Avian Genetic Resources at Risk: an Assessment and Proposal for Conservation of Genetic Stocks in the USA and Canada

Animal Science Publications Animal Science

9-1999

Avian Genetic Resources at Risk: An Assessment and Proposal for Conservation of Genetic Stocks in the USA and Canada

Jacqueline M. Pisenti University of California, Davis

Mary E. Delany University of California, Davis

Robert L. Taylor Jr. University of New Hampshire

Ursula K. Abbott University of California, Davis

Hans Abplanalp University of California, Davis

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This Report is brought to you for free and open access by the Animal Science at Iowa State University Digital Repository. It has been accepted for inclusion in Animal Science Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Avian Genetic Resources at Risk: An Assessment and Proposal for Conservation of Genetic Stocks in the USA and Canada

Abstract Genetic diversity, in both wild and domestic species, is a limited resource worth preserving for future generations (Oldfield 1984; Alderson 1990; AF O 1992; NRC 1993; Bixby et al. 1994). While many strong advocates promote the conservation of wild species, fewer are aware of the increasing loss of biodiversity in our major food species, particularly among domestic birds. Fortunately, breed conservation organizations have already made some progress in encouraging hobbyists and small-scale farmers in their role as conservators of unique and historically important breeds (Bixby et al. 1994), particularly the less common chicken and turkey breeds (Crawford and Christman 1992). These two species are considered more at-risk than most other livestock species (e.g., cow, pig, sheep, goat, or horse) due to recent and extraordinarily rapid expansion of the commercial poultry industry.

Disciplines Agriculture | Animal Sciences | Genetics | Poultry or Avian Science

Comments This report is published as Pisenti, Jacqueline M., Mary E. Delany, Robert L. Taylor Jr., Ursula K. Abbott, Hans Abplanalp, James A. Arthur, Murray R. Bakst, Colin Baxter-Jones, James J. Bitgood, Francine A. Bradley, Kimberly M. Cheng, Rodney R. Dietert, Jerry B. Dodgson, Ann M. Donoghue, Alan B. Emsley, Robert J. Etches, Richard R. Frahm, Roger J. Gerrits, Paul F. Goetinck, Allan A. Grunder, David E. Harry, Susan J. Lamont, Gail R. Martin, Patrick E. McGuire, Gary P. Moberg, Louis J. Pierro, Calvin O. Qualset, Muquarrab A. Qureshi, Fred T. Shultz, and Barry W. Wilson. Avian Genetic Resources at Risk: An Assessment and Proposal for Conservation of Genetic Stocks in the USA and Canada. University of California Division of Agriculture and Natural Resources, Genetic Resources Conservation Program, Davis, CA. Report No. 20 (1999).

Authors Jacqueline M. Pisenti, Mary E. Delany, Robert L. Taylor Jr., Ursula K. Abbott, Hans Abplanalp, James A. Arthur, Murray R. Bakst, Colin Baxter-Jones, James J. Bitgood, Francine A. Bradley, Kimberly M. Cheng, Rodney R. Dietert, Jerry B. Dodgson, Ann M. Donoghue, Alan B. Emsley, Robert J. Etches, Richard R. Frahm, Roger J. Gerrits, Paul F. Goetinck, Allan A. Grunder, David E. Harry, Susan J. Lamont, Gail R. Martin, Patrick E. McGuire, Gary P. Moberg, Louis J. Pierro, Calvin O. Qualset, Muquarrab A. Qureshi, Fred T. Shultz, and Barry W. Wilson

This report is available at Iowa State University Digital Repository: https://lib.dr.iastate.edu/ans_pubs/716 Avian Genetic Resources at Risk: An Assessment and Proposal for Conservation of Genetic Stocks in the USA and Canada Clockwise from above: • White Leghorn rooster from UCD 003, a highly inbred stock that serves as genetic background to a number of congenic chicken stocks. • Red Jungle Fowl rooster from UCD 001, a highly inbred stock derived from the wild chicken progenitor species. • Hybrid rooster from cross between Red Jungle Fowl (UCD 001) and White Leghorn (UCD 003). Offspring from the cross of this rooster and a White Leghorn hen were used as a reference population in developing the chicken genome map. (Photographs courtesy of J. Clark, University of California–Davis.)

Front cover: Chicken, turkey, and quail eggs. (Photograph courtesy of J.M. Pisenti, University of California–Davis) Avian Genetic Resources at Risk: An Assessment and Proposal for Conservation of Genetic Stocks in the USA and Canada

Authors J.M. Pisenti, M.E. Delany, R.L. Taylor, Jr., U.K. Abbott, H. Abplanalp, J.A. Arthur, M.R. Bakst, C. Baxter-Jones, J.J. Bitgood, F.A. Bradley, K.M. Cheng, R.R. Dietert, J.B. Dodgson, A.M. Donoghue, A.B. Emsley, R.J. Etches, R.R. Frahm, R.J. Gerrits, P.F. Goetinck, A.A. Grunder, D.E. Harry, S.J. Lamont, G.R. Martin, P.E. McGuire, G.P. Moberg, L.J. Pierro, C.O. Qualset, M.A. Qureshi, F.T. Shultz, and B.W. Wilson

Sponsored by the University of California Genetic Resources Conservation Program US Dept. of Agriculture US National Science Foundation Dept. of Animal Science, University of California–Davis

Report No. 20 K September 1999

Genetic Resources Conservation Program Division of Agriculture and Natural Resources University of California Davis, California USA This report is one of a series published by the University of California Genetic Resources Conservation Program (technical editor: P.E. McGuire) as part of the public information function of the Program. The Program sponsors projects in the collection, inventory, maintenance, preservation, and utilization of genetic resources important for the State of California as well as research and education in conservation biology. Further information about the Program may be obtained from: Genetic Resources Conservation Program University of California One Shields Ave. Davis, CA 95616 USA

Tel: (530) 754-8501 FAX: (530) 754-8505 email: [email protected] http://www.grcp.ucdavis.edu

CITATION: J.M. Pisenti, M.E. Delany, R.L. Taylor, Jr., U.K. Abbott, H. Abplanalp, J.A. Arthur, M.R. Bakst, C. Baxter-Jones, J.J. Bitgood, F.A. Bradley, K.M. Cheng, R.R. Dietert, J.B. Dodgson, A.M. Donoghue, A.B. Emsley, R.J. Etches, R.R. Frahm, R.J. Gerrits, P.F. Goetinck, A.A. Grunder, D.E. Harry, S.J. Lamont, G.R. Martin, P.E. McGuire, G.P. Moberg, L.J. Pierro, C.O. Qualset, M.A. Qureshi, F.T. Shultz, and B.W. Wilson. 1999. Avian Genetic Resources at Risk: An Assessment and Proposal for Conservation of Genetic Stocks in the USA and Canada. Report No. 20. University of California Division of Agriculture and Natural Resources, Genetic Resources Conservation Program, Davis, CA USA.

The University of California prohibits discrimination against or harassment of any person on the basis of race, color, national origin, religion, sex, physical or mental disability, medical condition (cancer-related or genetic characteristic), ancestry, marital status, age, sexual orientation, citizenship, or status as a covered veteran (special disabilities veteran, Vietnam-era veteran or any other veteran who served on active duty during a war or in a campaign or expedition for which a campaign badge has been authorized). University Policy is intended to be consistent with the provisions of applicable State and Federal laws. Inquiries regarding the University’s non- discrimination policies may be directed to the Affirmative Action/Staff Personnel Services Director, University of California, Agricultural and Natural Resources, 1111 Franklin, 6th Floor, Oakland, CA 94607-5200. Tel. (510) 987-0096. Table of Contents

Preface ...... vii Chapter 5: Genetic stocks: Current resources and recent losses..... 31 Executive Summary ...... ix Survey method Avian Genetic Resources Task Force Results from the survey Members...... xvii Lost stocks Charge to the Task Force ...... xviii Trends in poultry genetics stock development and conservation Chapter 1: Introduction ...... 1 Chapter 6: An Avian Genetic Resources Chapter 2: Avian genetic diversity: System: Proposal ...... 39 Domesticated species ...... 5 Task Force recommendation Target species Rationale Types of genetic stocks Components of an Avian Genetic Research genetic stocks Resources System (AVGRS) Commercial stocks Facilities and organizational aspects Fancy breeds and mid-level of AVGRS production stocks Financing the AVGRS Chapter 3: Avian genetic resources References...... 47 for biological research ...... 15 Avian reproductive biology Appendix 1: Instructions and survey Embryology form sent to researchers ...... 55 Models for human genetic diseases Appendix 2: Genetic stock Immunogenetics collection data...... 57 Cytogenetics Description of stock categories Genomics Notes on specific fields Developmental genetics Disclaimer Chapter 4: Conserving avian genetic resources ...... 25 Methods of conservation of genetic stocks Live animals Semen cryopreservation Blastodisc cryopreservation Primordial germ cell cryopreservation

iii List of boxes

1. Commercial value of the poultry 12. Small renaissance of old-style industry ...... 1 chicken breeds ...... 14

2. Dispersal of a genetically significant 13. Inherited muscular dystrophy poultry collection ...... 2 of the chicken ...... 16

3. Collections at risk: University of 14. Deep pectoral myopathy: One price California–Davis ...... 2 of intensive selection ...... 18

4. Successful conservation of at-risk 15. Ancona chickens give a new angle genetic stocks ...... 3 on disease resistance ...... 19

5. Parthenogenetic turkeys ...... 6 16. Government involvement in genome research ...... 20 6. Research with goose breeds in Canada ...... 8 17. Patterns in vertebrate limb development ...... 22 7. Highly inbred stocks in immunogenetics ...... 9 18. Patterns in skin development ...... 24

8. Chicken chromosome rearrange- 19. Mosaic chickens and genetic ment stocks ...... 10 stock preservation ...... 28

9. Economics of sex-linked genes 20. Orphaned CFAR stocks preserved and chicken genetics ...... 11 as frozen embryonic cells ...... 29

10. Development of egg-laying stocks ..... 12 21. The Jackson Laboratory model for vertebrate genetic stocks ...... 36 11. Development of meat-producing stocks ...... 13 22. Japanese quail at the University of British Columbia ...... 37

iv List of figures

ES1 Components of the Avian Genetic 9. Silkie rooster from UCD Silkie ...... 14 Resources System ...... xii 10. Chromosomes from a Red Jungle 1. Red Jungle Fowl rooster from Fowl hen from UCD 001 ...... 19 UCD 001 ...... 5 11. Wingless-2 chicken embryo from 2. White Leghorn rooster from UCD Wingless-2 X 331 ...... 21 UCD 003 ...... 6 12. Eudiplopodia embryo foot from 3. Flock with different turkey breeds ...... 6 UCD Eudiplopodia X 003 ...... 22

4. Japanese quail silver mutation from 13. Hens from UCD Scaleless-Low...... 24 UBC SI ...... 7 14. Stage X blastodisc (at time of 5. Japanese quail porcupine mutation oviposition)...... 27 from UBC PC-WB ...... 7 15. Diagram of avian blastodisc 6. White Leghorn hen ...... 12 cryopreservation and recovery ...... 28

7. Traditional broiler-type chicken 16. Components of the Avian Genetic carcass of the 1940s ...... 13 Resources System ...... 40

8. Commercial Large White turkey tom .. 13

List of tables

ES1 Estimated costs of Avian Genetic 4. Estimated costs of Avian Genetic Resources System ...... xv Resource System ...... 45

1. Summary by category of existing Appendix 2 poultry genetic stocks (live and cryopreserved) ...... 32 2.0. Stock categories ...... 57

2. Number of poultry genetic stocks 2.1. Stock information. kept as live birds in institutions ...... Separate pagination following 60 in the USA and Canada in 1998, and the number lost since 1984 ...... 34 2.2. Stocks listed by country, state or province, institution, and curator. 3. Summary by category and species ...... Separate pagination following 60 of poultry genetic stocks reported lost since 1984 ...... 35 2.3. Curator contact information...... Separate pagination following 60

Preface

IN 1984, AN INTERNATIONAL SYMPOSIUM and Work- vice (CSREES), convened a binational Task Force shop on Genetic Resources Conservation for in 1995 to address the problem. The Task Force California made the recommendations that pre- included representatives from the many public cipitated the establishment of the Genetic Re- institutions that have or had poultry research sources Conservation Program within the Uni- programs, from private companies, and from re- versity of California (UC/GRCP). These recom- search programs that have utilized poultry ge- mendations recognized that the avian genetic netic stocks. stocks developed in California, primarily chicken In support of the Task Force’s work, UC/ and coturnix quail, had been valuable in re- GRCP conducted a survey of existing genetic search and the commercial poultry industry and stocks in the US and Canada to provide an in- that continued conservation of such stocks de- ventory for analysis. This new inventory is pre- pended upon long-term support for live-bird sented in this document. The most recent prior maintenance and further research on cryopres- inventory was published in 1988 (R.G. Somes, ervation technology. At that time, there was no Jr. 1988. International Registry of Poultry Genetic national-level program, comparable to the Na- Stocks. Storrs Agr. Exp. Sta. Bull. 476. The Uni- tional Plant Germplasm System, directed to ani- versity of Connecticut, Storrs). It was not sur- mal genetic resources. By the early 1990s, the prising to find that many stocks had been lost in California situation was fast approaching a crisis the interval. Indeed, numerous stocks have been with the imminent retirement of the two primary lost over the course of this Task Force effort. developers and curators of poultry research ge- The majority of the Task Force convened at netic stocks at the University of California– an initial meeting in Davis in October 1995 and Davis, Ursula Abbott and Hans Abplanalp. No a subgroup met in Washington DC in May 1996. plan was in place for the continued support and Results of the survey and progress of the Task maintenance of the important and widely used Force have been presented and discussed at sev- genetic stocks developed and acquired by them. eral meetings including the annual NE–60 Re- Nationally, other collections were at risk as the gional Research Project meetings and the annual poultry and avian science departments in the US meetings of the Poultry Science Association and were losing faculty (to retirements) and financial the Society for Developmental Biology. An in- resources that had supported collection mainte- terim review of the issues was presented by nance in the past. The UC Davis campus re- M.E. Delany, co-chair of the Task Force, and cently followed this trend, with the merging of its J.M. Pisenti, UC/GRCP’s facilitator for the Task Avian Sciences Department into the Animal Sci- Force (M.E. Delany and J.M. Pisenti. 1998. Con- ence Department in 1997. Avian genetic stocks servation of poultry genetic research resources: in Canada are likewise imperiled. Consideration of the past, present, and future. Recognizing the drastic reductions in human Poultry and Avian Biol. Rev. 9:25–42). and financial resources for avian genetic resour- We thank Mary Delany (University of Califor- ces management in the US and Canada, UC/ nia–Davis) and Robert L. Taylor, Jr. (University GRCP, in cooperation with two agencies of the of New Hampshire) for serving as co-chairs of the US Dept. of Agriculture (USDA), the Agricultural Task Force and all the members for their contri- Research Service (ARS) and the Cooperative butions of information and editing of this report. State Research, Education, and Extension Ser- We especially acknowledge Jacqueline Pisenti, a

vii poultry developmental geneticist, who facilitated ity of existing genetic resources and support the this effort in every way. Her great familiarity with further development of new genetic resources. poultry stocks and expertise in maintaining the While Congress authorized the US National genetic stocks at UC Davis was a definite asset Genetic Resources Program with the Food, Agri- in carrying out the charge to the Task Force. Her culture, Conservation and Trade Act of 1990, persistence in pursuit of information for the sur- there still is no plan for ensuring the conserva- vey made it a successful venture. Her work in tion of poultry and other livestock genetic re- pulling together this report from components sources critical to the US. In Canada there has submitted by many different individuals has pro- been a loss of federal support for poultry genetic duced what we think is a document that speaks resources and now most of their important ge- in a uniform, strong voice for the value of these netic resources exist only as frozen embryo blas- genetic stocks and for the imperative of their todisc cells. With these uncertainties, it is continued conservation. doubtful if new genetic stocks from current re- The work of the Task Force could not have search will be conserved. This is a direct deter- been accomplished without financial support rent to new research on critical issues in avian from UC/GRCP and from grants from the Na- biology. At the same time, we recognize that tional Science Foundation and the Agricultural emerging technologies of molecular biology and Research Service. These grants both supported genomics have increased the value of existing the activities of the Task Force and contributed genetic stocks and provided the impetus to de- to the maintenance of at-risk poultry genetic velop new ones which will need conservation at- resource collections at the University of Califor- tention. The Task Force has made well consid- nia–Davis. ered and reasonable recommendations. UC/ The Task Force has defined the types of ge- GRCP and the USDA will work to make these netic stocks, made an excellent summary of the recommendations known and will support their extent of the use of avian genetic resources in adoption into a viable Avian Genetic Resources many different research disciplines, analyzed the System to protect and make available to all re- inventory for trends in stock development and searchers extant avian genetic stocks and, im- conservation, and finally made recommenda- portantly, to encourage new research in bio- tions designed to ensure the continued availabil- medicine, biology, and agriculture. Calvin O. Qualset, UC/GRCP Richard R. Frahm, USDA–CSREES Steven Kappes, USDA–ARS

viii Executive Summary

Background Findings

AMONG THE DOMESTICATED AVIAN species, tradi- This study documented the loss of more than tional breeds developed for meat or egg produc- 200 stocks since 1984. A detailed database was tion are a tremendous source of genetic diver- prepared for all extant stocks in the US and sity. Such breeds result from hundreds of years Canada, including 268 chicken, 20 turkey, 65 of selection by farmers and breeders, incorporat- Japanese quail, and 8 waterfowl or gamebird ing a variety of unique genes and gene combina- accessions. tions. Likewise, intense selection for odd and 1. The continuing loss of avian research interesting traits resulted in the array of fancy stocks is a significant concern, as in the breeds treasured by hobbyists. The relatively past 15 years more than 200 mutant, small size of most poultry species (particularly inbred, and selected avian genetic stocks the chicken and Japanese quail), along with were destroyed. More than one-third of their phenomenal reproductive capacity and ge- the remaining stocks are at risk of elimi- netic variability, make them particularly well nation within the next few years. suited to multi-generational studies with rigorous selection or high levels of inbreeding. This 2. While several research institutions in the has stimulated the development of many impor- US and Canada still maintain collections, tant genetic stocks of chicken, turkey, and quail they are at capacity and will likely face by researchers in agricultural departments at reduction in resources in the near future. public universities or in federal agricultural re- There is no facility currently available search organizations. These specialized genetic that can accommodate the needs of all stocks have contributed widely to research in currently at-risk stocks. basic, biomedical, and agricultural sciences. To date, no formal conservation plan exists 3. Without stock conservation facilities, for these stocks at any organizational level. In- there will be little incentive for invest- stead, conservation of these important avian ge- ment in lines of research that would pro- netic resources is largely dependent upon indi- duce new genetic stocks, particularly viduals, sometimes connected through breed highly inbred and selected stocks. This is associations or academic circles, but largely as a direct deterrent to research on critical independent efforts. This lack of a formal conser- issues in avian biology. vation plan is particularly perilous for research genetic stocks. Unlike the more widely dispersed 4. Many research stocks have unique ge- traditional or hobby breeds, specialized research netic properties which would be impos- stocks are often kept at only one location, which sible or very costly to recreate. Some of makes them far more vulnerable to extinction. In these have high potential value for future particular, when such stocks can no longer be genetic research in the basic, biomedical, maintained by their curating researcher, they and agricultural sciences, for example: are often perceived as an unnecessary drain on dwindling financial resources at that institution, • Uniform selected and inbred stocks are and may be eliminated at very short notice. genetically well suited for studies of the

ix immune system and other complex vation of dissociated early blastodiscs functional systems. and primordial germ cells, are the subject of recent research in Canada, • Strains that carry a wide variety of mu- Japan, and the US. These methods al- tations affecting specific developmental low the recovery of intact genomes in or metabolic processes provide a start- the first generation. ing point for research exploring the tissue or cellular source of defects in em- 8. Funding is difficult to secure for conser- bryonic development and metabolic vation-related research and for the main- function, leading to a better under- tenance of live animal collections and standing of the control of the normal germplasm repositories. processes. 9. It is difficult to predict which stocks will • Mutations that closely mimic certain be of value to commercial or academic human congenital defects or disorders researchers at some future time. So, de- provide animal models for detailed ex- spite the uniqueness and potential use- perimental analysis of such conditions. fulness of the existing avian genetic stocks, the tenuous nature of the “value” 5. Information regarding the properties and of many stocks has precluded sustained availability of research stocks is not financial support for their preservation readily accessible to researchers who from any single agency. could effectively use them. 6. Many researchers who utilize genetic 10. There is currently no organization in the stocks, especially in basic biological and US or Canada to monitor conservation medical research areas, do not have fa- status and availability of avian genetic cilities for maintaining stocks and require stocks and set priorities for their conser- consistent and reliable sources for live vation on a national or binational level. birds, tissues, or eggs. Recommendation 7. Avian genetic stocks can be conserved as live animals or cryopreserved germplasm An avian genetic resources management system, (specifically as embryonic cells, semen, or with strong leadership, but shared responsibil- embryos). ity, is proposed as the most efficient and secure way to conserve genetic stocks and address is- • Live bird maintenance is expensive and sues of risk and loss. The proposed Avian Ge- labor intensive, as many research netic Resources System (AVGRS) would be com- stocks require rigorous disease control prehensive and would require the cooperation measures with specialized rearing and and collaboration of scientists, funding agencies, adult bird housing conditions, yearly and research institutions. The System must be monitoring of specific performance oriented toward research objectives, but it could traits for selected stocks, and genetic also support the needs of breeders, breed hobby- testing for chromosomal-abnormality ists, and breed historians. and mutant-carrier stocks. • Although the annual storage cost for Rationale cryopreserved germplasm is relatively low, very little germplasm from avian Historic long-term collaboration between Cana- genetic stocks is currently cryopre- dian and US scientists provides a basis for col- served, and recovery of live birds from laboration in the formation and operation of an the cryopreserved semen can be quite Avian Genetic Resources System. The US Na- difficult. An additional disadvantage of tional Plant Germplasm System and its counter- semen cryopreservation is that only the part in Canada serve as excellent models for the male genome is conserved. This elimi- proposed Avian Genetic Resources System. A nates or severely limits the usefulness system on this binational level is necessary be- of this conservation technique with in- cause no dependable regional or local solution bred or selected stocks. exists. • Promising new methods for conservation of diploid germplasm, cryopreser-

x Components of an Avian Conservation Genetic Resources System This is the cornerstone activity of the AVGRS and of critical importance. A central facility is The Avian Genetic Resources System is envi- needed for conservation and distribution of ge- sioned as a multilocational organization that netic materials. The central facility would house would serve the avian genetic resources needs those living genetic stocks that could not be for the US and Canada. The AVGRS would fea- maintained elsewhere and would serve as a ture a central facility as a focal point for many of backup site for important stocks that are main- the activities of the System. The functional com- tained elsewhere. This would include a secure ponents are outlined in Executive Summary Fig- backup repository for privately owned lines or ure 1 and are briefly discussed here. populations, either as live birds or cryopreserved germplasm at the central or secondary centers Avian Genetic Resources Advisory on a fee basis. The central facility would also Committee (AVGRAC) physically maintain the various types of preserved genetic resources and would coordinate The AVGRS would be advised by this binational those maintained elsewhere. The cryopreserva- committee comprised of representatives of nation capabilities of the central facility would be tional and state/provincial agencies, stock cura- supplemented by a specialized cryopreservation tors, and researchers. It would consist of 12 to center, presently unused, at the USDA site in 15 individuals who have worked with avian ge- Beltsville, Maryland. No site for the central facil- netic resource issues, drawn from government, ity is identified at this time. industry, and academic institutions in the US The central facility would support and be and Canada. Specifically, they should have linked to secondary facilities located at active worked in close association with national, inter- research centers which have the capability of national and private research-oriented organiza- maintaining genetic stocks for their own re- tions, and be familiar with avian genetic stock search needs. Several locations in the US and conservation issues. The members should meet Canada would qualify as secondary sites. at least once a year and be in regular communication during the year. The Committee would Methods of conservation. Conservation meth- review reports and recommendations for conser- ods employed in the AVGRS would be live-bird vation of stocks received from species-oriented maintenance and cryopreservation. committees. It would make recommendations to Targets for conservation. Conservation empha- the management unit of the AVGRS. sis of the AVGRS should be on live birds, embryonic cells, gametes, DNA, and tissues. The target Coordination species for the system will be those of interest in agriculture for food production and for basic bio- The various government and research institu- logical and biomedical research. Thus, the focus tions involved in avian research and conserva- will be on chicken, turkey, and Japanese quail tion would use the AVGRS for coordination of genetic stocks. However, this system could also information about genetic resources and the consider wild turkey, jungle fowl, and game AVGRS would in turn be responsible for main- birds, as well as species commonly raised in taining and distributing this information. This captivity. The AVGRS will emphasize: function would also include strategic planning for conservation of particular stocks, based on • Genetic stocks having traits and genetic advice from advisory groups established for each characteristics useful in research, such species. For example, imperiled stocks would be as inbred lines, single-gene mutations, identified to the AVGRS and a plan for their con- chromosome aneuploidy, and DNA servation would be developed through coordi- marker sequences. nated analysis. International relationships would be coordinated through the AVGRS, including • Lines and populations developed by pri- conservation of stocks in other countries, import vate and public breeders by hybridization and export of genetic stocks, data sharing, and and selection for important production- development of conservation plans for landraces, related traits. wild species, and breeding populations. • Domesticated mid-level production and fancy breeds held by small producers

xi Figure ES1. Components of the Avian Genetic Resources System.

Avian Genetic Resources System

Binational Avian Genetic Coordination Resources Advisory Commmittee

USDA International US NIH organizations US NSF FAO A&AF Canada IUCN Collections Scientific societies NGOs Others

Database/ Importation/ Conservation Distribution Research Information Quarantine

Central facility Genomics Coordinated with US Eggs Cryobiology Websites and Canadian Sperm Reproductive Stock registry organizations Embryos physiology Breed registry Live birds Genetics Live birds DNA Stock Preserved tissues Preserved characterization Eggs tissues Blood DNA Cultured tissues Cryopreserved semen, embryonic cells

Cryopreservation

Beltsville MD Guelph ON Others

Stock colonies

US - CA, IA, NH, WI, MI, CT Canada - BC, ON Others xii and hobbyists in North America and from supporting an avian genetic stocks conser- Europe. vation program, while the basic research or disease model aspect of genetic stocks could be em- • Domesticated, but primitive, landraces phasized for organizations promoting basic and existing in Asia, Central and South biomedical research. Thus, the underlying goals America, and elsewhere, primarily as of presenting genetic stocks information at such scavenger birds. meetings is not only to attract the attention of researchers, but to engage the interest and pro- Archival preserved specimens of birds, or- mote funding from commercial sectors that can gans, skeletons, eggs, feathers, and tissues that benefit directly from research using avian ge- have been preserved as museum specimens are netic stocks. also a component of the genetic resources sys- Another outreach option for the AVGRS tem, since these materials provide for baseline would be an independent website that would observations and time-course monitoring of fac- promote the available avian genetic stocks to the tors such as environmental toxicants. scientific community by advertising what is An informal in situ system of conservation of available, and indicating those that are slated for landraces and breeds is well established in elimination. The effectiveness of such a site North America. A monitoring and database sys- could be multiplied by linking it with websites: tem may be the most important need for those the animal genetic map (Angen), the chicken genetic resources. This could become an activity map (ChickMap), various research organization of this proposed system. sites (e.g., Poultry Science Association, Society for Developmental Biology, various commercial Databases poultry sites, and sites for academic institu- Detailed information about all genetic stocks in tions). the US and Canada should be maintained and The AVGRS website information could be fur- updated by the AVGRS in a genetic resources ther promoted by a series of clearly written re- information system, similar to the Genetic Re- view articles in several of the major biological sources Information Network (GRIN) developed science journals. In each case, a specific area of for the US National Plant Germplasm System research would be targeted, such as animal and housed with the USDA National Agriculture models for human diseases, limb pattern de- Library. Additionally, database service would be fects, craniofacial defects, integumentary de- offered to the various breed conservancies and fects, or immunogenetic research. hobbyists groups for inventory and location of The outreach activity would also involve inter- conserved breeds, landraces, and specialty national contacts through FAO or various coun- stocks. It would also be logical for the AVGRS tries with respect to avian genetic resources. For database to include DNA sequence data as they example, there are genetic stocks at risk in other are developed. countries that should be considered for rescue While GRIN currently focuses on plant infor- in the AVGRS because of their value for re- mation, its goal is to include information on all search. of the common and endangered breeds of farm Bird care and housing animals, including the avian genetic stocks used primarily in research. Collaboration with the The housing and care of the live birds at all cen- AVGRS database would facilitate this goal. ters will follow American Association for Labora- tory Animal Care standards for a breeding Outreach colony. Essentially, the breeding stock should be Researchers can also be informed of the wide kept in a facility that approximates that of a variety of available genetic stocks at the annual well-run commercial poultry breeding farm. The meetings of a variety of organizations, including highest degree of automation for feeding, clean- the Poultry Science Association, the Pacific Egg ing, watering and climate control is recom- and Poultry Association, the Poultry Breeders mended. With most of the chicken genetic Roundtable, the Society for Developmental Biol- stocks, the adult birds will be housed in single- ogy, the American Association for the Advance- bird cages, and bred by artificial insemination. ment of Science, and the American Medical As- Other features of the facility may include: floor sociation. Presentations at the commercially ori- pens, with or without trap nests, to maintain ented meetings could be used to showcase the stocks that do not perform well in cages; and benefits the different companies could derive separation of males and the females (in different

xiii rooms or cage rows), so that appropriate, sex- cultural institution (land-grant university) with a specific breeder diets, lighting, and feeding regi- veterinary school that has a good avian medicine mens can be provided for each group. program, but reasonably isolated from commercial poultry stocks. The connection with a land- Importation and quarantine grant institution would give the center close ties to active research laboratories and faculty, who Movement of animals introduces risks of spread- could benefit from such a resource and be ing contagious diseases, obviously of great con- drawn upon in support of the center. Access to cern in long-term conservation of live birds. state-of-the-art poultry disease diagnostics and Movement of genetic resources as fertile eggs or veterinary care is critical, along with good, off- semen reduces disease transmission risk and site quarantine facilities for newly acquired ge- are preferred procedures. Importation of stocks netic stocks. Locating in a strong poultry pro- to the central facility will be done through on- ducing state would also provide an existing poul- site isolation and through national facilities un- try-oriented political and commercial infrastruc- der the direction of USDA Animal and Plant ture that could be mobilized to help support the Health Inspection Service. The central facility conservation center. will have appropriate isolation and sanitation This facility would include a hatchery, brood- capabilities. ing and growing areas, adult bird housing, an isolation area, a cryopreservation laboratory and Distribution storage facility, a database center, staff and administrative offices, and a laboratory to support A major function of the AVGRS will be to provide research and analytical services. genetic materials to users in the research com- Network of secondary genetic stock munity, breeders, and others. The genetic stocks may be transferred as live birds, semen, or eggs. centers These will be distributed on a cost-recovery ba- Secondary stock centers would be designated as sis. Some users require a continuing supply of part of the AVGRS at land-grant universities and genetic stocks and these needs would be sup- other institutions across the US and Canada plied by contractual stock reproduction pro- that fulfilled two criteria: (1) had adequate facili- grams. The distribution function would supply ties and support for the genetic stocks used in well-documented stocks to researchers, thus its own research programs and (2) had a long- contributing to the integrity of research projects. term interest in conserving genetic stocks. Such This functional component of the AVGRS is centers, approved as part of the AVGRS, would analogous to services provided by the Jackson receive funding from AVGRS for maintenance of Laboratories for mouse genetic stocks. stocks. These secondary centers would maintain live birds and would provide backup for at-risk Research stocks held in the central facility. As with the central facility, the secondary stock colonies The AVGRS should have a research capability would also have a distribution function on a fee within the central facility, especially for develop- basis. Researchers could also, on a fee basis, ing cryopreservation technologies. Research arrange to keep research flocks at the central would also be done on methods for documenting facility or one of the secondary centers, since genetic integrity or diagnostics with DNA mark- they may find it difficult or impossible to keep ers. Other research would be done as needed such stocks at their own institutions. Secondary and appropriate. The research activities would centers could specialize on one or a few classes be networked with research laboratories in the of genetic stocks. US and Canada for collaborative work. Management Facilities and organizational The central facility and the secondary centers aspects of AVGRS would be administered by the research institutions with which they are located. The central The central facility facility would have, at a minimum, a director or manager (research scientist), curator, an admin- Ideally, the primary AVGRS facility would be istrative assistant, database manager, cryopres- constructed de novo near or part of a major agri- ervation research scientist, and three or four

xiv laboratory and animal care technicians. The The AVGRS will be the major provider of ge- AVGRS would be guided by the advisory com- netic materials to researchers throughout the mittee on all management aspects. public and private sectors. For the most part, researchers do not have capacity to maintain live Stock evaluation guidelines bird colonies and depend upon stock colonies for their research. User-fees are an appropriate One of the more important activities of the means to recoup costs of stock maintenance. AVGRAC would be the evaluation of stocks for Donation funds can be expected to support conservation, cryopreservation, or elimination. the perpetual maintenance of particular genetic Guidelines for assessing the value of genetic stocks. These funds may be provided as annual stocks should be consulted. grants or through income derived from interest on endowment accounts. Financing the Avian Genetic Funding should be sought from the US government for construction of the central facility Resources System and for personnel support for operations as a part of the US National Animal Genetic Resour- Multiple sources of funding will be necessary to ces System. meet all of the needs of the AVGRS. Initial costs Long-term funding would be the most secure are those to construct the central facility and from endowment funds. Contributors could be upgrade the secondary stock centers. Annual encouraged from the private sector, from large costs of the central facility would be for its per- integrated commercial poultry companies to pri- sonnel and operations. It would also be neces- vate individuals with interests in preserving sary to support the annual activities of the poultry stocks or willing to promote the conser- AVGRAC. The central facility could also divert vation of stocks that can be used to study hu- funding for specific needs to the secondary cen- man diseases. ters by means of annual grants. Construction, personnel, and operational From the US side, the biological resource pro- costs have not been established, pending further grams of the National Science Foundation and analysis of potential sites for the central facility the National Institutes of Health would be ex- and other considerations. For illustrative pur- pected to provide operational funds through di- poses, rough order-of-magnitude estimates are rect grants and through grants to investigators given in Executive Summary Table 1. who use the avian genetic resources in their research. The USDA’s National Genetic Resources Table ES1. Estimated costs of Avian Genetic Resources System. System should participate in the AVGRS Startup costs through the Agricultural Research Service and Constructing and equipping central facility $15,000,000 the Cooperative State Research, Extension, and Upgrading and renovating secondary centers 2,000,000 Education Service. The various State Agricul- Total $17,000,000 tural Experiment Stations and land-grant and Annual costs other Universities should also participate. Cana- Personnel at central facility $400,000 dian support and participation should be forth- Operating costs at central facility 100,000 coming to the extent that the AVGRS provides Grants to secondary centers (8 x $25,000) 200,000 support to its research and development pro- Advisory Committee 25,000 grams. Total $725,000

Avian Genetic Resources Task Force Membership

Ursula K. Abbott, Dept. of Animal Science, Roger J. Gerrits, retired, USDA-ARS, National University of California, Davis, CA USA Genetic Resources Program, BARC-West, Beltsville, MD USA Hans Abplanalp, Dept. of Animal Science, University of California, Davis, CA USA Paul F. Goetinck, Cutaneous Biology Research Center, Dept. of Dermatology, Massachusetts James A. Arthur, Hy-Line International, General Hospital, Charlestown, MA USA Dallas Center, IA USA David E. Harry, Nicholas Turkey Breeding Murray R. Bakst, USDA-ARS-GGPL, BARC-East, Farms, Sonoma, CA USA Beltsville, MD USA Susan J. Lamont, Dept. of Animal Science, Colin Baxter-Jones, Arbor Acres, Inc., Iowa State University, Ames, IA USA Glastonbury, CT USA Gail R. Martin, Program in Developmental Biol- James J. Bitgood, Dept. of Poultry Science, ogy, Dept. of Anatomy, University of California, University of Wisconsin, Madison, WI USA San Francisco, CA USA Francine A. Bradley, Dept. of Animal Science, Patrick E. McGuire, Genetic Resources Conser- University of California, Davis, CA USA vation Program, University of California, Davis, Kimberly M. Cheng, Dept. of Animal Science, CA USA University of British Columbia, Vancouver, BC Gary P. Moberg, Dept. of Animal Science, CANADA University of California, Davis, CA USA Mary E. Delany (Co-Chair, AGRTF), Dept. of Jacqueline M. Pisenti (Facilitator, AGRTF), Animal Science, University of California, Genetic Resources Conservation Program, Davis, CA USA University of California, Davis, CA USA Rodney R. Dietert, Dept. of Microbiology, Immu- Louis J. Pierro, Storrs Agric. Experiment Station, nology, and Parasitology, Cornell University, Storrs, CT USA Ithaca, NY USA Calvin O. Qualset (ex officio), Genetic Resources Jerry B. Dodgson, Dept. of Microbiology, Conservation Program, University of California, Michigan State University, East Lansing, MI USA Davis, CA USA Ann M. Donoghue, USDA-ARS-GGPL, Muquarrab A. Qureshi, Dept. of Poultry Science, BARC-East, Beltsville, MD USA North Carolina State University, Raleigh, NC USA Alan B. Emsley, Poultry Consultant, Fred T. Shultz, Animal Breeding Consultant, Trumansburg, NY USA Sonoma, CA USA Robert J. Etches, Origen Therapeutics, Robert L. Taylor, Jr. (Co-Chair AGRTF), Dept. of South San Francisco, CA USA Animal and Nutritional Sciences, University of Richard R. Frahm, USDA-CSREES, New Hampshire, Durham, NH USA Washington, DC USA Barry W. Wilson, Dept. of Animal Science, Allan A. Grunder, CFAR, Ottawa, ON CANADA University of California, Davis, CA USA

xvii Charge to the Task Force

EVALUATE THE CURRENT STATUS of avian genetic stocks maintained in the US and Canada. The assessment should include the following aspects: Origin and history of avian genetic stocks. How avian genetic stocks have been utilized. Value of avian genetic stocks in agriculture, biomedical, and basic biological research. Strategies and techniques for long-term conservation.

Produce a report documenting these findings and include recommendations for organizational, fiscal, and administrative steps and personnel necessary to ensure the long-term security of avian genetic stocks for the US and Canada.

xviii 1

Introduction

GENETIC DIVERSITY, IN BOTH WILD and domestic The intense competition engendered by the species, is a limited resource worth preserving rapid growth and often narrow profit margins for future generations (OLDFIELD 1984; ALDERSON has served to eliminate the less competitive 1990; FAO 1992; NRC 1993; BIXBY et al. 1994). poultry breeders and to consolidate the high While many strong advocates promote the con- production industrial bloodlines in the hands of servation of wild species, fewer are aware of the a dozen or so poultry breeding organizations. increasing loss of biodiversity in our major food This has created a relatively limited genetic base species, particularly among domestic birds. For- for the chicken, derived primarily from two tunately, breed conservation organizations have breeds (Leghorn and Rhode Island Red) for egg already made some progress in encouraging production, and two breeds (Plymouth Rock and hobbyists and small-scale farmers in their role Cornish) for meat production (CRAWFORD 1990). as conservators of unique and historically im- A similar situation exists for the commercial tur- portant breeds (BIXBY et al. 1994), particularly key. These highly selected industrial stocks con- the less common chicken and turkey breeds siderably out-perform the old production breeds, (CRAWFORD and CHRISTMAN 1992). These two spe- given the correct feed and management. But the cies are considered more at-risk than most other relentless drive to improve the meat- (and egg-) livestock species (e.g., cow, pig, sheep, goat, or producing abilities of the commercial chicken horse) due to recent and extraordinarily rapid and turkey stocks has exacted a biological cost: expansion of the commercial poultry industry. disease susceptibility, leg weakness, muscle de- In just 50 years, poultry production went fects, and various other inherited conditions that from small, individually owned and reproduced interfere with the ability of the bird to hatch, farm flocks that formed a small but significant grow, and reproduce normally (CRAWFORD 1990). part of the farm income, to the huge commercial Despite these limitations, such stocks have al- meat- (turkey or broiler-chicken) or egg-produc- ready displaced or diluted some of the hardy, tion ranches that are generally owned or con- disease-resistant indigenous farm stocks kept in trolled by large corporations (CRAWFORD 1990). developing countries (MASON and CRAWFORD In 1997 this industry generated over $21 billion 1993). in poultry products in the US (Box 1 and USDA- The threat to genetic diversity extends beyond NASS 1998). the hobbyist, farm, and commercial poultry

Box 1. Commercial value of the poultry industry

THE CHICKEN AND TURKEY are the two most million laying hens that produced 77.4 ket, poultry production in Canada has commercially important poultry spe- billion eggs that year (USDA-NASS 1998). increased slowly but surely between cies in the US, having steadily increased This placed the 1997 poultry industry be- 1988 and 1996 (the most recent pro- in popularity with consumers for sev- low the beef industry in value, but well duction year available), from 370 to al- eral decades. In 1987 these two spe- above the pork or sheep industries, and most 480 million broilers; from 18.6 cies were the source of over $12.5 bil- about on par with the dairy industry. to 21.6 million turkeys; from 27.5 to lion in marketable products; in 1997, The Canadian poultry industry is also 28.2 million eggs. In 1995, the Cana- their total value was $21.6 billion, de- growing due to both increased consumer dian poultry industry was valued at rived from almost 8 billion broiler demand and a diverse export market. $3.7 billion Canadian dollars (approx. chickens, 300 million turkeys, and 311 More closely regulated than the US mar- $2.4 billion US) (AA-FC 1996).

1 stocks. Many of the genetically Box 2. Dispersal of a genetically significant poultry collection diverse avian genetic poultry stocks developed, maintained, ONE OF THE LARGEST commercially de- congenic lines for meat-bird-derived and studied by academic re- rived collections of chicken genetic endogenous viral genes (GRUNDER et al. searchers have disappeared or stocks in North America was located 1995). The stocks used in these stud- at the Center for Farm Animal Research ies included versions of both meat- and become at risk in recent years (CFAR) in Ottawa, Ontario. Many infor- egg-selected stocks that had been se- (Boxes 2, 3, and 4, and Chapter mative studies were conducted with questered from commercial stocks sev- 5). As these specialized stocks historical and modern commercial eral times since the 1950s, including vanish, unique opportunities for stocks that dated back to at least 1950. control strains, multitrait selected genetic advancement of the dif- Some of the accomplishments include strains, and specialty strains selected ferent species are lost, and sci- production of unique control strains for one trait such as endogenous viral from these stocks, improvement of pro- genes. Unfortunately, the facility in entific advancement in the agri- duction traits by selection with no evi- Ottawa lost its government support cultural, biomedical, and basic dence of plateaus, study of resistance and was shut down April 1, 1997. Em- sciences is hampered. Loss of to diseases including Marek’s disease bryonic blastodermal cells from some these unusual genetic stocks is and lymphoid leukosis, comparison of 30 CFAR stocks not transferred to not a trivial matter, since the methods of measuring eggshell qual- other institutions were frozen at the ity, and the development of semi- University of Guelph (Ontario, Canada). different forms (alleles) of each gene that underlie the observed differences in these stocks may be found only in tion, body shape, feed-use efficiency, leg a single population of birds; if that population is strength, and disease resistance. Ironically, it is lost, the unique alleles are also lost. these selected stocks that are particularly vul- Genetic stocks of chickens, turkeys, and nerable when funds become limiting, because Japanese (Coturnix) quail have played important improvements in production-related traits re- roles in both basic and applied research, often quire many years and a relatively large number serving as premier model organisms in the study of birds each year. Basic research can make use of fundamental questions in vertebrate biology. of all these types of stocks, but the various In the biomedical field, all three of these species single-gene mutations and genetically uniform have numerous mutant forms that have pro- inbred and congenic lines have proven to be par- vided animal models for the study of certain in- ticularly useful. herited human disorders (Appendix 2). These Despite recommendations for conservation include defects such as (glaucoma, macular de- (CAST 1984; NRC 1990), no formal conservation generation) various limb defects, cleft palate, plan exists in the US or Canada for such re- muscular dystrophy, and autoimmune forms of search stocks, and many have been lost or now thyroiditis, vitiligo, and scleroderma. face extinction as curating researchers either Agriculturally important genetic stocks in- retire or lose funding for stock maintenance. clude those selected for various production-re- The real and threatened loss of genetic diver- lated characteristics. These include egg produc- sity in chicken, turkey, and Japanese quail

Box 3. Collections at risk: University of California–Davis

AN EXAMPLE OF THE PROBLEMS confronting formerly maintained by their research sis, muscular dystrophy, scoliosis, and poultry genetic stocks is found at the grants and departmental funds. These scleroderma). In addition, Abbott has University of California–Davis (UCD). As stocks have been distributed widely to maintained and studied 14 mutations with other organizations across the researchers for use in such diverse ar- with defined effects on craniofacial country, UCD has reduced resource al- eas as studies of the immune system (the and/or limb development and two that locations for maintenance of genetic effects of the major histocompatibility affect the integument. Studies with stocks. This has become an acute prob- complex haplotypes on disease resis- these mutations have provided signifi- lem for poultry genetic stocks once tance and the characterization of the cant insights into mechanisms control- maintained by the Department of Avian physiological parameters of a chicken ge- ling vertebrate morphogenesis and Sciences. The department itself has netic immune-deficiency syndrome), the pattern formation. These stocks have been subsumed by the Deptartment of architecture of the chicken genome (two the potential to contribute significantly Animal Science. The retirements of of Abplanalp’s inbred lines were used to to our understanding of a variety of cur- Ursula Abbott and Hans Abplanalp of create reference backcross populations rent and future problems within the ba- the former Avian Sciences Deptartment and provide baseline DNA for the Chicken sic, biomedical, and commercial/agri- have put at risk over 50 inbred, mu- Genome Mapping Project), and the ef- cultural science realms of study, par- tant, and specialty lines of chickens col- fects of inbreeding on different repro- ticularly with the use of the rapidly lected or developed by these two re- ductive traits. Some of the mutations are evolving technology that allows researchers since 1955 (see Appendix 2 useful as animal models for the study of searchers to address the molecular ge- for descriptions of these stocks) and certain human genetic diseases (ichthyo- netic basis of such problems.

2 prompted the formation of the Avian Genetic Re- and Canada. A comprehensive genetic resources sources Task Force (AGRTF). Early in the discus- management strategy is herein proposed that sions, Task Force members realized that there can, in the future, provide support and services were several major, but different, conservation for all economically important avian species. issues. One is the protection of the ancestral This report discusses the history and uses of wild populations, another is the conservation of the different species, presents results of a survey unique breeds and landraces of domesticated of the genetic resources in the targeted species, poultry species, and finally, a more specialized gives overviews of major research areas depen- conservation effort is the preservation of unique dent on such genetic stocks, discusses the dif- genetic types developed for use in agricultural, ferent conservation methods currently available, biomedical, and basic biological research, in- and, finally, proposes a plan for a comprehen- cluding the various single-gene traits, highly in- sive Avian Genetic Resource System that would bred lines, and the populations or lines under insure long-term maintenance and accessibility improvement for various economic or other de- of these (and potentially other) endangered avian fined traits. While the preservation of wild pro- genetic stocks. genitors of domestic species is of critical importance, as is the conservation of nondomesticated avian species world-wide, the Task Force de- Box 4. Successful conservation of at-risk genetic stocks cided that the scope of this re- THE EXAMPLES OF THREE LINES (Trisomic, from one CSIRO facility (B. Sheldon) to port should be restricted to mPNU, and Triploid) serve as models another (R. Pym). Thus, these special- specialized genetic stocks. The of the traditional mode of curator trans- ized-cytogenetic lines represent suc- Task Force also recognized that fer from originating-investigator/insti- cess stories not only because of their rare breeds conservation, as tution to a new curating-researcher/in- significant contributions to basic and practiced by hobbyists and stitution. The Trisomic and mPNU lines applied research, but also in that new originated in the Poultry and Avian Sci- homes for the lines were established others, was already in place ences Department at Cornell University so that their use and availability for fu- in North America. The North (S.E. Bloom) and were recentl1y trans- ture research are secure, at least for American poultry stocks cur- ferred to the University of California– the foreseeable future. Unfortunately, rently most at-risk are the Davis (M.E. Delany). The Trisomic line this model of successful transfer of cu- unique genetic variants and is also maintained at the University of ratorship of genetic lines is the excep- specialty stocks held by re- New Hampshire (R.L. Taylor, Jr.). The tion today rather than the rule. CSIRO Triploid line was transferred search institutions in the US

Avian genetic diversity: Domesticated species

GENETIC DIVERSITY IS CONSIDERED crucial to the bird stocks (ring-necked pheasant and bobwhite continued survival of a species, be it wild or do- quail) have been developed and will be noted in mestic. Such within-species diversity has been this report. Noted below are salient features of the raw material of agriculturists over millennia. the most widely used domesticated species that In response to selective breeding and the differ- have the greatest need for conservation of ge- ential survival of less fit animals, preferred traits netic stocks. have been accentuated and clustered to produce distinct breeds and varieties of the modern do- Chicken mesticated species (NRC 1993). In more recent times, researchers have deliberately isolated First domesticated over 6,000 years ago, the various mutations in specialized stocks, permit- chicken (Gallus gallus or G. domesticus) presents ting the systematic study of such mutations and by far the greatest amount of genetic diversity of promoting a better understanding of the normal the domesticated avian species, with over 400 function of the affected genes. identified genetic variations (SOMES 1988). Many The totality of wild and domesticated species are showcased in the more-than 100 recognized form the gene pool or genetic resources base chicken breeds and commercial varieties, which necessary for the survival of the species. The variously integrate most of the naturally occur- genes and genotypes present in this pool repre- ring mutations affecting size, body type, produc- sent genetic resources which are accessible and tion characteristics, posture, color, feather can be exploited by biologists and breeders. In structure and location, comb shape, and behav- this report, we emphasize “genetic stocks” which ior (see Figures 1 and 2 for wild- and domestic- have been bred for specific traits and genes in type chickens). Some of the most extreme vari- contrast to breeds in which the individual birds ants include: the tiny, short-legged Japanese have many traits in common and can generally Bantam; the tall, aggressive Old English Game be maintained with randomly breeding populations. Genetic stocks are typically selected for traits of special interest to breeders and geneticists. Many of them are reproductively, physically, or physiologically compromised, and require special care in breeding and management, even for maintenance or conservation purposes. Target species While the AGRTF recognizes the need for conservation of undomesticated avian species, this report primarily addresses the need for conservation of specialty stocks of domesticated species, particularly chicken, turkey, and Japanese quail. A limited number of waterfowl (duck and Figure 1. Red Jungle Fowl rooster from UCD 001 goose) genetic stocks and semi-domestic game- (Photo courtesy of J. Clark, University of California–Davis).

5 Fowl; the light-weight Single- Box 5. Parthenogenetic turkeys comb White Leghorn hen that can lay more than 300 eggs in PERHAPS THE MOST SPECTACULAR use of tur- hatch, and grow into fully functional her first year of production; and keys in experimental biology was the males (OLSEN 1965). The existence of the large Rock-Cornish commer- study of meiosis, fertilization, and early this line has given rise to the notion embryonic development with a strain that genetic imprinting does not exist cial meat chicken, with its phe- of parthenogenetic turkeys. In the in birds, although this conclusion must nomenal rate of growth and 1960s and 1970s, M.W. Olsen of the be tentative in the absence of any for- well-fleshed carcass. These are United States Department of Agricul- mal investigation of imprinting in the all thought to share a common ture Agricultural Research Center at unique parthenogenetic stock. How- ancestor in the Red Jungle Fowl Beltsville developed a line of turkeys ever, this parthenogenetic stock exists in which an embryo would form in 30 precariously at only two research sta- (G. gallus gallus) (Figure 1) to 50% of the unfertilized eggs (par- tions in the world (the University of which is still found wild in parts thenogenesis). Most of these embryos Guelph (Ontario, Canada) and the Uni- of India and Southeast Asia die, but a small proportion of them versity of Oman). (CRAWFORD 1990; FUMIHITO et al. (about 0.5%) continue to develop, 1994), although some poultry specialists believe that several other jungle fowl species (G. sonnerati, G. lafay- ettei, and G. varius) also contributed to the ancestral gene pool (CRAWFORD 1990).

Turkey The one commercially important avian species originating in North America, the domestic turkey of commerce, is the product of hybridization between two subspecies of turkey: the domesticated Meleagris gallopavo gallopavo from Central America and the wild M. g. sylvestris from the eastern United States (CRAWFORD 1990). From these hybrids, birds were selected for size, tame- ness, carcass yield, and rapid growth, resulting in several distinct breeds and varieties (Figure 3). The modern commercial or exhibition turkeys are large, slow-maturing birds with a much lower reproductive potential than chicken or Figure 3. Flock with different turkey breeds (Photo Japanese quail (at one generation per year for courtesy of F.A. Bradley, University of California–Davis). the turkey). Although this species is far less popular with researchers or hobbyists than the chicken or the Japanese quail, at least six breeds are still kept for exhibition and a few unique research stocks have been developed (Box 5), including several commercial-type long- term selected and randombred-control lines kept at Ohio State University (see survey results, Ap- pendix 2, Tables 2.1 and 2.2). Perhaps as a consequence of the few researchers studying the turkey, relatively few mutations (49) have been reported in the turkey compared to the chicken and Japanese quail (SOMES 1988).

Japanese quail

Gaining in popularity as an experimental animal in both research and education, the Japanese quail (Coturnix japonica) is a small, early matur- Figure 2. White Leghorn rooster from UCD 003 (Photo ing, highly efficient egg and meat producer. Until courtesy of J. Clark, University of California–Davis). recently, the Japanese quail was classified as a

6 subspecies of the common European quail (C. productive life of an individual bird is quite coturnix). It is now classified as a distinct species short, frequently less than one year, and, unlike because of the nonhybridization of the two in the the chicken, close inbreeding is not tolerated. wild or in captivity (CHENG and KIMURA 1990). Thus, only one moderately inbred line exists (at According to all available documentation, the the University of British Columbia). domestic Japanese quail strains used in meat and egg production (even in Europe) are descen- Duck ded from C. japonica, which is still found in small wild populations in Japan. While gaining Almost all of the 15 or so domestic duck breeds popularity as a food animal in the US, its small recognized today are descended from the wild size has limited its use as a meat- or egg-pro- mallard duck (Anas platyrynchus platyrynchus), ducing animal to specialty markets. However, the exception being the Muscovy duck (Cairina the Japanese quail has other qualities that make moschata) (LANCASTER 1990). In addition to the it ideally suited for research. Usually reaching different plumage patterns and colors, a variety sexual maturity by six weeks of age, the females of body types and behavioral traits are found often lay an egg a day for several months. The among the duck breeds, ranging from the boat- males are aggressive breeders and maintain high shaped, vocal Call ducks to the cane-shaped In- fertility even when housed with four or more dian Runner ducks. Only 22 mutations have hens. The early maturity and short incubation been described in the domestic duck, most in- interval (16 to 17 days) permit as many as five volving feather color or pattern (LANCASTER generations in a single year, in contrast to the 1990). As such, these traits have been used in slower-maturing chicken (one to two generations defining breed and variety standards, especially per year) or the even slower maturing and less among the more ornamental duck breeds, such productive turkey (one generation per year). The as the Call, Indian Runner, Crested, Cayuga, quail is sometimes called the mouse of the bird and Swedish. While such breeds are usually world, since it has become extremely popular as only kept by hobbyists, a few are important in a model species for biological research in several commercial meat production, particularly White fields, including toxicology, cell biology, nutri- Pekins, Rouens, and, in some areas, Muscovy or tion, and selective animal breeding. Although Muscovy-domestic duck hybrids. most researchers use unselected or randombred birds, over 100 mutations are known in this spe- Goose cies, including many affecting feather color and shape (Figures 4 and 5), and several causing Six recognized domestic goose breeds were de- embryo-lethal deformities (SOMES 1988; CHENG rived from the western Greylag goose of Europe and KIMURA 1990). At present, most of these mu- (Anser anser anser). Several other breeds are tant strains are only maintained at the Univer- thought to have descended from the smaller sity of British Columbia or by hobbyists. Two Swan goose of central Asia (A. cygnoides). The drawbacks with this species are that the usual African breed is believed to be derived from a

Figure 4. Japanese quail silver mutation from UBC SI Figure 5. Japanese quail porcupine mutation from (Photo courtesy of K. Cheng, University of British Co- UBC PC-WB (Photo courtesy of K. Cheng, University lumbia). of British Columbia).

7 hybrid between these two species (HAWES 1990). and pheasant blood-type variants currently kept Strict herbivores, geese have a long history of at Northern Illinois University (JARVI et al. 1996). domestication, but their delayed maturity (two years) and low egg production rate make them Types of genetic stocks less attractive as an experimental animal or as a commercially viable species (Box 6). However, For the purposes of this report, genetic stocks due to the increasingly diverse consumer groups are classified into four categories that reflect the in the US and Canada, formerly noncommercial genetic composition and type and the breeding species are becoming popular on a small scale system used to maintain them. for specialty markets. One example is the demand from the Asian markets for a smaller, less • Randombred fatty meat goose. Until now, Europeans and • Highly inbred North Americans have traditionally raised Emb- den geese for market purposes. This large-bod- • Long-term selected ied, fatty bird is not well suited to the method of • Mutant (including cytogenetic variants cooking employed by Asian chefs. Therefore, wa- and transgenics) terfowl suppliers are now starting to grow the smaller Chinese geese for this market. We are primarily concerned in this report with conservation of genetic stocks developed for Gamebirds research purposes, which include all of these categories. Conservation of genetic stocks in the Several species of game birds are commonly different categories present different challenges bred commercially or by hobbyists, including for successful conservation, including: high em- many subspecies of the Ring-necked pheasant bryonic mortality, low viability, poor reproduc- (Phasianus colchicus) and the Bobwhite quail tive traits, pronounced susceptibility to one or (Colinus virginianus). Nine color mutations have more diseases, large and deleterious genetic been identified in the pheasant, along with sev- load, poor response to specific environmental eral affecting skin color and feather structure, stressors, poor recovery of cryopreserved semen, and 11 that produce biochemical polymorphisms and need for a very large gene pool (more than (SOMES 1990). For most populations, very little 100 birds per generation). selective breeding or inbreeding is deliberately practiced, and the development of gamebird Randombred lines are maintained as relatively stocks for genetic research is unusual. Excep- large populations of birds (usually over 100) in tions include the now-extinct inbred pheasant which little, if any, selection of breeding stock is lines developed at the University of California– done by the curator. Quite simply, the number Davis (WOODARD et al. 1983) and the Bobwhite of progeny from each male or female depends on the reproductive success of that bird at the time the eggs are col- Box 6. Research with goose breeds in Canada lected to reproduce the population. Such randombred stocks WHILE GEESE ARE NOT COMMONLY used for and improving egg production with experimental purposes, a relatively controlled lighting and trapnesting. are generally kept as closed large experimental population of geese Early studies with Pilgrim geese (the flocks, although new bloodlines was maintained at the Center for Food only goose breed that shows strong may be introduced to the popu- Animal Research (CFAR) in Ottawa. Sev- sexual dimorphism) included a demon- lation to improve the vigor of the eral distinct stocks of Chinese, Emb- stration of increased egg production flock, particularly if inbreeding den, and Chinese X Pilgrim hybrid with selection (MERRITT 1962), and use geese were developed in Ottawa to of light control to increase egg produc- depression is observed. The study production traits and DNA fin- tion. More recently, artificial insemina- birds may be reared and bred in gerprinting patterns (GRUNDER et al. tion techniques have been improved a single large enclosure, with all 1994). The stocks included standard (GRUNDER and PAWLUCZUK 1991) and males having access to all fe- breed control strains, stocks selected geese have been shown to lack endog- males. This is a common for for multiple traits, and the unselected enous viruses (i.e., viral DNA integrated pheasants, ducks, geese, some reference strains (SOMES 1988). As with into the host bird chromosomes) of the chicken and turkey research in the early avian leukosis type (GRUNDER et al. chickens, and naturally breed- part of this century, most studies with 1993). Unfortunately, with the loss of ing turkey stocks. Alternatively, the relatively undeveloped pure and funding from the Canadian govern- the birds may be randomly seg- crossed goose varieties have been re- ment in April of 1997, these stocks regated into smaller floor pens lated to agricultural objectives, includ- were either eliminated or dispersed. or randomly paired or grouped ing methods of rearing broiler geese in cages, as is common with

8 Japanese quail. A minimum of 25 pairs, usually Highly inbred genetic stocks are invaluable in more than 150 birds, is needed to keep inbreed- a wide range of research fields, particularly ing at a minimum. These stocks are often kept genomics (gene mapping) and immunogenetics as a source of “normal” control birds, and also (Box 7). A good example of the usefulness of in- function as a resource stock, from which inbred bred strains in genomics is the mapping of clas- or selected stocks can be derived or qualitative sical mutations. While over 80 classically identi- mutations isolated. fied genetic mutations have been assigned to the chicken linkage map, only a few have been lo- Inbred lines are produced by breeding together cated on the molecular map. This is due to the close relatives for many generations, resulting in lack of genetic characterization of the exhibition increasingly homozygous and homogeneous breeds and lines in which most of these muta- progenies. Different types of mating schemes are tions are found. Such nonuniform genetic back- used, depending on how rapidly the researcher grounds make them difficult to use in matings is attempting to approach complete homozygos- designed to integrate the maps. In contrast, ity. Disregarding parthenogenesis, the most congenic lines, mentioned above, are uniquely rapid inbreeding is produced by father-daughter, useful for such genetic mapping. The integration mother-son, or brother-sister (full-sib) matings. of genes in exhibition breeds into defined inbred These breeding schemes can also be used to ex- lines would provide the necessary uniformity for pose deleterious recessive traits or to fix pre- molecular mapping of these traits. ferred or beneficial single-gene traits in a population. Unfortunately, even in the absence of ma- Long-term selected stocks are the result of jor genetic defects, the fertility and viability of many generations of testing and selective breed- the inbred offspring are almost always lower ing for traits governed by multiple genes (the so- than the more outbred parent strain, a charac- called quantitative or polygenic traits). Many val- teristic called inbreeding depression. If selection ued heritable characteristics in the poultry and breeding strategies do not compensate for breeds belong in this category. These include egg this decline, inbreeding depression can result in production rate, egg size, feed efficiency, fertility, the extinction of the line within a few genera- hatchability, viability, disease resistance, body tions. This is a particular concern in lines propa- size and shape, and behavioral characteristics. gated by full-sib matings which also have large To change the population mean for one or more genetic loads (many deleterious alleles). How- of these quantitative traits requires rigorous ever, once the lethal and sub-vital alleles have testing and ranking of the individuals and family been purged from the inbred strain, it can theo- groups for the traits-of-interest each generation, retically be bred to essentially complete homozy- followed by selective breeding of the higher- gosity while maintaining reasonable reproductive ranked individuals and families to produce the performance traits (fertility, egg hatchability, egg next generation. Many factors can affect the rate production rates, viability, etc.). Such genetically of improvement in response to selection includ- uniform stocks can then be used as a standard ing 1) degree of heritability of the trait or traits genetic background in the study of individual involved, 2) selection stringency, 3) level of in- genes and gene complexes. Par- ticularly useful inbred lines are Box 7. Highly inbred stocks in immunogenetics those which have been bred for contrasting phenotypes due to BASIC INFORMATION ABOUT FACTORS control- including coccidiosis, Newcastle’s dis- allelic differences at single loci. ling disease resistance in the chicken ease, and the tumor-inducing viruses These lines, having the same has been gathered largely from stud- that cause Marek’s disease and lym- ies with congenic strains of chickens phoid leukosis. The congenic MHC genetic background for practi- (birds with identical, highly inbred strains, most requiring at least ten gen- cally all loci except for the alle- backgrounds but different major his- erations of back-crossing and blood- les of interest, are called tocompatibility complex (MHC) testing to develop, are key resources congenic lines. They are used to haplotypes; ABPLANALP 1992). A num- required for furthering our understand- study single-gene effects on pro- ber of these congenic strains have been ing of the way the MHC genes func- ductivity, for molecular charac- developed at the University of Califor- tion. Studies with these stocks have al- nia–Davis, the USDA Avian Disease and ready given the primary poultry breed- terization of genes affecting de- Oncology Laboratory in East Lansing, ers vital information to use in deter- velopmental traits or disease MI, the University of New Hampshire, mining the best of several alternative resistance, and many other uses and Iowa State University. Researchers breeding strategies to enhance disease in basic biological and biomedi- have shown how each MHC-haplotype resis-tance potential of their produc- cal research (ABPLANALP 1992). could directly affect the resistance of tion stocks. a bird to a variety of different diseases,

9 breeding, and 4) genetic variation in the original DNA, usually containing a gene of interest, into source population. Selected stocks usually re- one of the chromosomes of germline or somatic quire several generations to develop, tend to re- cells. While some transgenic chickens have been vert towards the original stock values if the se- produced in the past few years (SALTER et al. lection pressure is lifted (i.e., if random or non- 1986; 1987; SALTER and CRITTENDEN 1989), the selected pedigree reproduction is used), and creation of transgenics is still very much experi- usually need to be reproduced in large numbers mental in chickens and other avian species. (several hundred birds) each generation for the However, a number of research groups continue best selection differential with minimized in- to develop and refine transgenic methodologies, breeding. and report promising advances in the production of transgenic birds (SALTER et al. 1987; LOVE et Mutant stocks incorporate one or more of the al. 1994; THORAVAL et al. 1995; MARUYAMA et al. many single-gene mutations that have a major 1998). effect on specific morphological or physiological traits. These include variants (alleles) that affect Research genetic stocks eggshell color, feather color or shape, skin color, comb shape, metabolic function, major histo- Genetic stocks are used in three areas of re- compatibility complex (MHC) haplotype identity, search: agricultural, biomedical, and basic or and pattern formation in the developing embryo. fundamental biological research. The wide array of mutations affecting feather Agriculturally important avian genetic stocks color and shape are important for distinguishing primarily include those selected for various pro- between breeds and varieties within breeds. In duction-related characteristics (egg production, the poultry industry, eggshell color, skin color, body shape, feed-use efficiency, leg strength, dis- feather color, and feathering rate mutations, ease resistance). Another use for such stocks is and, more recently, MHC types, have all played to provide a flexible, rapidly responding model important roles in the development of commer- system for testing breeding techniques and sys- cial strains and varieties. Of particular interest tems that might also be useful with large live- to biomedical researchers are those mutations stock species (e.g., pigs, sheep, and cattle). These that cause disease conditions that mimic human stocks are particularly vulnerable to funding genetic disorders, including muscular dystrophy, cuts due to the long development period needed scoliosis, scleroderma, and a variety of develop- for most selected stocks, and the relatively large mental mutations (usually lethal) that affect the numbers that must be produced and monitored development of the face, limbs, integument, and annually to produce the selected population. internal organs. Biomedical research specifically uses animal Cytogenetic variants are birds that have chro- models for the study of various human diseases. mosomal abnormalities, such as aneuploidy, Avian models, mostly in the chicken, exist for polyploidy, translocations, and large insertions the autoimmune forms of vitiligo, scleroderma, or deletions. A small number have been estab- and thyroiditis, as well as for various develop- lished in the chicken, and these have provided mental defects, such as polydactyly, scoliosis, useful model systems for the study of meiosis, and cleft palate. Genetic stocks are also used in inheritance, recombination, linkage, transcrip- avian health research for studying the nature of tional regulation, and gene dosage effects. Such stocks include: aneuploidy for the chro- Box 8. Chicken chromosome rearrangement stocks mosome encoding the MHC and nucleolar organizer region FROM THE MID-1960S TO THE 1980s, ani- the sex chromosomes, and sources of mal genetics laboratories at Ohio State aneuploids). Unfortunately, with the (NOR), complete triploidy (three University, the University of Minnesota, lack of support by various agencies copies, instead of two, of all and New Mexico State University de- over the last ten years, over thirty of chromosomes), large deletions veloped about 40 different chromo- these unique genetic resources were (the mPNU line, in which there some rearrangement strains in the irretrievably lost. The seven still in ex- is segregation of an MHC/NOR chicken (ZARTMAN 1971; WOOSTER et al. istence, along with a recently isolated chromosome with a deleted 1977; WANG et al. 1982). A number of spontaneous translocation, are cur- studies by these laboratories made im- rently being maintained at the Univer- NOR), and various stocks carry- portant contributions to our under- sity of Wisconsin. However, with de- ing translocations between standing of chromosome behavior in partmental reorganizations and bud- macrochromosomes (Box 8). avian species (including recombination, getary difficulties, these stocks are also Transgenic stocks are chromosome segregation, identifica- threatened. formed by inserting foreign tion of pseudoautosomal regions on

10 disease resistance and effects of specific genes mercial importance, such as the sex-linked gene on productivity under disease stresses. controling the rate of feather growth that has Most of the genetic stocks are of value for been heavily utilized by modern chicken breed- studying questions in basic biology that may ers (Box 9). lead to more applied biomedical or agricultural In marked contrast to the general perception research, or by simply contributing to the knowl- that commercial poultry stocks all have a rela- edge of how different biological systems function tively small and diminishing genetic base, some in a wide variety of studies in the life sciences. researchers have reported the opposite. Specifi- Some of the specialized stocks have been cally, DUNNINGTON et al. (1994) used DNA finger- derived directly from commercial chicken, tur- printing to measure variability among commer- key, or Japanese quail lines, while others were cial chicken breeding populations and concluded developed from special breeds, landraces, or that a considerable reservoir of genetic diversity wild-types. yet remained. IRAQI et al. (1991) reported a great degree of polymorphism for endogenous viral (ev) Commercial stocks genes in five egg-type populations maintained by an Israeli commercial breeder. AARTS et al. (1991) The commercial poultry stocks have made re- also found variation for ev genes among and markable genetic progress in the last 50 years within six WL and four medium-heavy brown (Boxes 9, 10, and 11). At this time, selected eggshell lines. While none of these methods spe- stocks used in commercial egg or meat produc- cifically reflects the variation remaining in genes tion must fit very specialized production criteria. associated with economically important traits, To develop these criteria, each breeding company the recent substantial progress in the develop- has identified particular commercial goals (egg ment of the genetic map of the chicken (CHENG et production, weight gain, feed conversion, carcass al. 1995; CHENG 1997) should soon lead to more characteristics, etc.) and seeks to meet them in thorough and realistic assessment of the amount the shortest possible time (EMSLEY 1993). In this of economic trait variability remaining in com- way, the fundamental difference between basic mercial poultry populations. and applied research is highlighted. While a researcher may have a preferred outcome for an Fancy breeds and mid-level experiment, any result can provide useful information to that researcher or others in the reproduction stocks search community. For the commercial breeder, the only outcome that is acceptable is one that For at least 50 years, poultry fanciers have been improves the commercial product for the con- the main conservators of the majority of the sumer, and increases final prof- itability for the producer (HUNTON 1990). Box 9. Economics of sex-linked genes and chicken genetics From a commercial production point of view, the loss of IN 1908, SPILLMAN REPORTED that the fe- chicks are all fast feathering. Such unique avian germplasm has a male was the heterogametic sex in chicks can be easily sexed at hatch time chickens (now described as ZW, as com- by the relative feather growth by any- number of negative repercus- pared to mammals where the male is one with a minimum of training. Previ- sions. To start with, production heterogametic, XY). This was based on ously chicks were sexed using the vent objectives and economic stan- the finding that the barring gene was sexing method, whereby rudimentary dards are constantly changing, inherited as a sex-linked gene, being copulatory organs were examined to particularly for meat production passed from the dam to her sons. This determine sex. This was a costly pro- birds. This means that agro- early finding has played an important cedure, and at $0.03 per chick would role in commercial poultry breeding, cost a hatchery $3,000 for every nomic industries will continue as many lines are now sexed at hatch 100,000 chicks hatched. Over 600 mil- to need access to genetic diver- time using the sex-linked rate-of-feath- lion egg-type chicks are hatched an- sity to meet future market de- ering gene. This gene influences de- nually in the US. If only half of these mands, to adapt to adverse en- velopment of the early wing feathers are sexed by feather sexing, the vironmental conditions, to fight in the chick. If the dam carries the slow chicken industry saves over $9 million new diseases, and to meet the feathering mutation, K, she passes this per year. Broiler breeders are incorpo- on to all her sons, and her W chromo- rating this gene also, as sex-separate demands for different nutri- some to her daughters. If the sire is rearing becomes more prevalent. With tional values. Thus, an effort pure for the wild type gene, k+, all the over 9 billion broilers hatched in the must be made to identify and daughters receive the wild type fast- US each year, this also will have an eco- conserve all useful genetic re- feathering gene. The male chicks are nomic advantage to the industry. sources that could have com- all slow feathering and the female

11 poultry breeds and varieties in North America, aspects to this practice: small parcels of land particularly the old dual-purpose or mid-level can remain agriculturally productive; open space production breeds (Box 12). As the Leghorn is maintained, family farmers are aided; and chicken, Rock-Cornish cross chicken, and moneys go into the local economy. broad-breasted Large White turkey became the Biomedical researchers are starting to be- dominant commercial birds, commercial breed- come aware of the genetic reservoir available in ers could see no economic benefit to maintaining the fancy breeds. They usually seek specific other standard breeds and varieties of poultry standard breeds or feather patterns that can be recognized by the American Poultry Association used in exploring biological questions (see Chap- (APA 1998). Today, without fanciers, it would be ter 3) or problems related to human medical dis- very hard to find an Ancona or Silkie chicken or orders, e.g., a form of vitiligo in barred chickens a Royal Palm turkey. The Lamona chicken breed, (BOWERS et al. 1994). The Silkie breed (Figure 9) developed by the USDA, is a notable American is particularly useful, with six dominant muta- example of a once-useful old-fashioned produc- tions: crest (Cr), rosecomb (R), muffs-and-beard tion strain now fallen from favor. (Mb), polydactyly (Po), ptilopody (Pt), fibromel- In some cases, access to mid-level stocks can anosis (Fm); and one recessive mutation, hook- help small-scale producers stay in business. less (h). These mutant alleles produce: elongated While they cannot compete with the Rock-Cor- feathers on the crown of the head (Cr) and on nish meat cross or Leghorn egg-layer in the the face and chin (Mb), a broad, flattened comb highly commercial marketplaces, they can be- that is covered with small, fleshy nodules (R), come financially successful by raising some of extra toes (Po), feathered legs and feet (Pt), dark these heirloom birds to supply specialized niche skin, bones, and viscera (Fm), and loose, excep- markets (Box 12). There are many other positive tionally fluffy body feathers (h). Not only have

Box 10. Development of egg-laying stocks

COMMERCIAL EGG-LAYING chickens (Figure 1940s and 1950s was primarily due to 90% of all the egg-type chickens in 6) have shown a substantial increase the introduction of hybrid stock, utiliz- North America, and probably well over in productivity in the past 60 years. ing pure breeds which had been under half of the commercial egg-type chick- Some of this improvement has been development by numerous small breed- ens worldwide. due to developments in the areas of ers participating in the National Poultry Crosses among lines of the White management, nutrition, and disease Improvement Plan (NPIP). The more re- Leghorn (WL) breed produce nearly all control, but the effect of genetic im- cent increase has been primarily due to the commercially marketed white-shell provement is clear (ARTHUR 1986). Be- selection for increased egg numbers. chicken eggs in North America. The WL tween 1940 and 1955, the number of However, it should be remembered that lines in use today stem from the pure- eggs laid per hen in the United States the work of the small breeders and the bred stocks sold in the 1930s and increased from 134 to 192 (USDA-NASS formal testing parameters set by NPIP 1940s. Though there has been inter- 1998). By 1994, eggs per hen had in- shaped the foundation stocks, paving the crossing in many cases to develop new creased to 254. The change in the way for the phenomenal performance in strains, many of the currently used the modern commercial stocks appear to have been selected birds. without intermixing for 30 years or Today, only a few large more. Of particular note is the com- international poultry mon use of the Mount Hope strain, breeding companies pro- which is distinguishable by its large duce most of the world’s egg size and the B-19 and B-21 major commercial egg-type histocompatibility complex blood types chickens. Just 40 years which it carries (for an explanation of ago, the 1958-59 sum- the major histocompatibility complex mary of US random- (MHC) and B-blood types, see the sec- sample-egg-production tion on Immunogenetics in Chapter 3). tests (ARS 1960) listed In response to regional consumer 132 breeding firms. In the preferences, several commercial most recent egg-layer test brown-eggshell chicken lines have also still conducted in North been developed. Typically less efficient America, (NORTH CAROLINA than the White Leghorn strains, com- COOPERATIVE EXTENSION SER- mercial brown-eggshell chicken lines VICE 1996) only five breed- are usually produced by crossing ing companies were listed. Rhode Island Red males with high pro- These were actually duction White Leghorn females. Alter- Figure 6. White Leghorn hen (Photo courtesy owned by just three inter- natively, some high egg production national firms. These strains of Rhode Island Red or Barred of U.K. Abbott, University of California–Davis). three firms breed over Plymouth Rock may be used.

12 the hobby breeders helped in supplying such the hobby breeders and the different breed orga- research birds for one-time projects, but some of nizations, a number of problems are associated them have participated in long-term breeding with their conservation: 1) most of the amateur programs for researchers. conservators often only keep their stocks for a Although the majority of exhibition and mid- short period of time (typically just five years); level production poultry breeds have continued 2) small-scale hobby breeders who get breeding to exist under the rather informal stewardship of stock from a central clearing house of poultry

Box 11. Development of meat-producing stocks

IN 1950, A COMMERCIAL BROILER took 84 sumer ideal. The broiler-breeders were of the dual-purpose breeds. The out- days to grow to 1800 grams; by 1970, fortunate to have available the Cornish bred or crossbred parents have better this was cut to 59 days, and by 1988, breed (derived from fighting stock im- reproductive traits and general vigor it was down to 43 days (from HUNTON ported from India), which had many of than parents from the pure-lines, and 1990). As with the egg-type chickens, the desired carcass characteristics. The their offspring, a three- or four-way a large proportion of the improved per- breeders also found that the production cross, exhibit even more hybrid vigor. formance of meat birds can be attrib- characteristics (body type, rate of gain, Unfortunately, despite careful evalua- uted to developments in the areas of feed conversion) improved rapidly in re- tion of the breeding stock, some seri- management, nutrition, and disease sponse to selection. Unfortunately, im- ous structural and physiological prob- control. But choice of foundation provement in these areas had a strong lems have surfaced that appear to be breeding stock and early use of breed negative effect on the already poor re- the result of the intense selection for crosses were also important in the de- production characteristics of the Cornish desirable production characteristics. velopment of the broiler industry. lines (low egg production, low fertility, These include: leg weakness, cardio- More so than the egg market, the poor hatchability, reduced chick viabil- pulmonary insufficiency, breast blis- broiler market is strongly consumer- ity), and seriously impaired disease re- ters, increased fat deposition, and driven (POLLOCK 1999). Early consumer sistance (see section on immunogenet- muscle anomalies. input (chicken of tomorrow competi- ics, Chapter 3). The early breeders found While the turkey industry is consid- tions between 1946 and 1948) gave that crossing the Cornish roosters with erably smaller than the broiler chicken the broiler-breeders and growers a hens from improved dual purpose breeds industry, many of the same breeding good picture of consumer preferences: solved many of these problems. These methods have been used, and many compact, well-fleshed carcasses at af- “female” line breeds, including the Ply- of the same problems have been en- fordable prices. In other words, the mouth Rock and New Hampshire, have countered (HUNTON 1990). With a scrawny, angular cockerels (Figure 7) better body type than Single-comb White smaller genetic base, and a much available in large numbers from egg- Leghorns, yet lay eggs at a relatively high larger bird to start with (Figure 8), the selected Single-comb White Leghorn rate compared to the Cornish “male” structural and physiological problems lines did not even approach the con- lines. Today, the commercial sire is of- found in chickens are often magnified ten a cross between two in turkeys. Considering the small num- predominantly Cornish ber of primary breeders (three) and the strains, and the commer- scarcity of exhibition or research tur- cial dam is a cross be- key breeding stock, it is imperative to tween two strains de- safeguard the remaining genetic diver- scended from one or more sity of this domestic species.

Figure 7. Traditional broiler-type chicken Figure 8. Commercial Large White turkey tom (Photo cour- carcass of the 1940s (Photo courtesy of F.A. tesy of R.A. Ernst, University of California–Davis). Bradley, University of California–Davis).

13 stocks may never know their egg source or the degree of relationship of their foundation stock; 3) breeding populations are often very small, particularly for the rarer breeds, and pedigree information is frequently limited or not available; 4) some hobbyists deliberately inter-cross different breeds or varieties in attempts to improve or modify exhibition traits; 5) selection for production characteristics (e.g., fertility, viability, egg production, or disease resistance) may be largely ignored in these small-scale breeding programs, although de facto natural selection will tend to eliminate the infertile, disease-susceptible, or least-viable individuals; and 6) backyard breeders tend to have problems in controlling diseases Figure 9. Silkie rooster from UCD Silkie (Photo cour- and may have serious endemic diseases. If there tesy of J. Clark, University of California–Davis). were a formal conservation program for avian genetic resour- Box 12. Small renaissance of old-style chicken breeds ces, it would be logical for it to provide technical services to WITH THE INCREASING CULTURAL diversity ers are getting their stocks from the of our population, the white-feathered, few people who still maintain popula- these hobbyists who are a very highly selected meat- or egg-produc- tions of true Rhode Island Reds, Speck- important component of avian ing bird no longer meets the needs of led Sussex, New Hampshires, and so genetic resources conservation. all consumers. In response to a great on. Those supplying the specialty egg demand by ethnic markets and the markets are also looking for different many upscale restaurants searching for breeds to produce a colored egg that the “chicken of yesterday”, more and will be distinctive (brown, tan, green, more small producers are starting to or blue), such as Orpington, Rhode Is- raise “old fashioned” mid-level produc- land Red, and Ameraucana. Unfortu- tion or dual purpose breeds (those that nately, most of these so-called mid- are reasonably efficient at producing level production breeds have all but both meat and eggs). These produc- disappeared from American farms.

14 3

Avian genetic resources for biological research

ALTHOUGH MOST WIDELY KNOWN for their utility in Research with a variety of genetic stocks has the production of food (meat and eggs) and other produced many important discoveries in the ar- commercial products (feathers, vaccines, fertil- eas of genetics, virology, immunology, develop- izer, etc.), chicken, Japanese quail and other mental biology, and animal agriculture. (see domesticated avian species have long been a CRAWFORD 1990, for a review). These include the preferred experimental organism in applied and pioneering studies on Mendelian inheritance and basic life sciences. Some features contributing to sex determination of BATESON (1902), and BATE- their popularity are: SON and PUNNETT (1906, 1908). Not surprisingly, given its history of use in genetic studies, the • Availability (poultry, especially, are easily first linkage map reported for any domestic ani- raised and readily obtained, with inex- mal species was that for the chicken published pensive common strains providing cost- by HUTT (1936). The turkey has provided one of effective research animals). the few known vertebrate models for parthenogenesis (embryo formation in an unfertilized egg) • High rate of embryo production com- (Box 5), and the wide range of metabolic and de- pared to mammals. velopmental mutations in chicken (Boxes 8, 13) and quail have allowed researchers to start in- • Accessibility of the avian embryo (the ex- vestigating the molecular bases of these defects, ternally incubated avian embryo is avail- and, eventually, to determine the normal func- able for experimental manipulation dur- tion of the affected gene. In virology, chicken ing most stages of embryonic develop- hosts were used by ROUS (1911) to identify the ment). first tumor-causing virus, Rous sarcoma virus. Later, the genetics of host resistance to RNA vi- • Excellence as a higher vertebrate animal ruses was elucidated (CRITTENDEN et al. 1963), model. and the Marek’s-like herpes virus found in turkeys was used in the first successful vaccination • Ease of surgical manipulations (surgical program against a tumor-causing virus in the procedures on birds are much less likely chicken (OKAZAKI et al. 1970). More recently, to result in infections due, perhaps in BUMSTEAD and PALYGA (1992) described one of part, to their high body temperatures). the first molecular genetic maps of a domestic animal using DNA markers (RFLPs), and the • Extensive history of use (more than a chicken genome map continues to be among the century of research provides avian scien- best developed of those for agricultural animals tists with needed information and genetic (LEVIN et al. 1994; CHENG et al. 1995; CROOIJMANS stocks to ask specific experimental ques- et al. 1996; CHENG 1997). It is by far the best- tions). developed map for any avian species or any species with ZW sex chromosome determination. In • Animal welfare considerations are gener- particular, the usefulness of the chicken genome ally less complex for domestic birds than map in cross-species comparisons was high- they are for other vertebrates. lighted at the First International Workshop on Comparative Genome Organization (ANDERSSON

15 et al. 1996), although workshop participants also given proper conditions. In fact, chickens from expressed concern that the continuing loss of some commercial stocks that have been selected poultry genetic stocks will impair some impor- for egg production may average over 280 eggs in tant comparisons with the human and other ge- a one-year period, with fertility of greater than nome maps. The chicken gene library was the 95%. While genetic strains used in research are first one described for an agricultural animal usually less productive, most produce at least species and, along with the human gene library, 100 eggs per hen per year, providing researchers was the first constructed for any vertebrate with an abundant, dependable source of indi- (DODGSON et al. 1979). Critical early observations vidually packaged embryos of known genotype. of gene structure, organization, and expression The functional reproductive system of most were made using chicken ovalbumin (WOO et al. female birds, including the chicken, is composed 1978), globin (DODGSON et al. 1979), histone of the left ovary and the oviduct. The ovary con- (ENGEL and DODGSON 1981), insulin (PERLER et tains ova in varying stages of development, with al. 1980), and lysozyme (STEINER et al. 1987) the largest being released at regular intervals. genes, among others. The oviduct is a tubular organ, consisting of several parts: the funnel-shaped infundibulum, Avian reproductive biology where each ovum enters the oviduct and fertilization occurs; the wide, thick-walled, magnum, Birds such as the chicken are uniquely adapted where the albumen is produced and deposited for the production of large numbers of offspring, around each of the ova; the narrower, thinner- in the form of fertile eggs, over relatively long walled isthmus, where the shell membranes are periods of time. In the wild, birds will usually lay made; the large, pouch-like shell gland, where a series of eggs on sequential days until they the egg is “plumped” with fluids and electrolytes, have as many eggs as they can comfortably incu- before the calcium carbonate shell is deposited bate (a “clutch”). At that time, they will stop lay- on the shell membranes; and, finally, the vagina, ing eggs and start to incubate or brood the eggs. with its specialized sperm storage sites at the However, during their long domestication, chick- utero-vaginal junction, where spermatozoa can ens have been selected for large clutch size and remain viable for more than a week (VAN KREY nonbroody behavior, so that hens today will con- 1990; BAKST 1993). Thus, the oviduct is where tinue to lay at a high rate for at least a year, both the fertilization and the packaging of ovum

Box 13. Inherited muscular dystrophy of the chicken

GENETIC MUSCULAR DYSTROPHY (GMD) of bud transplants demonstrated that dys- The discovery of and sequencing of the chicken was first formally described trophic muscles grafted to a normal host dystrophin, the gene associated with in 1956 in selected New Hampshire and its nerve were phenotypically dys- Duchenne muscular dystrophy in the strains at the University of California– trophic, and normal muscles trans- human and the mdx dystrophy in the Davis. Since then, literally hundreds of planted to a dystrophic host were nor- mouse, added a new dimension to the reports have been published on the ab- mal, indicating the problem was in the study of muscle abnormalities. The normality. The disorder is caused by a muscle and not directly its innervation. dystrophin protein itself is absent in single gene; but little is known of the Thus, if neural influences are involved in humans with Duchenne dystrophy and molecular nature of the defect (PESSAH GMD, it is likely it is the dystrophic in the mdx mouse. This led the Muscu- and SCHIEDT 1990; WILSON 1990; muscle that is unable to respond prop- lar Dystrophy Association to focus its IANNACCONE et al. 1995). erly to signals from its phenotypically efforts on the human and mouse forms Symptoms of the disorder typically normal nerve. of the disease. But it is still not known appear during late embryogenesis and One of the major uses for the dystro- whether or not the dystrophin gene neonatal muscle maturation. Muscles phic chicken has been to test therapies, product is defective in GMD of the with fast twitch, alpha-white muscle fi- including an elevated oxygen levels chicken. It is known that dystrophin in bers such as the superior pectoralis (ASHMORE and SOMES 1966), the drugs D- normal chickens is closely homologous and biceps are most affected. These penicillamine (which affects collagen for- to the mammalian gene, and that a “white” muscle fibers exhibit irregular- mation; PARK et al. 1979), cyprohepta- dystrophin protein is present in GMD shaped rounded fibers, both larger and dine, methysergide, and diphenylhydan- chickens. It is not known if this pro- smaller than normal. Eventually the toin. A Muscular Dystrophy Association- tein is the same as the one in normal muscles atrophy and are replaced by supported drug screening program chickens. Future research focusing on fat and connective tissue. The early ap- achieved promising results with steroids the role of the dystrophin gene, estab- pearance of GMD in fast twitch but not such as corticosterone-21-acetate lishing expression of the abnormality in tonic fibers suggests it is expressed (C21A). The most effective treatments se- in cell culture, and studying the fac- in a particular myogenic lineage. verely reduced the growth rate of the tors that regulate maturation of nor- Studies have shown that the prob- chicks, as if the synthesis of defective mal muscle are worthy of study. lem with dystrophic muscle is not a proteins play a role in expression of the faulty set of neural instructions. Limb abnormality.

16 occurs, producing the neat, aseptic association differences between the appearance of chicken of nutrients and germplasm that will ultimately and Japanese quail cell nuclei. Selected early form the chick. Embryonic development pro- embryonic cells from quail have been grafted gresses as the egg moves down the oviduct, so into chicken blastodiscs, which, after careful that when the egg is laid 24 to 27 hours after incubation, reveal exactly how the donor quail fertilization, the embryo is a radial dome of cells are distributed in the later embryos (DIE- 40,000 to 60,000 cells that is already forming TERLEN-LIEVRE and LEDOUARIN 1993; DIETER- distinct layers (epiblast and hypoblast). At this LEN-LIEVRE 1997). Such studies have permitted stage of development, the embryo is comprised the development of a detailed fate map of the of cells that are morphologically undifferenti- early blastodisc. Additionally, avian embryos ated (EYAL-GILADI and KOCHAV 1976; WATT et al. have been used extensively in teratological 1993) and pluripotential, i.e., able to differenti- studies, in which their response to chemical, ate into a number of different cell types nutritional, hormonal, and environmental (PETITTE et al. 1990). challenges were evaluated to provide guide- Numerous studies on avian reproduction lines for identifying causes of nongenetic devel- have been conducted since the turn of the cen- opmental defects (LANDAUER 1967, 1973), and, tury, particularly on the control of fertility and eventually, for identifying the biochemical egg production (HUTT 1949; LERNER 1950, mechanisms disturbed by such exposures. 1958). Consequently, much is known about Avian embryos have also been of value in stud- genetic and environmental factors that influ- ies of cell proliferation related to cancer-like ence or govern reproduction in the male and cell growth or programmed cell death inherent female chicken, turkey, and Japanese quail. in certain stages of embryonic development Some of the genetic variants affecting repro- (SANDERS and WRIDE 1997). ductive traits that were studied include: restricted ovulator, multiple ovulator, riboflavin Models for human genetic transport deficient, and male infertility associated with the rose-type comb. diseases Embryology Animal genetic defects have long been used as model systems in the study of human dis- There is a long and rich history of use of the eases. A few of the avian genetic disorders that avian embryo as a model system for study of have proven especially useful include the au- vertebrate development (ROMANOFF 1960). Be- toimmune forms of avian vitiligo (AUSTIN et al. ginning with Aristotle (384–322 BC) whose 1992; AUSTIN and BOISSY 1995; ERF et al. Historia Animalium includes the first known 1995), scleroderma (GERSHWIN et al. 1981; fully preserved description of a chicken em- ABPLANALP et al. 1990; VAN DE WATER et al. bryo, researchers and natural science histori- 1994; SGONC et al. 1995), and thyroiditis (re- ans have found bird embryos to be a readily viewed by ROSE 1994), the polygenic avian available, dependable source of embryos that scoliosis (RUCKER et al. 1986; LIEN et al. 1990; could be manipulated and observed during the MOCHIDA et al. 1993), the autosomal recessive course of development independent of and form of muscular dystrophy (PESSAH and without harming the female parent (a major SCHIEDT 1990; WILSON 1990; IANNACCONE et al. issue when studying mammals). Its easy ac- 1995) (Box 13), and a polygenic muscle defect cess during organogenesis, relatively inexpen- in the broiler chicken (Box 14). Other known sive cost, and bilaterality providing opportuni- avian mutations mimicking human disorders ties for contralateral controls for microsurgery include: autosomal and sex-linked dwarfism, and other perturbations have made the avian lamellar ichthyosis, poly- and hypodactyly, embryo one of the best characterized verte- gouty uremia, genetic obesity, several types of brate models, both in classical and molecular micromelia, glaucoma, a non-autoimmune terms (MACCABE and NOVEROSKE 1997; MORGAN form of vitiligo (BOWERS et al. 1994), and a vari- 1997). Another factor that has made the avian ety of neurological disorders (SOMES 1988; embryo the model of choice for studies of ver- CRAWFORD 1990). tebrate development is the respectable catalog Japanese quail disease models have also of existing mutations (listed in ABBOTT 1967; attracted the attention of biomedical research- SOMES 1988; and CRAWFORD 1990). Avian em- ers. For example, at the University of British bryos have also proven uniquely adapted to Columbia, quail serve as a model in the study interspecific tissue grafting because of distinct of atherosclerosis, and in age-related macular

17 degeneration (AMD). This condition is the most derstanding of the complexities of the vertebrate common cause of blindness in humans over the immune system. They have also provided the age of 65. Except for primates, the quail is cur- framework for the development of disease-resis- rently the only suitable nonhuman species in tant poultry stocks (LAMONT 1994) and for under- which to study this disease. standing the differential effectiveness of certain Despite the proven utility of existing strains vaccines in chicken strains with different MHC of chickens, turkeys, and Japanese quail in bio- haplotypes (BACON and WITTER 1992). medical research, fewer and fewer researchers In studies which focused on cell-mediated are making use of these unique genetic stocks immunity and macrophage function, researchers (WILSON 1990). Contributing to this decline are showed that genetic differences between selected the increasing costs and the more technical (and strains can also affect the ability of a given bird costly) nature of many studies that have biased to promote or suppress Rous sarcoma tumor researchers towards smaller vertebrate labora- formation (QURESHI and TAYLOR 1993). tory species (rats and mice). Whether or not it is The relationship between MHC haplotype and the best possible choice, the default condition immunocompetence is currently attracting the for medical research continues to be the rodent, attention of the commercial sector. This is due to ultimately limiting the study of disorders and a strong negative correlation between character- diseases to those suitable to such animal mod- istics such as improved feed conversion and els. Enhanced use of exceptional avian models more rapid growth rates with a weaker antibody depends on the continued accessibility of exist- response to specific antigen challenges and a ing stocks and the development and mainte- decreased effectiveness of cell-mediated immu- nance of new genetic stocks. nity, both of which are related to MHC function (GAVORA 1990; HELLER et al. 1991). This trend in Immunogenetics immune responsiveness of commercial egg-laying Leghorn strains (small, slower-growing birds) Natural genetic variation in the major histocom- is compared with that of commercial broiler patibility complex (MHC) has been studied ex- strains. In addition, a distinct loss of immuno- tensively in the chicken, particularly as it relates competence was shown in a study that com- to disease resistance (GUILLEMOT et al. 1989; BA- pared two broiler-type lines, one descended from CON and DIETERT 1991; HELLER et al. 1991; SUNG commercial stocks developed in Canada in 1957, et al. 1993; KEAN et al. 1994; SCHAT et al. 1994; and the second from modern commercial stocks BACON and WITTER 1995; HEMENDINGER et al. (QURESHI and HAVENSTEIN 1994). Thus, commer- 1995). The different MHC haplotypes have been cial broiler-chicken breeders are now showing systematically integrated into highly inbred interest in improving immune system function to stocks to control or eliminate complications in offset the immune depression that has been immune response introduced by subtle differ- bred into their stocks with long-term, intensive ences in the genetic background (ABPLANALP selection for meat production traits. 1992; Box 7). These studies led to a better un-

Box 14. Deep pectoral myopathy: One price of intensive selection

DEEP PECTORAL MYOPATHY (DPM) is char- able in as little as 15 minutes when broil- with better circulation and a different acterized by death of the mid-region ers were induced to flap their wings for breast muscle configuration still ac- of the supracoracoideus muscle of the short periods of time. ceptable to the public which would large broilers and marketable turkeys. Polygenic physiological problems are probably require outcrossing to the un- It is also known as “Green Muscle Dis- not simply resolved. Food preferences of affected, unimproved genetic stocks. ease” and “Oregon Muscle Disease”. the public and the economic forces of DPM has its human counterpart. It A series of investigations by Siller, the poultry industry favor selection for is one of a class of pathological situa- Harper, and their colleagues (WIGHT large breasts maintaining a physiologi- tions known as “Compartment Syn- and SILLER 1980; WIGHT et al. 1981; cal situation in which deep pectoral dromes”. One of these is anterior tibi- HARPER et al. 1983; SILLER 1985; WILSON muscles predisposed to ischemia may alis syndrome or “March Gangrene” in et al. 1990) demonstrated that the my- continue to be a problem. Indeed, SILLER which hard exercise by untrained or opathy was due to an ischemia caused (1985) said that the disorder was a “pen- susceptible individuals (such as mili- by swelling of the muscle during exer- alty of successful selection”; “...wild tur- tary recruits on their first forty-mile cise. An enlarging muscle, an inelastic keys and less intensely selected old com- hike of basic training) results in per- muscle fascia, and a rigid sternum cre- mercial strains are apparently not sus- manent muscle damage similar to that ate a situation in which circulation is ceptible to DPM, it is obvious that this found in turkeys and large broilers. cut off to the mid-region of the muscle. disease is man-made”. One solution Ultrastructural changes were detect- would be to breed broilers and turkeys

18 As more is learned about the genetic mechanisms controlling Box 15. Ancona chickens give a new angle on disease resistance disease resistance and suscep- AN UNUSUAL GENE CONFERRING disease re- some Marek’s disease virus. This gene, tibility, researchers will be able sistance was recently discovered in the Rfp-Y, now also identified in other to narrow their focus to specific rare Ancona breed of chicken. A unique chicken breeds, is on the same chro- genes. A few of these genes are copy of a gene outside of the known mosome as the MHC, and is still being major histocompatibility complex characterized (BRILES et al. 1993; now known, but the majority (MHC) was identified that imparts re- WAKENELL et al. 1996; MILLER et al. 1994, remain to be identified. As with sistance to the commercially trouble- 1996). plant genetic stocks, some resistance genes may well be found in stocks not now commercially useful, which includes individuals with two (normal or e.g., wild or feral populations and breeds such disomic), three (trisomic), or four (tetrasomic) as Ancona chicken (Box 15) or other relatively copies of chromosome 16 (a microchromosome). unimproved populations (GAVORA 1990). The biological consequences of aneuploidy and gene dosage effects on growth, development and Cytogenetics immunity have been the subject of many studies (DELANY et al. 1988; QURESHI et al. 1989; HEMEN- The chicken has proven to be a good vertebrate DINGER et al. 1992; LEPAGE et al. 1996) and con- cytogenetic model, despite the complexity of its tinues to be important in current research. The karyotype (the majority of the 78 chromosomes Trisomic Line has been particularly useful in are exceptionally small microchromosomes; see studying chromosome dosage effects on regula- Figure 10). In particular, unique cytogenetic tion of MHC expression, with tetrasomics and conditions in the chicken have encouraged biolo- trisomics expressing distinctly higher levels of gists to use the chicken as a means to study al- MHC-products on their cell surfaces than disom- tered chromosome constitutions (e.g., gene dos- ics (MUSCARELLA et al. 1987; DELANY et al. 1988; age effects) on the biology of this and other HEMENDINGER et al. 1992). higher vertebrates. The chicken is exceptional The mPNU line segregates for a large deletion among the higher vertebrate animal group in in the nucleolar organizer region of chromosome that several viable genetic strains exist which 16, giving it a reduced number of rRNA genes showcase the effects of chromosomal aneup- (DELANY et al. 1995). This line was used to estab- loidy, polyploidy, or large deletions, several of lish the developmental threshold (i.e., lethal these occurring in microchromosomes. limit) for rRNA gene copy number for the first The linkage and chromosomal location of the time in a higher vertebrate (DELANY et al. 1994, major histocompatibility complex (MHC) with the 1995). The Trisomic and mPNU lines were in- single nucleolar organizer region (i.e., the rDNA strumental in establishing the location of a new locus) were determined in studies of birds from locus, Rfp-Y (Box 15) on this microchromosome the Trisomic Line (BLOOM and BACON 1985), (MILLER et al. 1994, 1996). The CSIRO Triploid line, maintained in Aus- tralia, is an important higher vertebrate polyp- loid model. Studies of the line have contributed information regarding errors of meiosis, genetic basis for inheritance of meiotic errors, sex determination, gonadal differentiation, sex reversal, and polyploidy effects on growth and development (LIN et al. 1986; THORNE et al. 1987, 1988, 1991, 1997; SOLARI et al. 1991; THORNE and SHELDON 1991). Genomics Genomics is a rapidly evolving field of science that emphasizes the study of complete genomes and chromosomes (Box 16). Genomic studies have also changed in focus, from the general or- Figure 10. Chromosomes from a Red Jungle Fowl hen ganization of the genome to the identification from UCD 001 (Photo courtesy of M.E. Delany, Univer- and localization of functional genes. Genomic sity of California–Davis). research is well advanced with the chicken.

19 Genome map development involves coordi- personal communication) have used inbred lines nated approaches (BURT et al. 1995): 1) expand- (RPRL 6I2 and 7I3) for mapping of non-MHC ing and improving the genetic linkage maps of genes which are responsible for resistance/sus- chickens and other poultry, 2) using markers, ceptibility to Marek’s disease virus. More gener- such as microsatellites, that have high utility, ally, BACON’s (1987) congenic MHC lines have improving the cytogenetic maps available for been critical for a variety of genetic analyses of birds, and 3) making new efforts towards inte- the avian immune system. Again, the speed with grated physical (recombinant DNA clone-based) which this work was accomplished was en- maps. Candidate gene research involves a vari- hanced and it could only have been accom- ety of genes of interest, including those encoding plished using the available well-characterized the major histocompatibility complex genes, genetic lines. other immune-response genes, ribosomal RNA One long-term objective of avian genomics is genes, cytokine and other hormone-encoding to develop an understanding of genes respon- genes, and genes related to muscle and mor- sible for economically important traits in poul- phology. Finally, several efforts are underway to try. These are variously known as quantitative map and identify anonymous genes associated trait loci (QTLs) (VERRINDER GIBBINS 1993) or eco- with disease resistance, growth and reproduc- nomic trait loci (ETLs). The ETLs are analogous tion, and general viability of poultry. to, and sometimes models of, complex genetic The interdependence of genome research and traits of humans and other species. In some genetic resource conservation can hardly be cases, the protein product of these genes is al- overstated. Inherent to all genetic experimenta- ready known. In other cases, researchers seek to tion and breeding is the fundamental require- identify and further characterize previously un- ment for allelic diversity. It is preferable that di- known ETLs (anonymous genes). Among the verse alleles be preserved in well-characterized, genes under study are those encoding disease inbred (homozygous) lines. As a concrete ex- resistance traits. These include major histocom- ample, it is widely agreed that one of the reasons patibility genes, cytokine genes, and anonymous that the laboratory mouse has become the most genes encoding Marek’s disease virus resistance. important model system for biomedicine has Other genes of interest include those which been the availability of diverse inbred lines (pio- regulate growth, reproduction and morphology neered most notably by the Jackson Laboratory). (e.g., endocrine genes, collagen and other bone COPELAND and JENKINS (1991) used such inbred and connective tissue genes, anonymous ETLs), mouse strains in their intraspecific backcross and genes which relate to general viability and reference family approach to gene mapping. A cellular function (e.g., ribosomal RNA genes, similar strategy was followed in developing the East Lansing chicken mapping reference population, derived from the segregating progeny of Box 16. Government involvement in genome research a cross between two inbred lines: Red Jungle Fowl (UCD THE US GOVERNMENT IS HEAVILY invested Avian Disease and Oncology Laboratory in genome research. In response to the (ADOL) in East Lansing, the National 001) and White Leghorn (UCD call for a USDA National Genetic Re- Research Iniative Competitive Grants 003), genetic stocks developed sources Program in the 1990 Farm Bill, Program, and limited funding through by H. Abplanalp at the Univer- the USDA created the National Animal CSREES to Regional Research Programs sity of California, Davis (CRIT- Genome Research Program (NAGRP), (e.g., NC-168) and a National Research TENDEN et al. 1993). The two administered by Cooperative State Re- Support Program, NRSP-8. NRSP-8 pro- lines are highly divergent, dis- search, Education, and Extension Ser- vides for coordination of animal ge- vice (CSREES) with Richard Frahm as nome research via the appointment of playing a high degree of inter- Direcctor. The NAGRP was developed Species (Poultry, Cattle, Sheep, Swine) line polymorphism. The diverse as an equal companion to the National Technical Committees and Coordina- and inbred character of these Animal Germplasm Program (NAGP), tors. Parallel developments in animal lines has been a major con- administered by Agricultural Research agriculture genomics have occurred tributor to their subsequent Service (ARS) with Roger Gerrits as di- world-wide, particularly in Europe (e.g., rector. The essential interrelationship Institute for Animal Health, Compton, utility. In contrast, BUMSTEAD of genome research and germplasm England; Roslin Institute, Edinburgh, and PALYGA (1992) used ani- resources is emphasized by the com- Scotland; University of Wageningen, mals from two divergent Leg- mon origin of and close ties between The Netherlands). One of the major horn lines as the parents for the NABRP and the NAGP. Suppport for goals of the NAGRP is to cooperate with their reference backcross panel. agricultural animal genomics comes international efforts to enhance Cheng and Bacon (Avian Dis- primarily from the USDA as direct sup- progress in animal genetics. port to ARS laboratories, such as the ease and Oncology Laboratory,

20 anonymous viability genes, and neuropeptide/ Developmental genetics neurotransmitter genes). Two major strategies are being used to locate Chicken developmental mutations played a sig- and characterize genes of interest. In the candi- nificant role in the early days of the science of date gene approach, potential ETL-associated genetics. Bateson’s work at the turn of the cen- genes are chosen based on the physiological or tury showed that different comb shapes in the genetic effects of the proteins or RNAs they en- chicken followed Mendelian inheritance pat- code as studied either in poultry or other spe- terns. This proved that Mendel’s principles, cies. The candidate gene is then isolated by re- though discovered in plants, also applied to ani- combinant DNA techniques, further character- mals (BATESON 1902; BATESON and PUNNETT ized, and used to generate markers to test its 1906, 1908). Today, there is increasing interest usefulness as an ETL indicator in appropriate in the molecular genetic analysis of such devel- populations. In the map-based approach, anony- opmental or pattern mutants to determine the mous ETLs are mapped in a test or resource basis of the developmental defects that produce population. Then a gene that is closely associ- these changes. The defined physical defects as- ated with a particular ETL can be isolated based sociated with the avian developmental muta- on its location in the map, or by a combination tions, exemplified in Figures 11 and 12 and Box of candidate and map-based techniques. A fun- 17, contrast strongly with many of the synthetic damental tool required for the latter approach (knock-out) mutations in the mouse, whose phe- (and also useful for the candidate-gene ap- notype is often simply characterized by the tim- proach) is a high quality, integrated genome ing of early embryonic death. map. High quality means densely spaced mark- Currently, developmental genetics is one of ers that are useful in many populations; inte- the most rapidly advancing areas in the biologi- grated implies that the poultry genetic, cytogenetic, and physical maps are also correlated with genome maps of other animal species. The identification of conserved syntenic groups between poultry genomes and those of humans and mice will facilitate the use of genetic and physiological data from these more highly studied species. A critical point with regard to genome research is the availability and suitability of poultry genetic resources. While commercial breeders maintain populations that presumably contain a wide variety of alleles, these populations are often not useful for research purposes if these breeders are unwilling to make populations (or data) available because of trade secrecy (proprietary) concerns, or the commercial lines are so outbred and therefore so heterogeneous at economic trait loci that it becomes impossible to measure specific effects at one or a reasonable number of candidate loci. Therefore, genetic mapping experiments require the availability of diverse populations of well-characterized, inbred, or partially inbred (or carefully randombred) germplasm. Public access to genetic stocks and information is essential for the advancement of science. Thus, the growing number of patent requests on such material by private corporations is a concern, as markers identified by researchers supported by funding from private organizations, using stocks that are privately owned (as with recent gene mapping studies by Figure 11. Wingless-2 chicken embryo from UCD the Groenen group (CROOIJMANS et al. 1996) may Wingless-2 X 331 (Photo courtesy of J.M. Pisenti, be restricted in their availability. University of California–Davis).

21 cal sciences (RIDDLE et al. 1993; FALLON et al. 1994; MORGAN 1997; SANDERS and WRIDE 1997; CHUONG 1998). Questions that have intrigued and puzzled embryologists and geneticists for decades can finally be addressed. The award of the 1995 Nobel Prize in Medicine/Physiology to E.B. Lewis, C. Nusslein-Volhard, and E.F. Wieschaus reflects the worldwide recognition of the fundamental importance of research in developmental genetics. Their work in identifying fruit fly (Drosophila melanogaster) developmental mutants and determining the molecular basis for some of these mutations provided key information for identifying a whole class of pattern- altering genes (the homeobox-containing genes) found in such diverse organisms as the fruit fly, nematode, echinoderm, fish, chicken, mouse, and human. Avian developmental geneticists interested in pattern formation have studied an array of morphological mutants, most of which are recognizable early in development. These mutants typically alter the beak, head, trunk (including the tail), limbs, and integument (skin, feathers, and Figure 12. Eudiplopodia foot from UCD Eudiplopodia scales) (ABBOTT 1967; ROMANOFF 1972; LANDAUER X 003 (Photo courtesy of J.M. Pisenti, University of 1967, 1973; SAWYER and GOETINCK 1988). In California–Davis). many instances, as exemplified by the wingless- 2 mutation in Figure 11, the mutations have a (the so-called phenocopy effect). A field with pleiotropic effect (alter more than one embryonic great potential then involved studies of the basis structure), with combinations of defects involv- of phenocopies and of means of overcoming ing the limbs, trunk, beak, feathers, heart, kid- them. Later, studies with pesticides provoked neys, and so on. Another tantalizing finding, additional interest, as many of these environ- much investigated by LANDAUER (1967, 1973), mental toxins could also produce phenocopies of reflected the close similarity of many known mu- different mutant syndromes. tant syndromes with those produced by treat- Currently, the genes affecting patterning in ments with a variety of chemicals or hormones, the avian embryo are increasingly important in or caused by nutritional deficiencies or excesses developmental studies (RIDDLE et al. 1993;

Box 17. Patterns in vertebrate limb development

LIMBLESS IS AN AUTOSOMAL recessive mu- prospective limb-forming territory to re- tremely important to bear in mind that tation that causes the complete ab- spond appropriately to the normal limb- the discovery that limbless encodes a sence of limbs in homozygotes; het- inducing signal, and as a consequence gene playing a critical role in limb de- erozygotes have normal limbs (PRAHLAD the apical ectodermal ridge does not velopment could not have been made et al. 1979). The earliest stages of limb form. In the absence of this important before the molecular markers for dor- development appear to occur normally signaling center, limb outgrowth does sal and ventral cell identities became in the mutant homozygotes, but not occur. The importance of these stud- available. Other mutations in avian shortly after the limb bud forms, it ies is that they have revealed a previously stocks may be equally valuable, but ceases to develop and soon regresses. unknown link between patterning along their importance cannot be assessed Two recent studies of this mutation the dorsal-ventral axis and the initiation at present because of limitations in our (GRIESHAMMER et al. 1996 and NORAMLY of limb bud formation. knowledge about limb development or et al. 1996) have provided evidence This breakthrough in understanding because the appropriate markers for that although the phenotype of the mu- the fundamental mechanism of limb de- assaying gene function are not avail- tant is a lack of limb outgrowth, the velopment in vertebrates would not have able. If we discard stocks because we primary defect in limbless embryos is been made were it not for the availabil- do not appreciate their value, we may a lack of normal dorsal-ventral pattern- ity of chicken stocks carrying the limb- be discarding the key to a more pro- ing at a very early stage of limb devel- less mutation, because similar mutations found understanding of a particular de- opment. This apparently results in an in other species such as mice and hu- velopmental or disease process. inability of the embryonic cells in the mans are not known. However, it is ex-

22 RODRIGUEZ et al. 1996). Specifically, these muta- these mutations to study perturbations in the tions can be used to study signaling, biological expression of developmentally regulated mol- clocks, interactions between different develop- ecules that could explain the pattern abnor- mental controls, and the relationship of the de- malities characteristic of such mutations fective patterns to similar syndromes produced (GRIESCHAMMER et al. 1996; NORAMLY et al. by chemical or other experimental means. Im- 1996; RODRIGUEZ et al. 1996; LAUFER et al. portantly, these mutants can be used to investi- 1997). Thus, there is still much to be gained gate directly various hypothetical models of gene from the analysis of the mutations that have action developed by other means. occurred in avian stocks and which have been maintained in university collections. Two par- Limb development ticularly useful chicken mutations are the For more than 50 years, vertebrate limb develop- limbless mutation, which has recently been ment has been a major focus of developmental used to gain a remarkable insight into the fun- biology (SAUNDERS 1948; ABBOTT 1967; SAWYER damental mechanism of limb initiation (Box and GOETINCK 1988; FALLON et al. 1993; LAUFER 17), and the eudiplopodia mutation (Figure 12), et al. 1997). Between 1972 and 1998, advances which has showcased the critical nature of in this field have been highlighted at six Interna- timing and location of signaling molcules in tional Conferences on Limb Development and early limb bud on the final patterning of the Regeneration. The limb bud has been of interest limb (LAUFER et al. 1997). because it provides an experimental paradigm for exploring fundamental mechanisms of verte- Feather and scale development brate tissue outgrowth and patterning (SAUNDERS 1972; EDE et al. 1977; HINCHLIFFE and JOHNSON The morphogenesis of cutaneous appendages, 1980; CONNELLY et al. 1981), and for identifying such as feathers, scales, and hair, depends on the molecules that mediate these processes. It a series of reciprocal interactions between the also provides a model for studying the mecha- epithelial and mesenchymal layers of the em- nism of embryonic induction (CONNELLY et al. bryonic skin (SENGEL 1976). Such epithelial 1981). Most of what is presently known about mesenchymal interactions also take place in vertebrate limb development has come from the development of the limb (RIDDLE et al. studies performed in avian species, primarily the 1993; FALLON et al. 1994; NISWANDER et al. chicken, but it is now clear that the mechanism 1994), tooth (VAINIO et al. 1993), kidney (PAT- of limb development has been highly conserved TERSON and DRESSLER 1994), lung (PETERS et al. throughout evolution, and what has been 1994), and mammary gland (CUNHA 1994). Evi- learned about limb development in the chick is dence is accumulating which indicates that the equally informative about limb formation in epithelial-mesenchymal signaling that occurs mammals (FALLON et al. 1993). Indeed, it appears during the early morphogenesis of these vari- that the early steps in limb development and the ous organs relies on common molecular mech- molecules that perform them are virtually identi- anisms (Box 18 and CHUONG 1998). Thus, in- cal in all vertebrate species (MORGAN 1997), and formation gained on the mechanisms for any it is only at relatively late stages that species- one of these organs systems is very likely to be specific differences become significant. A num- applicable to our understanding of patterning ber of researchers have used developmental mu- events in other systems. A future challenge is tations to test hypothetical control mechanisms to understand how different embryonic struc- governing limb pattern at the tissue level. More tures acquire their identity while relying on recently, still other researchers have returned to common signaling mechanisms.

23 Box 18. Patterns in skin development

THE SCALELESS MUTATION has contributed opment of the feathers and scales (SAW- 1996). Based on these observations, significantly to our understanding of YER and ABBOTT 1972; SAWYER et al. 1974; FGF-2 was hypothesized to be an ac- both the cellular and molecular mecha- SAWYER 1979). These classical studies in tive molecular component of the early nisms that control the formation of cu- the genetics, histology, and tissue and signaling between the dermal mesen- taneous appendages, particularly the cell biology of this mutation laid essen- chyme and the overlying epithelium feathers and scales in birds. Chickens tial groundwork for current molecular during feather morphogenesis. The ob- homozygous for the scaleless mutation studies that were designed to explore servation that FGF-2 can rescue the mu- (Figure 13), an autosomal recessive molecular control mechanisms governing tant phenotype of scaleless embryos trait, lack most feathers and scales feather and scale development. suggests that FGF-2 either is, or is (ABBOTT and ASMUNDSON 1957) as well In a recent study, the role of fibro- downstream from, the signal that the as the scleral ossicles (the precursors blast growth factor (FGF) signaling was ectoderm of the scaleless mutant fails to the bony eye ring) (PALMOSKI and examined in the epithelial-mesenchymal to generate. GOETINCK 1970). These defects have interactions during the initiation of The results obtained with the scale- made this mutant an ideal model sys- feather germ formation in genetically less skins indicate that this mutant is tem for studying the early development normal and scaleless embryos. A spatially an excellent system to elucidate sig- of cutaneous appendages, and, by ex- and temporally restricted pattern of tran- naling pathways by FGF and other sig- trapolation, other organ systems description was seen for the genes that en- naling molecules in the morphogenesis pending on epithelial-mesenchymal in- code FGF-2 and FGFR-1 in developing of cutaneous appendages. Mechanisms teractions. In some of the earliest stud- feather germs of the normal chick em- identified from this system may be ap- ies in which normal and scaleless ecto- bryo. FGF-2 expression is restricted to plicable to the understanding of devel- derm and mesoderm were recombined, the early feather epidermal placodes, opmental mechanisms in other organs researchers showed that the scaleless whereas, FGFR-1 expression is limited to in which epithelial-mesenchymal inter- mutation specifically affects the ecto- the dermal condensations underlying the actions play a role (PETERS et al. 1994). dermal epithelium (GOETINCK and placodes. Transcription of these genes ABBOTT 1963; SENGEL and ABBOTT 1963). could not be de- This ectodermal defect prevents the tected in skins of formation of the ectodermal placodes scaleless embryos in the skin of scaleless embryos that failed to de- (GOETINCK and SEKELLICK 1972), thus in- velop feathers as a terrupting the normal sequence of tis- result of their ecto- sue interactions. Despite the ectoder- dermal defect. How- mal defect, the mutant mesenchyme ever, when scaleless is fully capable of participating in skin was treated feather and scale development when with FGF-2, feathers recombined with genetically normal ec- would form at the toderm (GOETINCK and ABBOTT 1963; site of application of SENGEL and ABBOTT 1963; SONG and SAW- the growth factor, YER 1996). and the induced Interestingly, the mutant pheno- feathers express type can be greatly modified through FGFR-1 in their der- selection for increased or decreased mal condensations . number of feathers. The accumulated However, the re- modifier genes for increased feather- sponse was re- ing alter the expression of the scale- stricted to a narrow less gene by altering the response of window of time, the mesodermal signals (BROTMAN strongest around 1977a,b). A number of studies also ad- day seven and eight, dressed the cellular and subcellular and gone by day 11 Figure 13. Hens from UCD Scaleless-Low (Photo (histological) differences in the devel- (SONG and SAWYER courtesy of J. Clark, University of California–Davis).

24 4

Conserving avian genetic resources

CONSERVATION OF AVIAN WILDLIFE species receives tion strategies must be applied. The situation is global attention because of the large numbers of similar for domesticated breeds of birds, but species presently in decline, and because birds there is more concern for conservation of specific provide a focus for recreational activities through- combinations of traits and genes, with minimal out the world. Less known are the needs for con- changes in gene frequency. Even more restrictive servation of progenitor, landrace, and feral is conservation of genetic stocks where specific populations of domesticated birds. Even less genes are targeted. For these genetic entities, no well publicized is the critical situation of many of change in gene or genotype frequency can be the specialized stocks used in research, as dem- accepted. Thus, we recognize a distinction be- onstrated in Chapter 5. tween conservation and preservation. The former Safeguarding existing biodiversity is a com- allows utilization with minimal genetic changes mon theme in the conservation of all types of over time caused by human activity and the lat- avian genetic resources, but the strategies used ter requires that no genetic changes occur, ex- to meet this goal can be quite different, depend- emplified by nonliving materials, quiescent (e.g., ing on the speicies. Wild species are generally cryopreserved) specimens of gametes and em- conserved through natural habitat protection bryos, or closely bred living genetic stocks. and take regulations (i.e., hunting or harvesting Assays for DNA polymorphisms can be done limits for a given species), with captive breeding with nonliving biological materials, providing the used in only the most severe cases of species opportunity for assessment of genetic diversity decline. Measuring the genetic diversity in wild in historical times from museum specimens or species is being addressed in a relatively few preserved tissues, including blood serum. This cases with DNA markers. Such data contribute emphasizes the value of preserved biological ma- to the development of rational schemes for con- terials as a component of a conservation strategy serving genetic diversity. Wild progenitors of do- for birds. Cloned genomic or cDNA libraries can mesticated birds, such as the Red Jungle Fowl be preserved indefinitely at low temperatures. are treated similarly, but wild turkey conserva- This includes DNA clones used for preparing tion, as another example, is enhanced by re- molecular linkage maps and for discovery of stocking and translocation of individuals. This functional genes. Databases of DNA nucleotide activity is motivated by the need for conservation sequences of genes or expressed sequence tags of the species and its diversity, but the fact that are extremely rich sources of information be- turkey is a recreational game bird is perhaps a cause sequences from many species are avail- stronger motivation for conservation. able for screening and comparisons with un- The goal of genetic resource conservation is known sequences. the maintenance of genetic integrity of a species This report focuses on the conservation of or populations within a species. For populations genetic stocks, as defined earlier. However, a in nature, natural evolutionary processes remain holistic view of avian conservation is appropriate active, thus changes in gene frequency, popula- because the methods used for preserving genetic tion sizes, and geographic distribution are to be stocks and breeding populations, especially se- expected. Human interventions impact species men cryopreservation, can be adopted or modi- composition through disruption of habitat and fied for other species, including threatened or harvesting. In such cases, proactive conserva- endangered wild species. Conservation methods

25 need to be adopted which meet the specific re- Live animals quirements of the species or the trait (genes) being conserved. An avian genetic resource conser- The maintenance and periodic reproduction of vation system includes several components (ac- live animals is the most dependable alternative quisition, maintenance, utilization, distribution, available for preserving a genetic stock. This is documentation, and health and quarantine) particularly true for the inbred and long-term which can provide broader service than the con- selected stocks, with their integrated collections servation and distribution of genetic stocks. This of quantitative trait alleles. This is also the most is elaborated in Chapter 6. reasonable way to maintain stocks that are often used in research. However, due to financial con- Methods of conservation of straints, most researchers cannot justify the live maintenance of stocks that are used only spo- genetic stocks radically, and recent events have shown (Chap- ter 5) that many unique lines are terminated for Avian genetic materials may be preserved in the this reason. form of live birds, as cryopreserved semen and The average number of birds required to dispersed embryonic or primordial germ line maintain a given genetic stock depends upon its cells, as preserved tissues from which DNA can characteristics. Randombred and selected stocks be isolated, as cloned genomic or cDNA, or as require a larger base population (often several nucleotide sequence data. Of these methods, hundred birds) than those carrying single-gene living birds and cryopreservation methods per- mutations. The latter may be realistically contin- mit recovery of animals, while preserving DNA ued with fewer than ten mutant-carrier birds if a gives the potential of recovering selected genes robust outbred stock is used as one parent line or defined segments of chromosomes. However, each generation. Other factors that affect the it should be remembered that at best each DNA number and distribution of birds needed to sequence represents only a very small portion of maintain a viable population include bird live- a total genotype and that, while samples of total ability, amount of inbreeding depression, en- DNA from a population may be preserved, sort- demic diseases, and the risk of natural or man- ing out the genes useful for a particular purpose made disasters, which can literally wipe out ge- may be a difficult task, particularly when gene netic stocks in a very short period of time. interactions must be taken into consideration. Maintaining stocks as live animals is very ex- Cryopreservation of semen and embryonic cells pensive, especially the selected lines and ran- is gaining acceptance as a means of preserving dombred populations. Even temporary shifts in endangered genetic resources, including wild interests of the curator or sponsoring institution species, rare breeds, and mutant or specialty can quickly orphan such genetic stocks, often lines used in research. leading to stock elimination and extinction of Ultimately, the preferred conservation method valuable genes or gene combinations. These re- depends upon 1) the reliability of the method to alities are documented in Chapter 5, emphasiz- yield the desired number of live animals, 2) the ing the need for backup sites or a permanently characteristics of the stock, and 3) the availabil- dedicated conservation program. ity of technical support, instrumentation, and storage facilities. Ideally, more than one method Semen cryopreservation of conservation should be used, or there should be a backup site to reduce the risk of loss due to The technology for semen cryopreservation fire, equipment failure, and human errors. Below (BAKST 1990; BUSS 1993; HAMMERSTEDT 1995) are outlined some features of live-bird conserva- has been successfully adapted for the preservation and three methods of cryopreservation of tion and propagation of chickens and certain semen or embryonic cells from which live birds feral and endangered species (GEE 1995). Many may be recovered. Semen cryopreservation has different cryopreservation protocols have been the longest history, although not a highly effi- evaluated (SEXTON 1979, LAKE 1986, HAMMER- cient recovery rate. Dispersed blastodisc and STEDT and GRAHAM 1992, BUSS 1993, HAMMER- primordial germ cell cryopreservation are prom- STEDT 1995). According to HAMMERSTEDT (1995) ising emerging technologies that will require semen cryopreservation is the most cost-effective further research to improve recovery rates to germplasm conservation strategy. Hammerstedt more acceptable levels. outlined the benefits of semen cryopreservation for the commercial poultry industry, but this preservation technique has not yet been widely

26 adopted. An important feature of semen cryo- Unfortunately, the semen from inbred, specialty, preservation for unique or endangered poultry and mutant-carrier stocks most at risk often lines is that semen can be collected frequently does not respond well to cryopreservation proce- (twice weekly) from a small number of males for dures that worked reasonably well with commer- use when females become available or in the fu- cial stocks. Frozen-thawed semen from these ture establishment of founder flocks. Other ben- less-robust stocks often exhibit extremely high efits of semen cryopreservation are: or complete infertility associated with poor motil- ity and high numbers of freeze-damaged or killed • Frozen semen is not easily affected by spermatozoa. Obviously, further research is diseases or natural disasters. needed, not only in the development of improved semen cryopreservation procedures (improved • Semen cryopreservation from many birds diluents, cryoprotectants, and other supple- of several lines can be accomplished at a ments, and optimizing cooling and thawing relatively low cost rates), but also addressing the significance of species variation, male-line variation within a • The expense of maintaining a flock is species, and individual male variation within a reduced or eliminated. given strain. However, despite the potential utility of this procedure in preserving the germ- • Frozen semen is more easily transported plasm of rare or endangered stocks or species, nationally or internationally than live only a few researchers in Japan, England, and birds or fertile eggs (HAMMERSTEDT 1995). the US are currently conducting research on semen cryopreservation. There are obvious limitations to the routine use of semen cryopreservation. For some species Blastodisc cryopreservation and genetic stocks the method may not be reliable or yet suitably developed. Another consider- Cryopreservation of the cells from an avian blas- ation is that only the male genome is preserved, todisc (Figure 14, the embryonic cells in an un- which means that the complex genome of highly incubated fertile egg) is a new technique that inbred or selected stocks could not be preserved can be used to preserve the intact genome of intact if only maintained as frozen semen, be- poultry genetic stocks (REEDY et al. 1995, Box cause, of course, none of the corresponding in- 19). While the methods are still being perfected, bred or selected females would be available for frozen-thawed blastodisc cells have been suc- insemination with the cryopreserved material. cessfully integrated into the blastodiscs of host Thus, while semen cryopreservation permits the chicken eggs, and developed into reproductively incorporation of preserved gene complexes into competent adults. The long-term viability of diploid animals, these gene complexes would be cryopreserved blastodisc cells is not yet known, heterozygous in the progeny and subject to ge- although cryopreservation studies with semen netic recombination in subsequent intermatings of progeny. On the positive side, semen cryopreservation may prove to be the most appropriate method for preserving single-gene mutant stocks, particularly if the genetic background is not a great concern in the modification of the mutant gene expression. Another problem with cryopreserved semen is that the quality of thawed semen is currently quite low. This is reflected in fertility levels rarely exceeding 70%, and more typically less than 50%, due to sperm destruction and deformity caused by semen cryopreservation and recovery procedures. One researcher estimated that cryopreserved semen has less than 2% of the fecun- dity of fresh semen (WISHART 1985). This is in spite of the fact that most of the successful cryoprotectants, diluents, and freezing tech- Figure 14. Stage X blastodisc (at time of oviposition) niques were developed with semen from highly (Photo courtesy of M.E. Delany, University of Califor- productive commercial broiler chicken stocks. nia–Davis).

27 and other cell-types suggests that properly cryo- and germline chimeras. These chimeric chickens protected and frozen specimens will remain vi- hatch and mature normally, and, when inter- able indefinitely if kept in liquid nitrogen. bred, produce some offspring that are purebred The large size and complex structure of the Barred Rock (KINO et al. 1997). While frozen- avian embryo (already composed of 40,000 to thawed blastodermal cells form germline chime- 50,000 cells when the egg is laid) do not permit ras less frequently than fresh blastodermal cells, the application of techniques that have been de- a sufficient number of “reconstituted” birds of veloped for cryopreservation of mammalian em- lines maintained as cryopreserved blastodermal bryos. A different strategy is required which uses cells can be obtained to use the technology to dispersed cells isolated from the relatively undif- store valuable genetic material (KINO et al. 1997). ferentiated embryonic cells present in the newly Thus, this technique should eventually provide laid fertile egg (Box 19). Recent experiments an inexpensive long-term solution for preserving have demonstrated that frozen-thawed blasto- the intact genome of stocks (particularly inbred dermal cells from purebred chickens of the and selected stocks) that are considered to be Barred Plymouth Rock breed can successfully valuable genetic resources but are not currently integrate into an irradiated White Leghorn host required in an active research program (Box 20). blastoderm to form embryos that are somatic

Box 19. Mosaic chickens and genetic stock preservation

A NEW TECHNIQUE HAS BEEN developed at the University of Guelph (Ontario, Canada) that can be used to reclaim both freshly dissociated and cryopreserved chicken embryonic cells (Figure 15, REEDY et al. 1995). Briefly, cells from the stage X embryo (EYAL-GILADI and KOCHAU 1976) can be removed, dispersed, and injected into recipient blastodiscs that are at the same stage of development. The resulting chimeras (mixture of host and donor cells), which can be either male or female, produce donor-derived gametes at rates of up to 100% (PETITTE et al. 1990; 1993; CARSIENCE et al. 1993; THORAVAL et al. 1994; KAGAMI et al. 1995). Matings of male and female chimeras that each produce donor-derived gametes yield offspring with the complete donor genotype at a rate that is the product of the frequency of the production of donor-derived gametes by eachof the chimeric parents (KINO et al. 1997).

Figure 15. Diagram of avian blastodisc cryopreservation and recovery (from REEDY et al. 1995).

28 Research aimed at improving Box 20. Orphaned CFAR stocks preserved as frozen the rate of germline transmis- embryonic cells sion by cryopreserved blastodermal cells could increase the THE FIRST LARGE-SCALE DEPOSITION of fro- mal cells were harvested and frozen at effectiveness of this technology zen blastodermal cells was completed the Avian Physiology and Genetics in 1998, preserving over 30 of the Laboratory at the University of Guelph, and reduce the number of blas- stocks once kept at the Centre for Food (Ontario, Canada). If these stocks are toderms that are required to Animal Research (CFAR). This had been required in the future, trained techni- ensure that the genetic diver- the flagship research center for poul- cians can thaw the cells and make sity within a stock is main- try research for Agriculture and Agri- germline chimeras (see Box 19), which tained in the reconstituted Foods Canada. The cryopreserved can then be mated to obtain pure “re- population. While this would be CFAR stocks were among those that constituted” birds from the original could not be placed with other institu- CFAR lines. a welcome improvement in the tions before April 1, 1997. Blastoder- technology, it should be emphasized that the current technology can be used to conserve genetic resources embryonic germinal crescent into the blood ves- and that it is the only fiscally realistic way to sels. After a short period of time being carried maintain the genome of stocks in an unadulter- through embryonic and extra-embryonic circula- ated state at the present time. tory systems, these cells will migrate out of the In the future, the range of genetic diversity blood vessels and selectively colonize the gonad- may increase as transgenic stocks are produced. al ridges. While in the migratory phase (mostly Many of these stocks will be developed for spe- between HAMBURGER and HAMILTON (1951) stages cific experimental uses that have short-term 13 and 15), the PGCs can be removed from the utility in research. It would be prudent to store embryo in blood samples. Primordial germ cells these stocks as frozen blastodermal cells rather can be partially separated from the blood cells than discard the time and effort expended in by density gradient centrifugation and can then their production. be cultured (CHANG et al. 1995; KUWANA et al. 1996), cryopreserved (NAITO et al. 1994a), or im- Primordial germ cell mediately injected into a host embryo (TAJIMA et al. 1993; NAITO et al. 1994b). One of the benefits cryopreservation of this method of germplasm preservation is that a highly enriched population of germline cells of Cryopreservation of primordial germ cells (PGCs) approximately 60% PGCs (NAITO et al. 1994b) isolated from the blood of early-stage chick em- can be introduced into a host embryo. Thus, bryos is another way of preserving the intact ge- even when frozen-thawed PGCs were injected, nome of both male and female birds (NAITO et al. up to 25% of the gametes were shown to be from 1994a). The PGCs are the precursors of the the donor germline (NAITO et al. 1994a). This adult gametes (ova and spermatozoa) and form a germline recovery rate is substantially better distinct population of readily distinguishable than that obtained from frozen-thawed blasto- cells even before they move from the extra- disc cells (KINO et al. 1997).

Genetic stocks: Current resources and recent losses

ALMOST ALL OF THE GENETIC STOCKS of chicken, support from the National Science Foundation turkey, Japanese quail, and other domesticated and the USDA Agricultural Research Service. In birds that have been used in research in the US 1998 each curator was contacted again to pro- and Canada were developed and conserved by duce an updated report. A survey instrument public sector universities and federal govern- (Appendix 1) was sent to all of the curators men- ment research organizations in these two coun- tioned in SOMES (1988) and the participants in tries. Many in the research community have the CSREES Regional Research Project NE-60 on been aware of the gradual attrition, and occa- genetic basis for resistance and immunity to sional dramatic losses, of these specialized avian diseases. Individuals listed in the Poultry stocks over the years. Some important genetic Science Association 1995–96 membership direc- resources were discarded before relocation plans tory who indicated a focus on genetics or immu- could be developed or because a new stock cura- nology, and individuals on the 1997 Poultry Sci- tor could not be located. Current threats to addi- ence Resource List prepared by the Poultry Sci- tional abandonment of existing genetic stocks ence Association and R.D. Reynells (USDA/ gave impetus for a study of the true situation of CSREES) were also contacted (usually via email existing genetic stocks, where such stocks are or telephone) and queried. In all, survey forms located, and their status for conservation and were sent to 37 curators (11 in Canada and 26 use. The situation is dynamic, for not only are in the US) at 27 institutions listed in the SOMES established genetic resources at risk, but new (1988) registry and 72 additional individuals genetic stocks are also being developed in cur- were contacted by phone or email. All curators rent research programs that will in turn require were asked to report on the status of stocks that preservation or conservation in the years to had been included in the 1988 registry (i.e., come. SOMES (1988) provided a benchmark with which of these stocks had been retained, trans- his comprehensive, but not exhaustive, sum- ferred, or eliminated), and to list any new stocks mary of the state of genetic stocks up to 1988. acquired since1988. They were also asked to in- Hence the Task Force undertook an assessment dicate the prognosis for long-term security of of the current situation with the goal of produc- each stock. Finally, respondents were asked to ing a complete database inventory of extant ge- send the names of any poultry genetic stock cu- netic stocks, along with a summary of the ge- rators they were aware of, either at their institu- netic stocks that had been discontinued, aban- tions or elsewhere, and these individuals not doned, or lost since 1984. This information con- already contacted were also asked to respond to stitutes the basis for the proposal of a comprehen- the survey. sive strategy geared towards the conservation of avian genetic stocks important to basic biological Results from the survey research and education. (See Chapter 6). According to the survey, 361 genetic stocks are Survey methods currently maintained (Table 1 and Appendix 2). Of the 36 curators at 27 institutions listed in the The study was conducted by Jacqueline Pisenti 1988 registry (SOMES 1988), 31 of them (or their during 1995–97 at the UC Genetic Resources successors) responded; four no longer main- Conservation Program, with additional financial tained stocks, and 27 still had at least some of

31 the stocks listed in the 1988 registry. Of the 72 of the existing genetic stocks. The detailed data- other persons queried, 44 responded and 13 re- base in Appendix 2, Table 2.1, lists the charac- ported that they curated poultry genetic stocks. teristics of every genetic stock that was identified By species, there are 268 chicken stocks in the survey. These were grouped into ten main (with 38 existing only as cryopreserved material), categories. The largest category is single-gene 65 Japanese quail, 20 turkey, six waterfowl, and mutants, with 107 stocks that display color var- two gamebird. Table 1 shows the categorization iations or defects in developmental, immunologi-

Table 1. Summary by category of existing poultry genetic stocks (live and cryopreserved). Japanese Waterfowl, Category Chicken quail Turkey Gamebird Total Number of stocks Bloodtype-Gene pool 6 0 0 2 8 Bloodtype-Major Histocompatibility Complex (MHC) 13 0 0 0 13 Bloodtype-MHC-Inbred 51 0 0 0 51 subtotal 70 0 0 2 72

Chromosomal variant 5 0 0 0 5

Endogenous virus 1 0 0 0 1 Endogenous virus-Inbred 4 0 0 0 4 subtotal 5 0 0 0 5

Inbred 27 1 0 0 28

Mutant-Color, eggshell 0 2 0 0 2 Mutant-Color, feather 1 12 0 0 13 Mutant-Developmental defect-Eye 5 0 1 0 6 Mutant-Developmental defect-Face/limb 28 0 0 0 28 Mutant-Developmental defect-Skin/feather 8 6 0 0 14 Mutant-Developmental defect-Spine/tail 3 0 0 0 3 Mutant-Gene pool 7 1 0 0 8 Mutant-Immunological defect 5 0 0 0 5 Mutant-Neurological defect 3 0 0 0 3 Mutant-Physiological defect 12 0 0 0 12 Mutant-Reproductive defect 3 0 1 0 4 Mutant-Uncategorized 8 1 0 0 9 subtotal 83 22 2 0 107

Pure breed 12 0 5 6 23

Randombred 18 14 8 0 40

Selected-Behavioral trait 2 1 0 0 3 Selected-Egg trait 11 0 2 0 13 Selected-Growth trait 14 18 3 0 35 Selected-Immune trait 11 1 0 0 12 Selected-Physiological trait 2 8 0 0 10 subtotal 40 28 5 0 73

Transgenic 2 0 0 0 2

Uncategorized 6 0 0 0 6

Total 268 65 20 8 361

32 cal, neurological, physiological, or reproductive At the time this report went to press, approxi- characteristics. The selected stocks category, mately one-third of the stocks kept as live birds with 73 stocks, are products of long-term selec- were considered by their curators to be at high tive breeding and are characterized by above- or risk of elimination within the next few years below-normal performance in defined behavioral, (30% of the chicken, 35% of the turkey, and 49% growth, egg production, immunological, or of the Japanese quail stocks). Just over 40% physiological traits. The next largest category were considered to be in a secure situation, with 72 stocks consists of the bloodtype vari- including 42% of the chicken, 45% of the turkey, ants, representing most of the known forms of and 37% of the Japanese quail stocks. The chicken erythrocyte and leukocyte alloantigens. remainder of the stocks (about 30%) were con- The inbred category, with 28 stocks, consists of sidered to be only moderately at risk. stocks approaching genetic homogeneity as a result of crossing full sibs or other close relatives Lost stocks for many generations. In addition to the inbred category, highly inbred stocks can be found in In the last 15 years, some 238 avian genetic the bloodtype-MHC-inbred and endogenous vi- stocks were reported as lost or eliminated by rus-inbred categories. A few highly inbred stocks research institutions in the US and Canada are also found among the mutant-developmental (Table 3; this also includes those few stocks re- defect-face/limb category. The randombred cat- ported as transferred to private individuals or egory with 40 stocks and the pure breed cat- organizations). The actual number of lost stocks egory with 23 stocks are important as control or is probably much higher. The data in Table 1 reference populations and represent gene pools show the numbers and percentages of genetic from which many of the selected and mutant stocks lost, based on the current number of ex- stocks were derived. The uncategorized group isting stocks and documented numbers of lost with six stocks are those stocks for which no stocks. Some new stocks have been developed description was available. since the last survey, specifically in the MHC- Forty-one researchers at 27 institutions (24 defined endogenous virus and selected catego- in the US and 3 in Canada) maintain 323 genetic ries. These recent additions inflate the total stocks as living birds (Table 2). Six of these insti- numbers of existing stocks and bias downwards tutions maintain 20 or more stocks (University the estimated percentage of stocks lost. Even so, of Arkansas, University of British Columbia– stock losses have been substantial: close to 40% Vancouver, University of Connecticut–Storrs, of the reported living US stocks and over 60% of University of California–Davis, University of Wis- the Canadian stocks were discontinued since consin–Madison, USDA/ADOL East Lansing, 1984, 42% of all stocks (Table 2). Most notable Michigan). Six maintained between ten and 19, was the discontinuation of more than 30 genetic four had six to nine, and 11 had five or fewer stocks by Agriculture and Agri-Food Canada at genetic stocks. Two institutions in the US and its facility in Ottawa. This clearly reflects a dis- four in Canada no longer keep such stocks. turbing trend in avian genetic resources conser- In addition to the living bird collections, 87 vation. genetic stocks are maintained under semen or Of all lost stocks, 75% were chickens, 11% blastodisc cryopreservation at five institutions. were turkeys, 11% were Japanese quail, and 4% Such frozen reserves are kept at the University were gamebirds or waterfowl. Ironically, more of Guelph (Guelph, Ontario) (33), the University than one-third of these stocks were reported lost of California–Davis (31), the USDA Avian Disease between 1995 and 1998 while this survey was in and Oncology Laboratory at East Lansing, Michi- progress, including 50 chicken stocks, 19 turkey gan (17), Pennsylvania State University (4), and stocks, 10 Japanese quail stocks, and four of the the University of Wisconsin–Madison (2). Five of waterfowl stocks. The losses were heaviest (35% the cryopreserved stocks at University of Califor- of all lost stocks) among the mutant and chro- nia–Davis are no longer maintained as live birds. mosomal variant categories, although the se- The 33 cryopreserved stocks at the University of lected (25%) and the bloodtype-MHC-inbred Guelph are from the Canadian Food Animal Re- (21%) categories were not far behind. Some of search collection and also are no longer main- these lost stocks, such as the bloodtype-MHC tained as live birds. Thus, 51 stocks maintained specialized stocks, included genes that can be as live birds are also backed up by cryopreserva- recovered by breeding and selection from exist- tion, while 38 stocks now exist only under cryo- ing genetic resources, but at a great cost of preservation. money and time. The now-extinct lethal and

33 Table 2. Number of poultry genetic stocks kept as live birds in institutions in the USA and Canada in 1998 and the number lost since 1984.

Kept as living birds† Lost since 1984† Curating institution C JQ T W,G Total C JQ T W,G Total % all‡ USA Number of stocks Alabama: Auburn University 10 0 0 0 10 17 0 0 0 17 63 Arkansas: University of Arkansas 12 9 0 0 21 1 2 0 0 3 13 Arizona: University of Arizona 0 0 0 0 0 1 0 0 0 1 100 California: University of California 46 1 0 0 47 15 7 1 4G 27 36 Connecticut: University of Connecticut 20 0 0 0 20 8 1 1 0 9 31 Delaware: University of Delaware 1 0 0 0 1 0 0 0 0 0 0 Georgia: University of Georgia 4 9 0 0 13 2 6 0 0 8 38 Illinois: Northern Illinois University 7 0 0 2G 9 0 0 0 0 0 0 Illinois: University of Illinois 2 0 0 0 2 0 0 0 0 0 0 Indiana: Purdue University 2 1 0 0 3 6 0 0 0 6 67 Iowa: Iowa State University 17 0 0 0 17 5 0 0 0 5 23 Iowa: USDA National Animal Disease Center 0 0 1 0 1 0 0 0 0 0 0 Louisiana: Louisiana State University 0 3 0 0 3 2 0 0 0 2 40 Maryland: University of Maryland 0 1 0 0 1 0 0 0 0 0 0 Massachusetts: University of Massachusetts 4 0 1 0 5 10 0 1 0 11 69 Michigan: USDA Avian Disease & Oncology Lab. 37 0 0 1W 38 2 0 0 0 2 5 Minnesota: University of Minnesota 0 0 0 0 0 5 0 0 0 5 100 Nebraska: University of Nebraska 1 1 0 0 2 0 0 0 0 0 0 New Hampshire: University of New Hampshire 14 0 0 0 14 14 0 0 0 14 50 New York: Cornell University 7 0 0 1W 8 7 1 0 0 8 50 North Carolina: North Carolina State University 5 0 7 2W 14 0 0 2 0 2 13 Ohio: Ohio State University 2 7 6 0 15 15 0 2 0 17 53 Oregon: Oregon State University 1 0 0 0 1 0 0 17 0 17 94 Pennsylvania: Pennsylvania State University 6 0 0 0 6 0 0 0 0 0 0 Virginia: Virginia Polytechnic Inst. & State Univ. 4 0 0 0 4 0 3 0 0 3 43 Wisconsin: University of Wisconsin 19 1 3 0 23 6 0 0 0 6 21

Total in USA 221 33 18 4W 278 116 20 23 4G 163 37 2G Canada British Columbia: Univ. of British Columbia 3 32 0 0 35 0 5 0 0 5 13 Ontario: University of Guelph 3 0 1 0 4 10 0 0 0 10 71 Ontario: AA-FC Center for Food Animal Research 0 0 0 0 0 30 0 0 6W 36 100 Quebec: McGill University 0 0 0 0 0 4 0 0 0 4 100 Quebec: University of Lavale 0 0 0 0 0 1 0 0 0 1 100 Quebec: Deschambault Research Station 0 0 0 0 0 4 0 3 0 7 100 Saskatchewan: University of Saskatchewan 3 0 1 2W 6 11 0 1 0 12 6 7

Total in Canada 9 32 2 2W 45 60 5 4 6W 75 63

Total 230 65 20 6W 323 176 25 27 6W 238 42 2G 4G †C = chicken, JQ = Japanese quail, T = turkeys, W = waterfowl, G = gamebird. ‡“% all” indicates the proportion of total stocks at that institution that were lost since 1984.

34 subvital mutant stocks, along with the large • The collection of stocks at the University number of discontinued translocation stocks, of Massachusetts went into dispersal in appear rarely, are difficult to detect, and are of- 1997, due to the retirement of its cura- ten discovered serendipitously. A number of the tor. While several important mutant viable mutations that were kept in gene pools or stocks have found new curators, includ- as specialized stocks in research collections can ing the auto-immune vitiligo (DAM) still be found among hobbyist breeds or exhibi- chickens and their normal controls, the tion stocks, but they present problems in use feather color and comb-type gene pool because there is a risk of transferring diseases and tester stocks have been eliminated. or they have background genotypes that may be inappropriate for use in research. • At Oregon State University (Corvallis), a Individual stocks and whole collections that large and unique collection of 17 stocks have been lost in recent years include: carrying feather-color and embryo-lethal turkey mutations was eliminated in • Inbred, specialty, and historical commer- 1995, due to funding difficulties. A simi- cial stocks once maintained by Agricul- lar problem contributed to the loss of an- ture and Agri-Food Canada in Ottawa other collection of turkey stocks in the that were dispersed or eliminated in 1960s, this one held at the University of 1997, due to loss of government support. California–Davis. While some of these specialized stocks were sent to other institutions or private • Fires at bird-care facilities have killed off companies, 33 were retained only as at least two turkey stocks at the Desch- cryopreserved blastodisc cells kept at the ambault Research Station and one Japa- University of Guelph, (Ontario, Canada) nese quail mutation at University of Cali- (Box 20) and 30 were eliminated. How- fornia–Davis. Five other quail mutations ever, one-half of these 30 were bloodtype salvaged from that fire at Davis (three stocks that are still available elsewhere. unique to University of California–Davis) • Five stocks (long-term inbred lines and were subsequently eliminated due to one gene pool of dominant mutations) funding difficulties. maintained at the University of Minne- sota, were eliminated in 1996, although • At the University of California–Davis, the two (the dominant marker stock and the retirement of two researchers with large inbred Rhode Island Reds) had been collections of research stocks has put transferred to the University of British over 40 stocks in jeopardy (Box 3); these Columbia a few years earlier. include over 20 mutations and an array of MHC-defined inbred lines, many of which are found nowhere else.

Table 3. Summary by category and species of poultry genetic stocks reported lost since 1984. Japanese Waterfowl, Category Chicken quail Turkey Gamebird† Total No. %‡ No. %‡ No. %‡ No. %‡ No. %‡ Bloodtype-MHC-Inbred 49 28 0 0 0 0 0 0 49 21 Chromosomal variant 33 19 0 0 0 0 0 0 33 19 Inbred 6 3 0 0 0 0 3G 30 9 4 Mutant 25 14 11 42 19 70 0 0 55 23 Pure breed 18 10 0 0 3 11 4W 40 25 10 Randombred 3 2 3 12 0 0 1W 10 7 4 Selected 42 24 11 46 5 19 1W ,1G 20 60 5 Total 176 74§ 25 11§ 27 11§ 6W,4G 4§ 238 100§ †W=waterfowl; G=gamebird. ‡This column indicates the percentage of lost stocks in a category out of the total of lost stocks for that species. §This value is the percentage of total lost stocks over all species accounted for by the total lost stocks for a given species.

35 Trends in poultry genetic stock been eliminated or merged with other departments, leaving only eight poultry science depart- development and conservation ments today (PARDUE 1997; DELANY and PISENTI 1998). With reorganization of these departments Only a few large collections of vertebrate genetic and their resources, genetic stock losses were stocks have been assembled, including the inevitable as a result of loss of long-term support mouse (Mus musculus) collection that is cur- funds, reallocation of funding and resources to rently kept at the Jackson Laboratory in Bar other areas, condemnation of poultry housing Harbor, Maine (Box 21) and the Japanese quail facilities without construction of adequate re- collection at the University of British Columbia placement housing, retirement of researchers (Box 22). But it is the chicken mutant collections who served as curator of stocks, shifts in re- that probably have the longest history, starting search interests, and new research on exotic in the 1920s with Landauer and Dunn at the avian species as research models or companion University of Connecticut, Storrs Agricultural birds. Experiment Station (a collection that still exists, The number of genetic stocks reported by in part). These early researchers in vertebrate SOMES (1988) is nearly the same as that detected embryology used classical embryological tech- in the present survey. However, the present sur- niques to study mutant gene expression, the ef- vey documented the loss of nearly 200 chicken fect of background genes on mutant phenotype, stocks, 23 turkey stocks, and at least 8 Japa- and the production of environmentally induced nese quail stocks, so it is evident that a consid- phenocopies (genetically normal embryos that erable number of new stocks have been pro- resemble mutants) of specific mutant syndromes duced during the past decade, possibly displac- (LANDAUER 1973). Ironically, it is these areas of ing some of the older ones. Most curators faced study that attract the attention of researchers with the need to reduce or disperse inventory try today, just as the remaining academic avian ge- to find alternate conservators for stocks that are netic stock collections have become threatened. slated for elimination (Boxes 2, 3, 4), although This underscores the need for preserving these this is not always successful (Box 8). Informal unique gene pools and identified single-gene networking for new curators has worked well mutations for the benefit of future researchers. enough with single-gene mutation stocks when Similar arguments can be made for other re- curating researchers had funding to support a search stocks, particularly inbred and selected number of these unique stocks, but this is often strains. Both require many years and large, no longer an option. pedigreed populations during their development; Clearly, planned and unplanned stock losses factors that place formidable barriers to the re- are impacting the availability of specialized ge- generation of such stocks because of short-term netic resources to researchers. Stock elimina- and limited funding commitments. tions are increasingly driven by funding prob- Traditionally, poultry stocks were maintained lems, more will be lost. Particularly at risk are at the research institutions where they were de- the selected lines and mutant stocks, which re- veloped and studied. These institutions, fre- quire either larger numbers or special handling quently in states with a large or growing poultry to propagate. industry, often had poultry or avian science departments that were independent of the larger Box 21. The Jackson Laboratory model for vertebrate genetic animal science departments. stocks This served to encourage re- A GOOD EXAMPLE OF A SUCCESSFUL genetic worldwide. In addition to providing the search on the different poultry stocks conservation program is the genetic stocks, the Jackson Laboratory species and the development Jackson Laboratory, a non-profit, also maintains and serves a computer- independant research institution, in Bar ized database system available any- and maintenance of unique Harbor, Maine. Along with research and where in the world that enables fast, poultry genetic stocks. In the training, its third mission is the main- efficient access to a single comprehen- early 1960s, some 45 poultry tenance and distribution of a huge in- sive archive on the mouse. Supported science departments existed in ventory of mouse genetic stocks. They partly by government grants and partly the US; since that time and in are maintained as either live animals by user fees, the Jackson Laboratory is or frozen embryos and are distributed a good model for long-term preserva- spite of the tremendous growth either as live animals or DNA prepara- tion of avian genetic stocks. Further in economic value of the the tions. Annually, the Laboratory sup- information on the Laboratory and the poultry industry and great con- plies about two million mice from over databases can be accessed from their sumer interest in poultry prod- 1,700 stocks to universities, medical web site (URL: http://www.jax.org/). ucts, most departments have schools, and research laboratories

36 Box 22. Japanese quail at the University of British Columbia

PRIOR TO 1980, A JAPANESE quail colony the Centre have been widely utilized for tory animal, and consultation for local was maintained at the Department of research, teaching, and extension. producers and raptor rehabilitation Animal Science, University of British Co- Areas of research include genetics, centers on management of the flocks lumbia (UBC) for research and teach- physiology, developmental biology, can- and/or marketing. In the latter cases, ing in genetics. In 1980, the goal was cer, atherosclerosis, eye defects, neurol- birds from the Centre were sometimes set to expand this colony and manage ogy, animal behavior, and animal ecol- provided as breeding stocks. With the it as a genetic resource collection, and ogy. In the past three years, the Centre increase in consumption of quail prod- to make it available to users outside assisted or collaborated in more than 35 ucts in metropolitan areas in Canada the department. In 1982, the Quail Ge- research projects. Currently, there are and also in the southern US, there has netic Resource Centre was formally es- two on-going research projects using been a significant increase in requests tablished with the support of the de- quail as a model to study atherosclero- for information from other parts of partment and the Natural Sciences and sis and another project using quail to Canada and from the US. Engineering Research Council of study age-related macular degeneration The Centre has been partially sup- Canada (NSERC). In the last 14 years, (AMD). Except for monkeys, the quail is ported by an infrastructure grant from many new mutations and strains have the only suitable model to study this dis- NSERC, which provided the salary for been incorporated into the collection. ease which is the most common cause the full-time technician. This grant cov- At present, the quail populations at the of blindness in humans over the age of ered 25% of the operating costs. Be- Centre harbor 27 morphological and 65. The Centre has also started screen- sides capital investments, the Univer- physiological mutations, close to 50% ing chicken microsatellite DNA primers sity provided 40% of the operating of all the mutations (not including obtained from Hans Cheng to detect costs through department funds. The isozyme variants) ever reported in the polymorphism in quail. remaining 35% of the operating costs literature for this species. Detailed de- Teaching uses include courses in bi- were covered by income from sales of scriptions of the mode of inheritance, ology, genetics, poultry management, products and users’ fees. The NSERC the phenotype, and possible applica- and animal behavior at University of Brit- support was terminated in 1995, and tions of these mutations can be found ish Columbia and other universities and income generated from egg sales and in CHENG and KIMURA (1990). In addi- colleges in the province. These stocks research contracts are not sufficient to tion, they also maintain 12 random- have also been used by students from sustain the operation. An endowment bred populations and specially devel- local secondary schools for their senior will be sought to generate Canada oped strains that are useful for biologi- science projects. The Centre staff also $30,000 Cdn a year to keep the opera- cal research or as breeding stocks for provides consultation for researchers and tion going. meat and egg production. Stocks from teachers on managing quail as a labora-

An Avian Genetic Resources System: Proposal

Task Force recommendation Resources System. A System on this binational level is necessary because no dependable re- IT HAS BECOME ABUNDANTLY CLEAR from the analy- gional or local solution exists. sis of extant genetic stock collections and from the information obtained from task force mem- Components of an Avian Genetic bers and others that many avian genetic stocks have been lost and many others are at serious Resources System risk of being lost. Further, the prognosis for maintaining new research stocks as they are be- The Avian Genetic Resources System is envi- ing developed in current research programs is sioned as a multilocational organization that not good. In fact, when maintenance facilities for would serve the avian genetic resources needs research stocks are not available, there will be for the US and Canada. The AVGRS would fea- no incentive for investment in lines of research ture a central facility as a focal point for many of that would produce such stocks. An avian ge- the activities of the System. The functional com- netic resources management system, with strong ponents are outlined in Figure 16 and are briefly leadership, but shared responsibility, is pro- discussed here. posed as the most efficient and secure way to conserve genetic stocks and address the con- Avian Genetic Resources Advisory cerns raised in this evaluation effort. The pro- Committee (AVGRAC) posed Avian Genetic Resources System (AVGRS) would be comprehensive and would require the The AVGRS would be advised by this binational cooperation and collaboration of scientists, fund- committee comprised of representatives of na- ing agencies, and research institutions. The Sys- tional and state/provincial agencies, stock cura- tem must be oriented toward research objec- tors, and researchers. It would consist of 12 to tives, but it could also support the needs of 15 individuals who have worked with avian ge- breeders, breed hobbyists, and breed historians. netic resource issues, drawn from government, industry, and academic institutions in the US Rationale and Canada. Specifically, they should have worked in close association with national, inter- Historic long-term collaboration between Cana- national and private research-oriented organiza- dian and US scientists provides a basis for col- tions, and be familiar with avian genetic stock laboration in the formation and operation of an conservation issues. The members should meet Avian Genetic Resources System. No compre- at least once a year and be in regular communi- hensive system exists in North America, nor any- cation during the year. The Committee would where else for that matter, for the conservation review reports and recommendations for conser- and distribution of avian genetic stocks (prima- vation of stocks received from species-oriented rily chicken, turkey, and Japanese quail) of committees. It would make recommendations to value for agricultural, biomedical, or biological the management unit of the AVGRS. research. The US National Plant Germplasm System and its counterpart in Canada serve as excellent models for the proposed Avian Genetic

39 Figure 16. Components of the Avian Genetic Resources System.

Avian Genetic Resources System

Binational Avian Genetic Coordination Resources Advisory Commmittee

USDA International US NIH organizations US NSF FAO A&AF Canada IUCN Collections Scientific societies NGOs Others

Database/ Importation/ Conservation Distribution Research Information Quarantine

Cryopreservation

Beltsville MD Guelph ON Others

Stock colonies

US - CA, IA, NH, WI, MI, CT Canada - BC, ON Others

40 Coordination agriculture for food production and for basic biological and biomedical research. Thus, the focus The various government and research institu- will be on chicken, turkey, and Japanese quail tions involved in avian research and conserva- genetic stocks. However, this system could also tion would use the AVGRS for coordination of consider wild turkey, jungle fowl, and game information about genetic resources and the birds, as well as other species commonly raised AVGRS would in turn be responsible for main- in captivity. The AVGRS will emphasize: taining and distributing this information. This function would also include strategic planning • Genetic stocks having traits and genetic for conservation of particular stocks, based on characteristics useful in research, such advice from advisory groups established for each as inbred lines, single-gene mutations, species. For example, imperiled stocks would be chromosome aneuploidy, and DNA identified to the AVGRS and a plan for their con- marker sequences. servation would be developed through coordinated analysis. International relationships would • Lines and populations developed by pri- be coordinated through the AVGRS, including vate and public breeders by hybridization conservation of stocks in other countries, import and selection for important production- and export of genetic stocks, data sharing, and related traits. development of conservation plans for landraces, wild species, and breeding populations. • Domesticated mid-level production and fancy breeds held by small producers Conservation and hobbyists in North America and Eu- rope. This is the cornerstone activity of the AVGRS and of critical importance. A central facility is • Domesticated, but primitive, landraces needed for conservation and distribution of ge- existing in Asia, Central and South netic materials. The central facility would house America, and elsewhere, primarily as those living genetic stocks that could not be scavenger birds. maintained elsewhere and would serve as a backup site for important stocks that are main- Archival preserved specimens of birds, or- tained elsewhere. This would include a secure gans, skeletons, eggs, feathers, and tissues that backup repository for privately owned lines or have been preserved as museum specimens are populations, either as live birds or cryopreserved also a component of the genetic resources sys- germplasm at the central or secondary centers tem, since these materials provide for baseline on a fee basis. The central facility would also observations and time-course monitoring of fac- physically maintain the various types of pre- tors such as environmental toxicants. served genetic resources and would coordinate An informal in situ system of conservation of those maintained elsewhere. The cryopreserva- landraces and breeds is well established in tion capabilities of the central facility would be North America. A monitoring and database sys- supplemented by a specialized cryopreservation tem may be the most important need for those center, presently unused, at the USDA site in genetic resources. This could become an activity Beltsville, Maryland. No site for the central facil- of this proposed system. ity is identified at this time. Databases The central facility would support and be linked to secondary facilities located at active Detailed information about all genetic stocks in research centers which have the capability of the US and Canada should be maintained and maintaining genetic stocks for their own re- updated by the AVGRS in a genetic resources search needs. Several locations in the US and information system, similar to the Genetic Re- Canada would qualify as secondary sites. sources Information Network (GRIN) developed for the US National Plant Germplasm System Methods of conservation. Conservation meth- and housed with the USDA National Agriculture ods employed in the AVGRS would be live-bird Library. For example, all of the information in- maintenance and cryopreservation. cluded in Appendix 2 should become part of the Targets for conservation. Conservation empha- AVGRS database. Additionally, database service sis of the AVGRS should be on live birds, embry- would be offered to the various breed conservan- onic cells, gametes, DNA, and tissues. The target cies and hobbyists groups for inventory and lo- species for the system will be those of interest in cation of conserved breeds, land-races, and spe-

41 cialty stocks. It would also be logical for the countries that should be considered for rescue in AVGRS database to include DNA sequence data the AVGRS because of their value for research. as they are developed. Bird care and housing While GRIN currently focuses on plant information, its goal is to include information on all The housing and care of the live birds at all cen- of the common and endangered breeds of farm ters will follow American Association for Labora- animals, including the avian genetic stocks used tory Animal Care (AALAC) standards for a breed- primarily in research. Collaboration with the ing colony. Essentially, the breeding stock AVGRS database would facilitate this goal. should be kept in a facility that approximates that of a well-run commercial poultry breeding Outreach farm. The highest degree of automation for feed- Researchers can also be informed of the wide ing, cleaning, watering and climate control is variety of available genetic stocks at the annual recommended. With most of the chicken genetic meetings of a variety of organizations, including stocks, the adult birds will be housed in single- the Poultry Science Association, the Pacific Egg bird cages, and bred by artificial insemination. and Poultry Association, the Poultry Breeders Other features of the facility may include: floor Roundtable, the Society for Developmental Biol- pens, with or without trap nests, to maintain ogy, the American Association for the Advance- stocks that do not perform well in cages; and ment of Science, and the American Medical As- separation of males and the females (in different sociation. Presentations at the commercially ori- rooms or cage rows), so that appropriate, sex- ented meetings could be used to showcase the specific breeder diets, lighting, and feeding regi- benefits the different companies could derive mens can be provided for each group. from supporting an avian genetic stocks conser- To minimize the disease problems in the ge- vation program, while the basic research or dis- netic stocks and reduce the risk of spreading ease model aspect of genetic stocks could be em- pathogens when stocks are shipped, all conser- phasized for organizations promoting basic and vation centers should follow the National Poultry biomedical research. Thus, the underlying goals Improvement Plan guidelines (USDA-APHIS of presenting genetic stocks information at such 1998). These procedures impact on the design of meetings is not only to attract the attention of the facility, such as: researchers, but to engage the interest and pro- • All incoming stocks should be acquired mote funding from commercial sectors that can only as fertile eggs, which are formalde- benefit directly from research using avian ge- hyde-fumigated, then incubated, netic stocks. hatched, and reared in a facility isolated Another outreach option for the AVGRS from all other avian species, including would be an independent website that would those already shown to be free of the tar- promote the available avian genetic stocks to the geted disease agents. After the birds in scientific community by advertising what is isolation are at least six weeks old, they available, and indicating those that are slated for should be blood-tested for the presence elimination. The effectiveness of such a site of egg-transmitted pathogens (in chick- could be multiplied by linking it with websites: ens, this usually includes Salmonella the animal genetic map (Angen), the chicken pullorum, S. typhimurium, Mycoplasma map (ChickMap), various research organization gallisepticum, and M. synoviae; turkeys sites (e.g., Poultry Science Association, Society would also be tested for M. gallinarium), for Developmental Biology, various commercial before being moved to the stock center. poultry sites, and sites for academic institutions). The AVGRS website information could be fur- • A random-sample of 10% of the adult ther promoted by a series of clearly written re- birds should be tested each year for evi- view articles in several of the major biological dence of the important poultry diseases, science journals. In each case, a specific area of including the disease pathogens listed research would be targeted, such as animal mod- above. els for human diseases, limb pattern defects, craniofacial defects, integumentary defects, or im- • Replacement birds should be raised in munogenetic research. strict isolation for the first month after The outreach activity would also involve inter- hatch. national contacts through FAO or various countries with respect to avian genetic resources. For • The stock center should be physically example, there are genetic stocks at risk in other well-isolated from other poultry (commer-

42 cial or hobby flocks) and from facilities in Facilities and organizational which other captive bird species are housed. aspects of AVGRS

• The bird houses should prevent entry of The central facility wild birds and vermin. Ideally, the primary AVGRS facility would be • Access to the facility should be restricted constructed de novo near or part of a major agri- and closely monitored, complying with cultural institution (land-grant university) with a full necessary sanitary restrictions. veterinary school that has a good avian medicine program, but reasonably isolated from commer- Importation and quarantine cial poultry stocks. The connection with a land- grant institution would give the center close ties Movement of animals introduces risks of spread- to active research laboratories and faculty, who ing contagious diseases, obviously of great con- could benefit from such a resource and be cern in long-term conservation of live birds. drawn upon in support of the center. Access to Movement of genetic resources as fertile eggs or state-of-the-art poultry disease diagnostics and semen reduces disease transmission risk and veterinary care is critical, along with good, off- are preferred procedures. Importation of stocks site quarantine facilities for newly acquired ge- to the central facility will be done through on- netic stocks. Locating in a strong poultry pro- site isolation and through national facilities un- ducing state would also provide an existing poul- der the direction of USDA Animal and Plant try-oriented political and commercial infrastruc- Health Inspection Service. The central facility ture that could be mobilized to help support the will have appropriate isolation and sanitation conservation center. capabilities. This facility would include a hatchery, brood- ing and growing areas, adult bird housing, an Distribution isolation area, a cryopreservation laboratory and storage facility, a database center, staff and ad- A major function of the AVGRS will be to provide ministrative offices, and a laboratory to support genetic materials to users in the research com- research and analytical services. munity, breeders, and others. The genetic stocks Bird housing should be designed to minimize may be transferred as live birds, semen, or eggs. disease and pest control problems, and maxi- These will be distributed on a cost-recovery ba- mize caretaker efficiency and bird well-being. sis. Some users require a continuing supply of Initially the facility should accommodate 1,000 genetic stocks and these needs would be sup- adult birds, with options for expansion. Several plied by contractual stock reproduction pro- design schemes will be evaluated to accommo- grams. The distribution function would supply date the genetic diversity of the stocks and their well-documented stocks to researchers, thus special requirements and for efficiency in man- contributing to the integrity of research projects. agement. This functional component of the AVGRS is an- Network of secondary genetic stock alogous to services provided by the Jackson Laboratories for mouse genetic stocks. centers Secondary stock centers would be designated as Research part of the AVGRS at land-grant universities and other institutions across the US and Canada The AVGRS should have a research capability that fulfilled two criteria: (1) had adequate facili- within the central facility, especially for develop- ties and support for the genetic stocks used in ing cryopreservation technologies. Research its own research programs and (2) had a long- would also be done on methods for documenting term interest in conserving genetic stocks. Such genetic integrity or diagnostics with DNA mark- centers, approved as part of the AVGRS, would ers. Other research would be done as needed receive funding from AVGRS for maintenance of and appropriate. The research activities would stocks. These secondary centers would maintain be networked with research laboratories in the live birds and would provide backup for at-risk US and Canada for collaborative work. stocks held in the central facility. As with the central facility, the secondary stock colonies would also have a distribution function on a fee basis. Researchers could also, on a fee basis,

43 arrange to keep research flocks at the central • Species coordinating committee facility or one of the secondary centers, since organization they may find it difficult or impossible to keep such stocks at their own institutions. • Promotion of the use of these genetic Secondary centers could specialize on one or stocks a few classes of genetic stocks (e.g., inbred strains, congenic series, randombred stocks, se- • User fees and maintenance contract lected stocks, single-gene mutant stocks, or guidelines chromosome translocation stocks). In fact, many of the existing poultry collections at both aca- Stock evaluation guidelines demic and government institutions are already quite specialized. The restricted number of One of the more important activities of the classes and species of stocks at each secondary AVGRAC would be the evaluation of stocks for live bird center would simplify reproduction and conservation, cryopreservation, or elimination. maintenance for the curators, since each type of Guidelines for assessing the value of genetic stock often has different needs in relation to stocks have been outlined in a report by the Na- population sizes, selection criteria, inbreeding tional Research Council Committee on Preserva- considerations, and testing techniques. tion of Laboratory Animal Resources (NRC 1990). The report suggests that value of a given Management stock should be established by considering: The central facility and the secondary centers would be administered by the research institu- 1. Importance of the disease process or tions with which they are located. The central physiological function exemplified by the facility would have, at a minimum, a director or stock (especially when used as an animal manager (research scientist), curator, an admin- model for a human disorder). istrative assistant, database manager, cryopreservation research scientist, and three or four 2. Validity of the model and continued ge- laboratory and animal care technicians. netic integrity of the stock. The AVGRS would be guided by the advisory committee on such matters as: 3. Replaceability of the stocks (those developed after many years of selection or • Information system and website arising from a spontaneous mutation management would be considered relatively irreplace- • Inventory control able).

• Conservation status determination 4. Versatility of the stock (the variety of (cryopreserved stocks only) problems that can be addressed with a given stock). • Stock accessioning strategies 5. Number of users. • Importation targets and necessary international cooperation agreements The advisory committee would also formulate other criteria specifically relevant for the conser- • Appropriate stock-specific conservation vation of avian species. protocols Financing the Avian Genetic • Management of grant funds for research and preservation efforts Resources System

• Curator training programs Multiple sources of funding will be necessary to meet all of the needs of the AVGRS. Initial costs • Program expansion decisions are those to construct the central facility and upgrade the secondary stock centers. Annual • Budgets costs of the central facility would be for its personnel and operations. It would also be neces- • Fund raising sary to support the annual activity of the AVGRAC. The central facility could also direct

44 funds for specific needs to the secondary centers Funding should be sought from the US gov- by means of annual grants. ernment for construction of the central facility From the US side, the biological resource pro- and for personnel support for operations as a grams of the National Science Foundation and part of the US National Animal Genetic Resour- the National Institutes of Health would be ex- ces System. pected to provide operational funds through di- Long-term funding would be the most secure rect grants and through grants to investigators from endowment funds. Contributors could be who use the avian genetic resources in their re- encouraged from the private sector, from large search. The USDA’s National Genetic Resources integrated commercial poultry companies to pri- System should participate in the AVGRS through vate individuals with interests in preserving the Agricultural Research Service and the Coop- poultry stocks or willing to promote the conser- erative State Research, Extension, and Educa- vation of stocks that can be used to study hu- tion Service. The various State Agricultural Ex- man diseases. periment Stations and land-grant and other Uni- Construction, personnel, and operational versities should also participate. Canadian sup- costs have not been established, pending further port and participation should be forthcoming to analysis of potential sites for the central facility the extent that the AVGRS provides support to and other considerations. For illustrative pur- its research and development programs. poses, rough order-of-magnitude estimates are The AVGRS will be the major provider of ge- given in Table 4. netic materials to researchers throughout the public and private sectors. For the most part, Table 4. Estimated costs of Avian Genetic Resources System. these researchers do not have capacity to main- Startup costs tain live bird colonies and depend upon stock Constructing and equipping central facility $15,000,000 colonies for their research. User-fees are an ap- Upgrading and renovating secondary centers 2,000,000 propriate means to recoup costs of stock mainte- Total $17,000,000 nance. Annual costs Donation funds can be expected to support Personnel at central facility $400,000 the perpetual maintenance of particular genetic Operating costs at central facility 100,000 stocks. These funds may be provided as annual Grants to secondary centers (8 x $25,000) 200,000 grants or through income derived from interest Advisory Committee 25,000 on endowment accounts. Total $725,000

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53 THORAVAL, P., M. AFANASSIEFF, F.L. COSSET, F. structural changes in male chickens by the LASSERRE, G. VERDIER, F. COUDERT, and G. alkylating agents: triethylene melamine and DAMBRINE. 1995. Germline transmission of ethyl methanesulfonate. Mut. Res. 96:53–66. exogenous genes in chickens using helper- WATT, J.M., J.N. PETITTE, and R.J. ETCHES. 1993. free ectropic avian leukosis virus-based vec- Early development of the chick embryo. J. tors. Transgenic Res. 4:369–377. Morph. 214:1–18. USDA-APHIS. 1997. National Poultry Improve- WIGHT, P.A. and W.G. SILLER. 1980. Pathology of ment Plan and Auxiliary Provisions. APHIS deep pectoral myopathy of broilers. Vet. Pa- 91-55-038, USDA Animal and Plant Health thology 17:29–39. Inspection Service. Washington, DC. WIGHT, P.A., W.G. SILLER, and L. MARTINDALE. USDA-NASS. 1998. Agricultural Statistics, 1998. 1981. March gangrene: deep pectoral myopa- United States Department of Agriculture, thy, Oregon disease, green muscle disease. National Agricultural Statistics Service. Gov- Am. J. Pathol. 103:159-161. ernment Printing Office, Washington DC. WILSON, B.W. 1990. Developmental and matura- VAINIO, S., I. KARAVANOVA, A. JOWETT, and I. tional aspects of inherited avian myopathies. THESLEFF. 1993. Identification of BMP-4 as a Proc. Soc. Exp. Biol. Med. 194:87–96. signal mediating secondary induction between WILSON, B.W., P.S. NIEBERG, R.J. BUHR, B.J. epithelial and mesenchymal tissues during KELLY, and F.Z. SHULTZ. 1990. Turkey muscle early tooth development. Cell 75:45–58. growth and focal myopathy. Poult. Sci. VAN KREY, H.P. 1990. Reproductive biology in 69:1553-1562. relation to breeding and genetics. p. 61–90 WISHART, G.J. 1985. Quantitation of the fertiliz- In: R.D. Crawford (ed.) Poultry Breeding and ing ability of fresh compared with frozen and Genetics. Elsevier. New York. thawed fowl spermatozoa. Brit. Poult. Sci. VAN DE WATER, J., R. BOYD, G. WICK, and M.E. 26:375–380. GERSHWIN. 1994. The immunologic and ge- WOO, S.L., A. DUGAICZYK, M.J. TSAI, E.C. LAI, J.F. netic basis of avian scleroderma, an inher- CATTERALL and B.W. O’MALLEY. 1978. The ited fibrotic disease of line 200 chickens. Intl. ovalbumin gene: cloning of the natural gene. Rev. Immunol. 11:273–282. Proc. Natl. Acad. Soc. (USA) 75:3688–3692. VERRINDER GIBBINS, A.M. 1993. Future interac- WOODARD, A.E., H. ABPLANALP, J.M. PISENTI, and tions between molecular biologists and the L.R. SNYDER. 1983. Inbreeding effects on re- poultry industry, illustrated by a comparison productive traits in the ring-necked pheas- of the genome mapping and gene targeting ant. Poult. Sci. 62:1725–1730. paradigms. p. 285–309 In: R.J. Etches and WOOSTER, W.E., N.S. FECHHEIMER, and R.G. JAAP. A.M. Verrinder Gibbins (eds.) Manipulation of 1977. Structural rearrangements of chromo- the Avian Genome. CRC Press. Boca Raton, FL. somes in the domestic chicken: experimental WAKENELL, P.S., M.M. MILLER, R.M. GOTO, W.J. production by X-irradiation of spermatozoa. GAUDERMAN, and W.E. BRILES. 1996. Associa- Can. J. Genet. Cytol. 19:437–446. tion between the Rfp-Y haplotype and the ZARTMAN, D.L. 1971. X-ray-induced chromo- incidence of Marek’s disease in chickens. somal aberrations in chickens. Genetics 68 Immunogenet. 44:242–245. (Suppl.):77. WANG, N., R.N. SHOFFNER, J.S. OTIS, and K.M. CHENG. 1982. The induction of chromosomal

54 Appendix 1. Instructions and survey form sent to researchers

INSTRUCTIONS FOR COMPLETING THE AVIAN GENETIC RESOURCES SURVEY We appreciate your willingness to assist us in this survey. Below are some suggestions and clarifica- tions for the enclosed survey form. If you need more space to complete your catalog of genetic stocks, please feel free to copy the survey form. We would also be interested in any relevant information you wish to attach that concerns your stocks (previously published summary information, references, expanded descriptions, etc.). 1. Curating researcher or person in charge of these stocks: this is the name of the person responsible for the poultry stocks recorded in the survey. This person can be contacted for further information on these stocks. If more than one person is responsible for a given stock or group of stocks, please write in the other names and addresses/phone numbers at the top of the page, and indicate the stocks that each person controls.

2. Name of Stock: how the stock is identified. 3. Species: chicken, turkey, coturnix quail or other avian species. 4. Stock Description/Characteristics: breed and any special stock characteristics, including degree of inbreeding (for inbred stocks), selection criteria, and/or mutations or chromosomal abnormalities present. If this stock is unchanged since it was listed in the 1988 International Registry, just write in “see 1988 registry” under this category. If you need more space to adequately describe a stock, please attach the expanded description to the survey form. 5. Eliminated? Date/Reason: if a stock has been eliminated, please indicate date of and reason for elimination (i.e., loss of funding, housing no longer available, stock no longer needed, etc.). 6. # Birds for Maint. (M & F): how many male and female birds are needed in a core flock to maintain a viable breeding population of each stock. 7. Funding Situation: security of the funding for that stock, at present and projected five years. If possible, please indicate source of funding: Government (NIH, NSF, USDA, etc.); Academic (university or institution, Hatch funds); Private (private organizations or individuals). 8. Other Loc.? (Y/N): is the stock maintained at one or more other institutions/locations? If yes, please give the name and address of the person(s) responsible for this stock at the other location(s), if available. 9. Cryo.? (Y/N): is the stock also (or only) kept as cryopreserved cells? If yes, please indicate the type of cells that have been cryopreserved (semen, blastodiscs, etc.), and where this material is kept.

55 Cryo? (Y/N)* (Y/N)* Other Loc? [email protected] f this form, or ask them Funding Situation # Birds for Maint. (M & F) Eliminated? Date/Reason Species Curating Researcher or person in charge of these stocks: Address: Phone Number: Fax: Email: SURVEY OF AVIAN GENETIC RESOURCES, 1996 Name of Stock* Stock Description/Characterstics 1. Do you make your stocks available to other researchers (for reproduction or research? 2. Do you know of other researchers who maintain avian genetic stocks? If so, please write their name and address on the back o to contact me. Thank you, Jacqueline M. Pisenti, GRCP, University of California, Davis, CA 95616, Fax (916) 754-8505, email: jm * please see instructions on the back of this form.

56 Appendix 2. Genetic stock collection data

THE INFORMATION PRESENTED HERE was collected 1995 and 1998. Over half of these discarded through a survey initiated in 1995 by the Uni- stocks were not represented in collections at versity of California Genetic Resources Conser- other institutions and thus, are lost to science. vation Program. Many stocks developed before Most stocks are maintained as living birds, but 1988 were listed in the International Registry of 38 chicken genetic stocks are maintained only in Poultry Genetic Stocks (SOMES, R.G., JR. 1988. the form of cryopreserved semen or blastodermal International Registry of Poultry Genetic Stocks. cells. Storrs Agr. Exp. Sta. Bull. 476. The University of The survey data are presented in three tables. Connecticut, Storrs). Therefore, curators listed Table 2.1 is a listing of the 361 reported stocks in the Somes registry were the starting point for grouped first by species (chicken, Japanese this survey. In addition, queries were sent to quail, turkey, and waterfowl/gamebird), then by members of the NE-60 Regional Research Project category of genetic stocks (the 28 categories (a USDA-organized group of researchers working used are listed in Table 2.0, then described be- on the genetic basis for resistance and immunity Table 2.0. Stock categories. to avian diseases), academic and government members of the Poultry Science Association Bloodtype-Gene pool (source list: PSA Membership Directory, 1995- Bloodtype-Major Histocompatibility 98) who indicated a focus on genetics or immu- Complex (MHC) nology, and individuals listed by the 1997 Poul- Bloodtype-MHC-Inbred try Science Resource List (prepared by the Poul- Chromosomal variant Endogenous virus try Science Association and R.D. Reynnells Endogenous virus-Inbred (USDA/CSREES)) who specialized in genetics or Inbred immunology and were affiliated with academic Mutant-Color, eggshell institutions with poultry, avian, or animal sci- Mutant-Color, feather ence departments. Mutant-Developmental defect-Eye Altogether, a total of more than 100 individu- Mutant-Developmental defect-Face/limb als were polled. Seventy-five responded and, of Mutant-Developmental defect-Skin/feather those, 40 currently maintain poultry genetic Mutant-Developmental defect-Spine/tail stocks as researcher-curators. These curators Mutant-Gene pool Mutant-Immunological defect represent 27 different institutions (24 in the US, Mutant-Neurological defect 3 in Canada). Approximately one-half of the in- Mutant-Physiological defect stitutions maintain 10 or fewer genetic stocks Mutant-Reproductive defect and only six maintain more than 20 stocks (Uni- Mutant-Uncategorized versity of Arkansas–Lafayette, University of Cali- Pure breed fornia–Davis, University of Connecticut–Storrs, Randombred Univerisity of Wisconsin–Madison, USDA-ADOL Selected-Behavioral trait East Lansing, MI, and University of British Co- Selected-Egg trait lumbia–Vancouver). About one-third of the re- Selected-Growth trait Selected-Immune trait ported stocks are considered to be at serious Selected-Physiological trait risk of loss in the near future, and at least 94 of Transgenic the surveyed stocks were eliminated between Uncategorized

57 low). Table 2.2 lists stocks grouped by institution Mutant stocks are classified into the following and curator, species, and category. Finally, Table categories: 2.3 lists curators and their contact information. Mutant-Color, eggshell Accordingly, the most important information Mutant-Color, feather necessary to look up a given genetic stock in- Mutant-Developmental defect-Eye cludes 1) the species and type of stock or 2) the Mutant-Developmental defect-Face/limb Mutant-Developmental defect-Skin/feather institution or curator who keeps that type of Mutant-Developmental defect-Spine/tail stock. Mutant-Gene pool Mutant-Immunological defect Description of stock categories Mutant-Neurological defect Mutant-Physiological defect Bloodtype refers to cell-surface antigens that Mutant-Reproductive defect have been characterized on red or white blood Mutant-Uncategorized cells. Bloodtype-Major Historcompatibility Color variation for feather and eggshell also Complex (MHC) consists of stocks with a de- occur in the pure breed and randombred catego- fined MHC or B-haplotype, and may be defined ries, particuarly among the different chicken for a variety of other erythrocyte alloantigens. breeds. Researchers interested in such variants Bloodtype-MHC-Inbred is congenic (genetically should look up the color genetics for these identical) to an established highly inbred line, breeds or discuss this with the pure breed stock except for the specified bloodtype. Bloodtype- curators. Gene pool stocks contain a variety of different Some developmental defect mutations may bloodtypes. Leukocyte cell surface antigens are actually fit into more than one category (e.g., also defined for one gene pool stock (NIU Male wingless-2 affects face, limbs, feathers, and kid- Breeder Alloantigen Reservoir). neys, but was listed by its effect on the face and limbs). Some of the mutations listed under neu- Chromosomal variant refers to stocks with al- rological, physiological, and reproductive defects terations in chromosome structure. These varia- can also cause developmental defects. On the tions include: insertions, deletions, transloca- other hand, a few of the mutations or variants tions, inversions, aneuploidy, and polysomy. did not clearly fit into any of the above specific Stocks with specific insertions (naturally occur- categories, so were classified as Mutant- ring or as a result of genetic engineering) are Uncategorized. A close reading of the mutant listed under the Endogenous virus or Transgenic descriptions is recommended. categories. Mutant-Gene pool refers to stocks that contain Endogenous virus (EV) stocks are characterized two or more mutations, which may or may not by specific viral insertions (one or more inser- affect affect the same structures or systems. tions of a defined endogenous virus), and En- Some unique mutations are only maintained in dogenous virus-Inbred stocks are congenic (ge- gene-pool stocks, and so do not appear under netically identical) to an established highly in- the more specific mutant categories. However, bred line, except for the specified viral insertion. brief descriptions of all mutations carried within that stock are listed for each of the pooled Inbred stocks usually have a level of inbreeding stocks. exceeding 95% (F>0.95), although one exception is UCD 001 (F is approximately 0.90). Other in- The Pure breed category includes all stocks that bred stocks include congenic stocks developed are maintained as a closed flock of an identified by continued back-crossing to a given inbred breed. It is usually not highly inbred, selected, or stock. Such congenic stocks are categorized by otherwise characterized. Some overlap occurs be- the unique gene or gene complex isolated in the tween the Pure breed category and the Random- inbred background (e.g., Bloodtype-MHC-Inbred, bred category. However, if an otherwise Pure Endogenous virus-Inbred, and Mutant-Develop- breed stock is commonly used as a control/stan- mental defect-Face/limb). In such stocks, the dard for another stock, it will be listed as Ran- inbred ancestral stock is listed under “Origin dombred. and History”. Randombred stocks are usually purebred or synthetic (mixed commercial) stocks that are kept in large, closed populations (100 birds or more).

58 Typically propagated with little or no selection of its current and historical genetic background (if breeding stock each generation, the number of available), and any other possibly useful back- progeny from each male or female usually de- ground information. In particular, for stocks that pends upon their reproductive success at the time are congenic, the specific inbred stock with which eggs are collected to produce the next generation. it is essentially identical is noted.

Stocks that have been selectively bred for a Breed: The source breed(s) or genetic back- quantitative characteristic are termed Selected- ground for stocks is noted here. along with the identified trait: Selected-Behav- ior trait, Selected-Egg trait, Selected-Growth Genetic characteristics: For those stocks that trait, Selected-Immune trait, and Selected- are characterized by a distinct mutation or set of Physiological trait. Each stock usually has an mutations, this field presents information on the unselected control paired with it, and two diver- pattern of inheritance (autosomal, sex-linked), gently selected stocks (e.g., for high or low body penetrance and expressivity (dominant, co-domi- weight at 6 weeks) from the same source may be nant, recessive, incomplete penetrance, mater- grouped together here. nal effect, sex-limited), and effect on viability (lethal, semi-viable; if a mutation is fully viable, no Transgenic stocks are the product of genetic notation is provided). engineering. Such stocks have successfully integrated the introduced genetic material into their Allele symbol: Here the short notation for the chromosomes. mutant form of the gene is listed. If the symbol is in question or has not yet been officially as- Finally there is disparate group of stocks classi- signed, the allele symbol is written in parenthe- fied as Uncategorized, either for want of better ses (i.e., (wgr) for the wing-reduced syndrome). descriptive information or because there may be too few representatives of a type to warrant an Status: This field provides a subjective evalua- additional category. tion of the potential for continued financial support of each stock, assessed by the curator of While most stocks clearly belong to a single de- that stock. ‘Good’ indicates dependable institu- scriptive category, some logically could be classi- tional or government support for at least the fied in more than one. In such situations, the next two to three years. ‘Fair’ indicates less cer- stock was listed under the category that most tain support. ‘Poor’ describes a stock which is closely fit the stock description. The distribution seriously at risk of elimination. When the spe- of all listed stocks according to these categories cific source of funding support for the stock was is summarized in Chapter 5 of this report. provided, that information was noted: USDA, Industry, Institutional, State Agricultural Ex- Notes on specific fields periment Station (Exp. Sta.), Hatch funds (Hatch), research funds (regional), or other Table 2.1 contains the fields described below. (misc.). In some cases, a stock is no longer main- Stock name is also used in Table 2.2. tained as living birds, only by germplasm cryopreservation. For such stocks, the notation in Stock name: The designation used usually in- the status field is ‘No live birds’. Finally, some corporates the name of the institution where the once-distinct mutant stocks are no longer car- stock is housed or was developed, and the name ried as separate accessions, but were recently that the curator assigned to the stock. In Table combined with another accession, and the name 2.2, the stock name is followed by the words of the recipient stock is indicated in the status ‘Cryo. only’, if that stock is only maintained by field (e.g., ‘Combined with UBC G’). For the pur- cryopreservation. This information is given in the poses of Table 2.1 and this report, the original Status field for Table 2.1 (see below). mutant is still counted as a separate accession.

Stock description: Only a brief description of Number of birds: When available, this is the the unique characteristics of the stocks is pro- number of birds (males and females) kept to vided; for more information, the curator should maintain the stock. be contacted. Cryopreservation: If no germplasm has been Origin and history: Information in this field in- cryopreserved for a given stock, the entry in this cludes when a stock was established or acquired, field is ‘No’. If germplasm has been cryopreserved,

59 then the cell type is indicated (semen, germ cells, Resources Task Force present this information blastodisc cells (for dissociated blastodiscs)). as a service to those interested in poultry genetic Stocks that are only maintained as cryopreserved stocks that can be found at academic and gov- germplasm can be identified by the remark ‘No ernment institutions in the USA and Canada. No live birds’ in the Status field. Curators can be con- certification is implied for the stocks listed tacted for details on recovery of these stocks and herein, either their status with regard to freedom costs associated with the recovery. from egg-borne disease agents, or their current availability (note that availability at the time the Available: Many curators provide eggs or chicks to survey was conducted is indicated). Inquiries other researchers for collaborative projects; some will regarding particular stocks should be directed to provide eggs or chicks for a fee (usually to offset bird the individual curator(s). In addition, readers are maintenance costs), while other stocks may not be reminded that it is not possible to guarantee the available because of proprietary concerns. Curators authenticity or scientific accuracy of the infor- should be contacted for details. mation presented herein. Those wishing to acquire any of these stocks Curator: The surname of the researcher in or genetic material derived from these stocks are charge of the given stock is indicated here. Con- reminded that they must obtain the appropriate tact information for them is listed in Table 2.3, customs forms and documentation, and follow alphabetically, by surname. the protocols governing such shipments. Even transfer between different states in the US or Disclaimer provinces in Canada may require health certification or other documentation. In the US, the The University of California Genetic Resources USDA Veterinary Services can provide some of Conservation Program and the Avian Genetic this information.

60 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken Bloodtype-Gene pool Auburn DAX Kept as closed flock SCWL see Fair 240 No With Ewald MHC: B5; other erythrocyte alloantigens: A/E4, C4, D3, since 1965 description collaboration H2, I3, K3, P3, “Q”2. NIU B haplotypes Derived from Ancona synthetic Mixed Ancona see Fair N/A No With Briles Pool of MHC B-haplotypes: 1, 3, 4, 6, 8, 10, 11, 12, 13, stocks homozygous for most description collaboration 14, 15, 17, 22, 23, 24, 26, 30, 31, 32, 33, 24r1, 2r1, 2r2, non-MHC genes 2r3, 21r1, 21r2, 2r4, 2r5, 24r2, 24r3, 21r6, 8r1. NIU B-haplotype Recombinants Derived from Ancona synthetic Mixed Ancona see Fair N/A No With Briles Recombinant B haplotypes: R1, R2, R3, R4, R5, R6, R7, stocks homozygous for non-MHC description collaboration R8, R9, R10, R11, R12. system genes NIU Male Breeder Alloantigen Reservoir Segregating for erythrocyte and SCWL see Fair 200+ No With Briles Pool of cell surface erythrocyte alloantigen (# alleles): leucocyte alloantigens description collaboration A(8), B(40), C(8), D(5), E(10), H(2), I(7), K(2), L(2), P(10), R(2); Leukocyte alloantigens: M(5), N(2), Q(3), T(3), U(4), W(2), Z(2). NIU Segregating Male Breeder Line SCWL see Fair N/A No With Briles MHC: B2/B5 or B19/B21; A4E1/A5E2; C2/C5; D1/D3; description collaboration H1/H2; I2/I8; K2/K3; L1/L2; P1/P4. UNH 105 Kept as closed flock New Hampshire see Good 10M/150F No Yes Taylor Closed flock with four MHC B haplotypes: 22, 23, 24, 26. since 1981 description

Bloodtype-MHC Auburn M Derived from commercial meat stock Commercial B8 Fair 35 No No Ewald MHC: B8. in 1982 meat stocks (proprietary) Auburn N Derived from commercial meat stock Commercial B13 Fair 100 No No Ewald MHC: B13. in 1982 meat stocks (proprietary) Auburn RM Cross of Auburn R and Auburn M SCWL X B2 Good 70 No With Ewald MHC: B2. stocks commercial collaboration meat stocks Auburn RMH Derived from cross of Auburn R SCWL B3 Fair 50 No With Ewald MHC: B3. and Auburn MH stocks collaboration Auburn RN Derived from cross of Auburn R SCWL X B13 Good 840 No With Ewald MHC: B13. and Auburn N lines in 1988 commercial collaboration meat stocks Cornell N2a Specific pathogen-free SCWL B21, C2 Good 23M/100F No Yes, fee Schat MHC: B21; erythrocyte alloantigen C2; highly resistant to Marek’s disease virus. Cornell P2a Specific pathogen-free SCWL B19, C2 Good 30M/110F No Yes, fee Schat MHC: B19, erythrocyte alloantigen C2; highly susceptible to Marek’s disease virus. NIU Female Breeder Parent Stock B19 Derived from Ancona synthetic Mixed Ancona B19 Fair N/A No With Briles MHC: B19; used as female parent in immunological stocks homozygous for non-MHC collaboration challenges. system genes

Chicken genetic stocks Appendix 2 Table 2.1 1 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Bloodtype-MHC (cont.) NIU Female Breeder Parent Stock B2 Derived from Ancona synthetic Mixed Ancona B2 Fair N/A No With Briles MHC: B2; used as female parent in immunological stocks homozygous for non-MHC collaboration challenges. system genes NIU Female Breeder Parent Stock B5 Derived from Ancona synthetic Mixed Ancona B5 Fair N/A No With Briles MHC: B5; used as female parent in immunological stocks homozygous for non-MHC collaboration challenges. system genes RPRL-Cornell JM-N Derived from Cornell JM randombred SCWL B21 Good: 6M/42F Semen Yes Bacon MHC: B21; resistant to Marek’s disease virus strain JM. stock; specific pathogen-free USDA RPRL-Cornell JM-P Derived from Cornell JM randombred SCWL B19 Good: 6M/42F Semen Yes Bacon MHC: B19; susceptible to Marek’s disease virus strain stock; specific pathogen-free USDA JM. UNH 192 Derived from cross of SCWL and SCWL X B19 Good 10M/150F No Yes Taylor MHC: B19. Ancona; kept as closed flock Ancona since 1988

Bloodtype-MHC-Inbred ISU 19-13 Derived from crosses of 1920s ISU SCWL B13 Good 2M/16F No With Lamont Inbreeding coefficient (F)>0.98; MHC: B13. inbred stocks before 1935 collaboration ISU 19-15.1 Derived from crosses of 1920s ISU SCWL B15.1 Good 2M/16F No With Lamont Inbreeding coefficient (F)>0.98; MHC: B15.1. inbred stocks before 1935 collaboration ISU 8-15.1 Derived from crosses of 1920s ISU Barred Leghorn B15.1 Good 2M/16F No With Lamont Inbreeding coefficient (F)>0.98; MHC: B15.1. inbred stocks before 1935 collaboration ISU G-B1 Congenic with ISU GH SCWL B13 Good 3M/30F No With Lamont Inbreeding coefficient (F)>0.99; MHC: B13. collaboration ISU G-B2 Congenic with ISU GH SCWL B6 Good 3M/30F No With Lamont Inbreeding coefficient (F)>0.99; MHC: B6. collaboration ISU GH-1 Derived from a cross of Ghostley SCWL B1 Good 2M/16F No With Lamont Inbreeding coefficient (F)>0.99; MHC: B1. Hatchery (MN) females and HN collaboration males in 1954 ISU GH-13 Derived from a cross of Ghostley SCWL B13 Good 2M/16F No With Lamont Inbreeding coefficient (F)>0.99; MHC: B13. Hatchery (MN) females and HN collaboration males in 1954 ISU GH-15.1 Derived from a cross of Ghostley SCWL B15.1 Good 2M/16F No With Lamont Inbreeding coefficient (F)>0.99; MHC: B15.1. Hatchery (MN) females and HN collaboration males in 1954 ISU HN-12 Derived from a pure Kimber line from SCWL B12 Good 2M/16F No With Lamont Inbreeding coefficient (F)>0.99; MHC: B12. H&N in 1954 collaboration ISU HN-15 Derived from a pure Kimber line from SCWL B15 Good 2M/16F No With Lamont Inbreeding coefficient (F)>0.99; MHC: B15. H&N in 1954 collaboration ISU M15.2 Imported from Egypt in 1954 Fayoumi B15.2 Good 2M/16F No With Lamont Inbreeding coefficient (F)>0.98; MHC: B15.2; original collaboration stock thought to be resistant to lymphoid leukosis.

Chicken genetic stocks Appendix 2 Table 2.1 2 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Bloodtype-MHC-Inbred (cont.) ISU M5.1 Imported from Egypt in 1954 Fayoumi B5.1 Good 2M/16F No With Lamont Inbreeding coefficient (F)>0.98; MHC: B5.1; original collaboration stock thought to be resistant to lymphoid leukosis. ISU Sp21.2 Imported from Spain in 1954 Spanish B21.2 Good 3M/30F No With Lamont Inbreeding coefficient (F)>0.98; MHC: B21.2. collaboration NCSU GB-1 Acquired from Iowa State U; SCWL B13 Good 40M/100F No Yes Qureshi MHC: B13. congenic with ISU GH NCSU GB-2 Acquired from Iowa State U; SCWL B6 Good 40M/100F No Yes Qureshi MHC: B6. congenic with ISU GH RPRL 15.15-5 Congenic with RPRL 15I5; specific SCWL B5 Good: 6M/35F Semen Yes Bacon MHC: B5 from RPRL 15I4. pathogen-free USDA RPRL 15.6-2 Congenic with RPRL 15I5; specific SCWL B2 Good: 6M/35F Semen Yes Bacon MHC: B2 from RPRL 6I1. pathogen-free USDA RPRL 15.7-2 Congenic with RPRL 15I5; specific SCWL B2 Good: 6M/35F Semen Yes Bacon MHC: B2 from RPRL 7I2. pathogen-free USDA RPRL 15.C-12 Congenic with RPRL 15I5; specific SCWL B12 Good: 6M/35F Semen Yes Bacon MHC: B12 from Reaseheath line C. pathogen-free USDA RPRL 15.N-21 Congenic with RPRL 15I5; specific SCWL B21 Good: 6M/35F Semen Yes Bacon MHC: B21 from Cornell JM-N. pathogen-free USDA RPRL 15.P-13 Congenic with RPRL 15I5; specific SCWL B13 Good: 6M/35F Semen Yes Bacon MHC: B13 from Cornell JM-P. pathogen-free USDA RPRL 15.P-19 Congenic with RPRL 15I5; specific SCWL B19 Good: 6M/35F Semen Yes Bacon MHC: B19 from Cornell JM-P. pathogen-free USDA RPRL 15I5 Specific pathogen-free SCWL B15, Good: 9M/63F Semen Yes Bacon Inbreeding coefficient (F)>0.999; MHC: B15; endogenous ALVE1,USDA viruses ev1, ev6, and ev10 or ev11; susceptible to ALVE6, avian leukosis viruse A and B and Marek’s disease ALVE10, virus. ALVE11 RPRL 7I1 Specific pathogen-free SCWL B2, ALVE1, Good: 12M/84F Semen Yes Bacon Inbreeding coefficient (F)>0.999; MHC: B2; endogenous ALVE3 USDA viruses ev1 and ev3; susceptible to avian leukosis viruse C and Marek’s disease virus. RPRL Line 0 Specific pathogen-free SCWL B21 Good: 12M/84F Semen Yes Bacon MHC: B21; free of all known endogenous viruses; USDA susceptible to avian leukosis viruses A, B & C. UCD 003 Full-sib crosses since 1956; one of SCWL B17, A4/E7 Poor 10M/12F Semen Yes Abplanalp Inbreeding coefficient (F)>0.99; A/E blood types 4/7; the reference lines in the East MHC: B17; shown to be resistant to Rous sarcoma and Lansing Chicken Genome Mapping susceptible to Marek’s disease virus . Project, and forms the genetic background for a number of congenic strains that carry various MHC haplotypes or developmental mutations (see UCD stock list)

Chicken genetic stocks Appendix 2 Table 2.1 3 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Bloodtype-MHC-Inbred (cont.) UCD 253 Congenic with UCD 003 SCWL B18 Poor 5M/6F Semen Yes Abplanalp MHC: B18; shown to be resistant to Rous sarcoma and Marek’s disease viruses. UCD 254 Congenic with UCD 003 SCWL B15 Poor 5M/6F Semen Yes Abplanalp MHC: B15; shown to be susceptible to Rous sarcoma and Marek’s disease viruses. UCD 312 Congenic with UCD 003; MHC from SCWL B24 Poor 5M/6F Semen Yes Abplanalp MHC: B24; shown to be susceptible to Rous sarcoma New Hampshire chicken strain and Marek’s disease viruses. UCD 313 Congenic with UCD 003; died out as SCWL B3 No live 0 Semen With Abplanalp MHC: B3; shown to be resistant to Rous sarcoma virus. live birds in 1996 birds permission UCD 330 Congenic with UCD 003; MHC from SCWL B21 Poor 5M/6F Semen Yes Abplanalp MHC: B21; shown to be resistant to Rous sarcoma and Australorp inbred line Marek’s disease viruses. UCD 331 Congenic with UCD 003; MHC from a SCWL B2 Poor 5M/6F Semen Yes Abplanalp MHC: B2; shown to be resistant to Rous sarcoma and dwarf SCWL Marek’s disease viruses. UCD 335 Congenic with UCD 003; MHC from a SCWL B19 Poor 5M/6F Semen Yes Abplanalp MHC: B19; shown to be susceptible to Rous sarcoma commercial Richardson Mt. Hope and Marek’s disease viruses. SCWL UCD 336 Congenic with UCD 003; MHC from SCWL BQ Poor 5M/6F Semen Yes Abplanalp MHC: BQ (similar to B21); shown to be resistant to Rous Red Jungle Fowl sarcoma and Marek’s disease viruses. UCD 342 Congenic with UCD 003; MHC from a SCWL BO Poor 5M/6F Semen Yes Abplanalp MHC: BO; shown to be susceptible to Rous sarcoma cross of Ceylon Jungle Fowl and virus. Red Jungle Fowl UCD 361 Congenic with UCD 003 SCWL B17, A2/E7 Poor 5M/6F No Yes Abplanalp A/E blood types 2/7. UCD 380 Congenic with UCD 003 SCWL B17, A4/E7 Poor 5M/6F No Yes Abplanalp A/E blood types 4/7; resistant to Rous sarcoma. UCD 386 Congenic with UCD 003 SCWL BR4/R4 Poor 5M/6F No Yes Abplanalp MHC: BR4/R4 (B15/B21 recombinant); shown to be resistant to Rous sarcoma and Marek’s disease viruses. UCD 387 Congenic with UCD 003 SCWL BR5/R5 Poor 5M/6F No Yes Abplanalp MHC: BR5/R5 (B21/B15 recombinant); shown to be susceptible to Rous sarcoma and Marek’s disease viruses. UNH 6.15-5 Congenic with UNH 6-1 SCWL B5 Good 10M/40F No Yes Taylor Inbreeding coefficient (F)>0.999; MHC: B5. UNH 6.6-2 Congenic with UNH 6-1 SCWL B2 Good 10M/40F No Yes Taylor Inbreeding coefficient (F)>0.999; MHC: B2. UNH-UCD 003 Acquired from U California-Davis in SCWL B17 Good 10M/40F No Yes Taylor Inbreeding coefficient (F)>0.999; MHC: B17.1986

Chicken genetic stocks Appendix 2 Table 2.1 4 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Bloodtype-MHC-Inbred (cont.) UNH-UCD 003.R1 Congenic with UCD 003 SCWL BF24-BG23 Good 10M/40F No Yes Taylor MHC: BF24-BG23 (B complex recombinant); backcrossed eight times to UCD-003. UNH-UCD 003.R2 Congenic with UCD 003 SCWL BF2-BG23 Good 10M/40F No Yes Taylor MHC: BF2-BG23 (B complex recombinant); backcrossed eight times to UCD-003. UNH-UCD 003.R3 Congenic with UCD 003 SCWL BF2-BG23 Good 10M/40F No Yes Taylor MHC: BF2-BG23 (B complex recombinant); backcrossed eight times to UCD-003. UNH-UCD 003.R4 Congenic with UCD 003 SCWL BF2-BG23 Good 10M/40F No Yes Taylor MHC: BF2-BG23 (B complex recombinant); backcrossed eight times to UCD-003. UNH-UCD 003.R5 Congenic with UCD 003 SCWL BF21-BG19 Good 10M/40F No Yes Taylor MHC: BF21-BG19 (B complex recombinant); backcrossed eight times to UCD-003. UNH-UCD 003.R6 Congenic with UCD 003 SCWL BF21-BG23 Good 10M/40F No Yes Taylor MHC: BF21-BG23 (B complex recombinant); backcrossed eight times to UCD-003. UNH-UCD 386 Acquired from U California-Davis in SCWL BF15-BG21 Good 10M/40F No Yes Taylor MHC: BF15-BG21 (B complex recombinant). 1995; congenic with UCD 003 UNH-UCD 387 Acquired from U California-Davis in SCWL BF21-BG15 Good 10M/40F No Yes Taylor MHC: BF21-BG15 (B complex recombinant). 1995; congenic with UCD 003 UNH-UCD 3C.1 Congenic with UCD 003 SCWL B17 Good 10M/40F No Yes Taylor MHC: B17, with recombined B complex.

Chromosomal variant Ottawa B-19/B-19 M13 Also referred to as Ottawa B19 SCWL B19 No live 0 Blastodisc cells With Etches MHC: B19; segregating for DNA banding patterns using birds permission M13 phage. Ottawa B-21/B-21 M13 Also referred to as Ottawa B21 SCWL B21 No live 0 Blastodisc cells With Etches MHC: B21; segregating for DNA banding patterns using birds permission M13 phage. UCD-Cornell Mono-PNU Acquired from Cornell in 1995 SCWL Good 120 No With Delany Embryos homozygous for a large deletion on the MHC collaboration chromosome (16) lack most of the rDNA genes and die early in embryogenesis; heterozygotes develop normally and are viable. UCD-Cornell Trisomic Acquired from Cornell in 1995 SCWL Good 120 No With Delany Trisomy or tetrasomy of the MHC-containing collaboration chromosome (16); such aneuploids can hatch and reach maturity, but are often small and have poor production characteristics.

Chicken genetic stocks Appendix 2 Table 2.1 5 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Chromosomal variant (cont.) Wisconsin Chromosomal Rearrangements Kept in genetic background of New Hampshire Fair: 4M/6F No With Bitgood Six chromosomal translocations and two inversions Wisconsin New Hampshire institutional collaboration involving chromosomes 1 through 4 and Z. Endogenous virus RPRL 15B1 Specific pathogen-free SCWL B5, B15, Good: 6M/42F Semen Yes Bacon Non-inbred; MHC: B5 and B15; susceptible to avian ALVE1 USDA leukosis viruses A, B & C and Marek’s disease virus; contains endogenous virus ev1. Endogenous virus-Inbred RPRL 100B Congenic with RPRL 7I2; specific SCWL B2, ALVE1, Good: 6M/42F Semen Yes Bacon Inbreeding coefficient (F)>0.999; MHC: B2; endogenous pathogen-free ALVE3 USDA viruses ev1 and ev3; susceptible to avian leukosis viruses B, C, and E, and Marek’s disease virus. RPRL 6I3 Specific pathogen-free SCWL B2, ALVE1, Good: 12M/84F Semen Yes Bacon Inbreeding coefficient (F)>0.999; MHC: B2; endogenous ALVE3 USDA viruses ev1 and ev3; susceptible to avian leukosis viruses A,B, &C, and resistant to Marek’s disease virus. RPRL 7I2 Specific pathogen-free SCWL B2, ALVE1, Good: 12M/84F Semen Yes Bacon Inbreeding coefficient (F)>0.999; MHC: B2; endogenous ALVE3 USDA viruses ev1 and ev3; susceptible to avian leukosis viruse C and Marek’s disease virus. RPRL Reaseheath Line C Specific pathogen-free SCWL B12, Good: 6M/42F Semen Yes Bacon Inbreeding coefficient (F)>0.999; MHC: B12; endogenous ALVE1,USDA viruses ev1, ev7, ev10; susceptible to leukosis B and C. ALVE7, ALVE10

Inbred ADOL 6C.7A ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7B ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7C ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7D ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters).

Chicken genetic stocks Appendix 2 Table 2.1 6 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Inbred (cont.) ADOL 6C.7F ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7G ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7I ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7J ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7K ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7L ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7M ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7N ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7P ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7R ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7S ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters).

Chicken genetic stocks Appendix 2 Table 2.1 7 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Inbred (cont.) ADOL 6C.7T ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7V ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7W ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). ADOL 6C.7X ReCon 12% RPRL 7I2, 88% RPRL 6I3 SCWL B2 Good: 4M/10F No Yes Bacon One of 19 different recombinant lines (primarily congenic USDA with RPRL 6I3), each subline with 12.5% of genome from RPRL 7I2 (sublines identified by letters). Ottawa GF Derived from Ottawa 3 SCWL No live 0 Blastodisc cells With Etches Inbreeding coefficient (F)>0.8. birds permission Ottawa GH Derived from Ottawa 3 SCWL No live 0 Blastodisc cells With Etches Inbreeding coefficient (F)>0.8. birds permission Ottawa M2 Derived from Ottawa 4 SCWL No live 0 Blastodisc cells With Etches Inbreeding coefficient (F)>0.7. birds permission Ottawa WG Derived from Ottawa 8 SCWL No live 0 Blastodisc cells With Etches Inbreeding coefficient (F)>0.7. birds permission Ottawa XP Derived from Ottawa 9 SCWL No live 0 Blastodisc cells With Etches Inbreeding coefficient (F)>0.7. birds permission UCD 001 One of the reference lines used in Red Jungle Good 50M/50F No With Delany Inbreeding coefficient (F)>0.8; from wild-type jungle fowl. the East Lansing Chicken Genome Fowl collaboration Mapping Project Wisconsin Ancona Kept as closed flock for Ancona Fair: 4M/15F No With Bitgood Inbreeding coefficient (F)>0.9; half-sibling inbreeding more than 20 generations institutional collaboration since the mid-1940s. Wisconsin Leghorn line UW-Sp2 Derived from 1940/1950 Canadian SCWL Fair: 4M/15F No With Bitgood Inbreeding coefficient (F)>0.9; half-sibling inbreeding Spruceleigh strains institutional collaboration since the mid-1940s.

Mutant-Color, feather Wisconsin Autosomal Albino Acquired from U SCWL Autosomal recessive. ca Fair: 4M/12F No With Bitgood Homozygotes have white feathers and red eyes. Massachusetts-Amherst in 1997 institutional collaboration (UMass Autosomal Albino)

Chicken genetic stocks Appendix 2 Table 2.1 8 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Mutant-Developmental defect-Eye UBC RC Found in Minnesota Rhode Island Rhode Island Autosomal recessive. rc or rd Poor 12 M/40F No Yes Cheng Retinal degeneration homozygotes do not form rods or Red in 1980; backcrossed yearly to Red cones in the retina, causing blindness. UBC-Minnesota Rhode Island Red UMass Pink Eye Also has dominant extension of Mixed Autosomal recessive. pk Dispersal 25 No Yes Smyth Pink-eye homozygotes have pink eyes and a high melanin (E) in 1998 incidence of cataracts; feather color is also diluted. Wisconsin Blind/Cataract Kept in genetic background of SCWL Autosomal recessive bc Fair: 6M/12F No With Bitgood Homozygous chicks are blind at hatch, with visible Wisconsin SCWL semi-viable. institutional collaboration cataracts. Wisconsin Pink-eye Acquired from U Mixed Autosomal recessive. pk Poor 4M/12F No Yes Bitgood Homozygotes have pink eyes and a high incidence of Massachusetts-Amherst in 1998 cataracts; feather color is diluted, even with dominant extension of melanin (E). Wisconsin Pop-eye Kept in Wisconsin New Hampshire New Hampshire Sex-linked recessive. pop Fair: 6M/12F No With Bitgood Homozygotes have a conical protrusion of the cornea genetic background institutional collaboration (keratoconus) first seen at 5 wk posthatch. Mutant-Developmental defect-Face/limb Storrs Chondrodystrophy Mutation reported in SCWL in 1942; SCWL Autosomal recessive ch Poor 5M/19F No Yes Pierro Homozygotes have short upper beaks, shortened long kept at Storrs since late 1940s embryonic lethal. bones, and bent tibiae. Storrs Creeper Held at Storrs since the 1920s; Mixed Rose R and Pt are autosomal Cp, R, Pt Poor 10M/39F No Yes Pierro Heterozygotes have shortened limbs, and homozygotes mutation present in a few exhibition comb WL dominants; cp is an die before hatch; stock also carries rose comb (R) and breeds autosomal incomplete ptilopody (leg feathering: Pt). dominant, lethal in homozygotes. Storrs Diplopodia-3 Mutation reported in inbred SCWL in Mixed SCWL Autosomal recessive dp-3 Poor 5M/22F No Yes Pierro Homozygotes display moderate preaxial polydactyly, 1972; acquired from U embryonic lethal. dwarfing, exposed viscera, and shortened upper beak. Saskatchewan in the 1960s Storrs Diplopodia-5 Mutation reported in 1983; acquired Mixed SCWL Autosomal recessive dp-5 Poor 5M/21F No Yes Pierro Homozygotes display moderate preaxial polydactyly, from U Saskatchewan in late 1980s embryonic lethal. dwarfing, exposed viscera, and shortened upper beak. Storrs Limbless Mutation reported in 1979 in a flock Mixed SCWL Autosomal recessive ll Poor 5M/20F No Yes Pierro Homozygotes do not form limb buds or limbs, and of Rhode Island Reds; acquired from embryonic lethal. usually have a shortened upper beak. U Wisconsin in late 1980s Storrs Micromelia-Abbott Mutation reported in crooked-neck Mixed SCWL Autosomal recessive mm-A Poor 5M/17F No Yes Pierro Homozygotes have distinctly shortened long bones. dwarf stock from U California-Davis embryonic lethal. Storrs Micromelia-Hays Mutation reported in Rhode Island SCWL Autosomal recessive mm-H Poor 5M/20F No Yes Pierro Homozygotes have distinctly shortened long bones. Red stock in 1944; held at Storrs embryonic lethal. since 1950s Storrs Nanomelia Mutation reported in SCWL stock by Mixed SCWL Autosomal recessive nm, Pt Poor 5M/20F No Yes Pierro Homozygotes have severely shortened long bones in the Landauer in 1965; held at Storrs embryonic lethal. limbs; may also carry the mutant allele for leg-feathering since then; also has ptilopody (Pt).

Chicken genetic stocks Appendix 2 Table 2.1 9 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Mutant-Developmental defect-Face/limb (cont.) Storrs Perocephaly Mutation reported in flock of SCWL Mixed SCWL Autosomal recessive per Poor 5M/22F No Yes Pierro Homozygotes show variable effects, from abnormal by Landauer in 1956; held at Storrs embryonic lethal with upper beaks to microcephaly, synophthalmia, and since then low penetrance. cyclopia. Storrs Polydactyly Mutation long known in exhibition Mixed SCWL Autosomal incomplete Po Poor 5M/22F No Yes Pierro Homozygotes and heterozygotes may have one or two stocks and reported in several dominant. extra preaxial toes, or a longer-than-normal first digit. ancient breeds Storrs Talpid-2 Mutation reported in SCWL stock in SCWL Autosomal recessive ta-2 Poor 2M/10F No Yes Pierro Homozygotes display extreme preaxial polydactyly (up 1959; acquired from U California embryonic lethal. to 10 digits per limb), overall dwarfing, exposed viscera, Davis in 1996 and cleft palate with a parrot-like upper beak. Storrs Wingless-2 Mutation reported in flock of SCWL SCWL Autosomal recessive wg-2 Poor 5M/22F No Yes Pierro Homozygotes lack wings, have reduced legs, by Landauer in 1956; held at Storrs embryonic lethal. balloon-like feathers, short upper beak, cleft palate and since then small kidneys. UCD Cleft Primary Palate/Scaleless Derived from crosses of: SCWL, Mixed Autosomal recessive cpp, sc Poor 5M/5F Semen Yes Abbott Cleft primary palate (cpp) homozygotes lack most of the UCD Scaleless-High and UCD embryonic lethal (cpp); upper beak, may also have limb reductions if Scaleless-Low; cpp was originally autosomal recessive homozygous for scaleless; for scaleless (sc ): scaleless called ectrodactyly when found in semi-viable (sc). homozygotes do not form spurs, scales or most UCD Scaleless stocks in 1966 feathers. UCD Coloboma X 003 Congenic with UCD 003; mutation SCWL Autosomal recessive cm Poor 5M Semen Yes Abbott Hemizygous females are moderately to severely dwarfed first reported in 1970 at U embryonic lethal. with mildly to severely cleft palates; some are lacking California-Davis preaxial digits or have trucated wings and legs; some are edemic; the expression may be highly variable, even with the same parents. UCD Diplopodia-1 X 003 Near-congenic with UCD 003; SCWL Autosomal recessive dp-1 Poor 5M/5F Semen Yes Abbott Homozygotes display moderate preaxial polydactyly, mutation first reported in 1947 at U embryonic lethal. dwarfing, exposed viscera, and shortened upper beak. California-Berkeley UCD Diplopodia-3 X 003 Near-congenic with UCD 003; SCWL Autosomal recessive dp-3 Poor 5M/5F No Yes Abbott Homozygotes display moderate preaxial polydactyly, mutation first reported in 1972 at U embryonic lethal. dwarfing, some with exposed viscera, occasional cleft California-Berkeley palate, and shortened upper beak. UCD Donald-duck Beak/Scaleless Reported in 1967 in New Mixed Autosomal recessive dd-2, sc, Poor 4M/3F Semen Yes Abbott Donald duck beak homozygotes have upward curled Hampshire-type chickens at U embryonic lethals (cpp may also upper beaks, may have downward curled lower beaks; California-Davis and dd-2); autosomal include cpp some hatch, but do not survive long; no known recessive semi-viable interaction with scaleless; for sc, see: UCD (sc). Scaleless-Low; may also carry cleft primary palate (cpp), see: UCD Cleft Primary Palate/Scaleless.

Chicken genetic stocks Appendix 2 Table 2.1 10 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Mutant-Developmental defect-Face/limb (cont.) UCD Eudiplopodia X 003 Congenic with UCD 003; mutation SCWL Autosomal recessive eu Poor 5M/5F Semen Yes Abbott Homozygotes have extra digits on the dorsal surfaces of first reported 1959 in SCWL flock at embryonic lethal. the limb buds, which develop into extra, bidorsal toes U California-Berkeley on the feet and occasional dorsal knobs or digits on the wings. UCD Limbless X 003 Near-congenic with UCD 003; SCWL Autosomal recessive ll Poor 5M/5F No Yes Abbott Homozygotes do not form limb buds or limbs, and mutation first reported in 1979 at U embryonic lethal. usually have a shortened upper beak. Wisconsin

UCD Polydactyly X 003 Near-congenic with UCD 003; mutant SCWL Autosomal dominant Po Poor 3M/3F Semen Yes Abbott Homozygous and heterozygous mutants may have one allele common in exhibition with incomplete or two extra preaxial toes, or a longer-than-normal first chickens penetrance. digit. UCD Stumpy X 003 Congenic with UCD 003; mutation SCWL Autosomal recessive stu Poor 5M/5F Semen Yes Abbott Homozygotes have conical leg buds and a poorly to reported at U California-Davis in embryonic lethal. non-vascularized allantois that never gets larger than the 1966 in New Hampshire X Cornish head; embryo death, typically between the fifth and seventh day, is associated with massive multiple hemorrhages. UCD Talpid-2 X 003 Congenic with UCD 003; mutation SCWL Autosomal recessive ta-2 Poor 5M/5F Semen Yes Abbott Homozygotes display extreme preaxial polydactyly, first reported in 1959 at U embryonic lethal. dwarfing, exposed viscera, and cleft, parrot-like upper California-Davis in a SCWL flock beak. UCD Wing-reduced X 003 Syndrome found in UCD 413 SCWL Multifactorial, not yet Poor 3M/3F No Yes Abbott A complex syndrome; affected birds lack toenails and (muscular dystrophy) in 1990; fully defined. some phlanges (usually on digit 3, sometimes digit 4) crossed several times to UCD 003 and may have truncated wings. UCD Wingless-2 X 331 Congenic with UCD 331; mutation SCWL Autosomal recessive wg-2 Poor 5M/5F Semen Yes Abbott Homozygotes lack wings, have reduced legs, first reported in 1956 at U embryonic lethal. balloon-like feathers, short upper beak, cleft palate and Connecticut-Storrs small metanephric kidneys. Wisconsin Ametapodia Acquired from U Mixed Autosomal dominant, Mp Fair: 4M/12F No With Bitgood Heterozygotes lack metatarsals in the legs and Massachusetts-Amherst in 1997 lethal in homozygotes. institutional collaboration metacarpels in the wings; homozygotes usually die (UMass Ametapodia) early in development. Wisconsin Limbless Kept in Wisconsin Leghorn genetic SCWL Autosomal recessive ll Fair: 6M/20F No With Bitgood Homozygotes do not form limb buds or limbs, and background embryonic lethal. institutional collaboration sometimes have a short upper beak. Wisconsin Talpid-2 Mutation first reported in 1959 at U SCWL Autosomal recessive ta-2 Fair: 6M/12F No With Bitgood Homozygotes display extreme preaxial polydactyly, California-Davis; acquired in 1990s; embryonic lethal. institutional collaboration dwarfing, exposed viscera, and cleft, parrot-like upper kept in Wisconsin Leghorn genetic beak. background Wisconsin Wingless-2 Mutation first reported in 1956 at U SCWL Autosomal recessive wg-2 Fair: 6M/12F No With Bitgood Homozygotes lack wings, have reduced legs, Connecticut-Storrs; now kept in embryonic lethal. institutional collaboration balloon-like feathers, short upper beak, cleft palate and Wisconsin Leghorn genetic small kidneys. background Chicken genetic stocks Appendix 2 Table 2.1 11 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Mutant-Developmental defect-Skin/feather Storrs Ottawa Naked Mutation first reported by R. Crawford New Hampshire Autosomal recessive. nk Poor 3M/17F No Yes Pierro Homozygotes are naked at hatch with occasional in 1982; acquired from U syndactyly of toes 2 and 3; some feathers may form on Saskatchewan in late 1980s adults. Storrs Ptilopody Mutation common in exhibition Mixed SCWL Autosomal dominant Pt Combined see: Storrs No Yes Pierro Homozygotes and heterozyotes have feathers replacing breeds; introduced into Storrs with multifactorial with Storrs Nanomelia some of the scales on lower leg, foot, and toes. Nanomelia with Buff Cochin cross; modifiers. Nanomelia also in Storrs Creeper; and Creeper Storrs Scaleless Mutation reported in New Mixed New Autosomal recessive sc Poor 10M/30F No Yes Pierro Homozygotes do not form spurs, scales or most feathers. Hampshire-type stock in 1957; Hampshire semi-viable. acquired from U California-Davis in 1965 UCD Ichthyosis X 003 Near-congenic with UCD 003; SCWL Autosomal recessive dehy Poor 5M/5F Semen Yes Abbott Ichthyosis (dehy) homozygotes develop lamellar mutation first reported in 1957 at U semi-viable. ichthyosis: chicks dehydrate rapidly after hatch, and California-Berkeley have characteristic stringy/greasy down feathers; adults do not slough leg scales, and develop chronic skin lesions. UCD Naked-neck Mutation common in exhibition Mixed SCWL Autosomal dominant. Na No live 0 Semen With Abbott Causes a reduction in size of feather tracts on the head, breeds and in some commercial birds permission neck and ventral trunk, usually giving the bird a bare or strains nearly bare neck. UCD Scaleless-High Mutation first reported at U Mixed Autosomal recessive sc Poor 15M/15F Semen Yes Abbott Scaleless-high homozygotes do not develop scales or California-Davis in 1957; originally semi-viable, with spurs, but selection for increased feather development non-viable, but crossbreeding and multifactorial modifiers. has resulted in abundant down-like feathers forming on selection dramatically increased the body and sparse feathers forming on the legs. viability; background breeds include Cornish, SCWL, Barred Rock, New Hampshire, Red Jungle Fowl UCD Scaleless-Low Mutation first reported at U Mixed Autosomal recessive sc Poor 15M/15F Semen Yes Abbott Scaleless-low homozygotes do not develop spurs, California-Davis in 1957; originally semi-viable, with scales or most feathers, a condition that was enhanced non-viable, but crossbreeding and multifactorial modifiers. by selection for low feather number. selection dramatically increased viability; background breeds include Cornish, SCWL, Barred Rock, New Hampshire, Red Jungle Fowl Wisconsin Tardy Feathering Kept in genetic background of SCWL Autosomal recessive. t Fair: 6M/12F No With Bitgood Homozygotes have very slow growing flight feathers Wisconsin Leghorn crossed with institutional collaboration after hatch, but this is only detectable if chicks are also Wisconsin New Hampshire expressing sex-linked rapid feather growth (k+).

Chicken genetic stocks Appendix 2 Table 2.1 12 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Mutant-Developmental defect-Spine/tail Storrs Dominant Rumplessness Mutation reported in 1925; held at SCWL Autosomal dominant. Rp Poor 6M/21F No Yes Pierro Homozygotes lack pygostyle, caudal vertebrae, Storrs since then uropygial gland and tail feathers; fertility is usually low if naturally mated. Storrs Recessive Rumpless Mutation reported in SCWL stock in Mixed SCWL Autosomal recessive rp-2 Poor 10M/67F No Yes Pierro Homozygotes have fused or absent pygostyle and 1945; held at Storrs since then; also with incomplete caudal vertebrae, and some kyphoscoliosis with extra has perocephaly (per); kept penetrance. ribs. homozygous for rp-2 UCD Scoliosis Multifactorial syndrome uncovered in Mixed Rose At least two (maybe No live 0 Semen With Abbott Affected birds show moderate to severe kyphoscoliosis the 1950s during inbreeding of comb WL three) autosomal birds permission starting at 5 weeks, and clearly visible in x-rays at 12 stocks at U California-Berkeley recessive genes. weeks; males are more severely affected than females.

Mutant-Gene pool OSU Dwarf Leghorn Mutation kept in commercial SCWL SCWL All recessive; one dw, blr, bld, Fair 20M/50F No Yes Savage Includes seven mutations: sex-linked dwarf; four background, but as closed flock sex-linked viable (dw), ed-a, ed-b autosomal mutations that cause: blastoderm for seven generations; four autosomal lethal degeneration (bld), blood ring and early embryo death developed by P. Bernier or semi-lethal (blr), and semi-lethal chick edema (when hom. for ed-a (blr,bld,ed-a,ed-b). and ed-b); and two new mutations that have not yet been reported: transient congenital tremor and ectopia. UBC-Minnesota Marker Acquired from U Minnesota-St. Paul Mixed Gene pool of various Po, Pt, P, Poor 8M/40F No Yes Cheng Gene pool with 13 dominant mutations: polydactyly, dominant and R, U, M, ptilopody, pea and rose comb, uropygial bifurcation, recessive mutations; Na, Cr, S, multiple spurs, naked neck, crest, silver, sex-linked see description. B, I, Mb, O, barring, dominant white, muffs and beard, and blue egg Cp, pr shell; may also contain recessive mutations creeper (Cp) and protoporphyrin inhibitor (pr). UCD Diplopodia-3/Scaleless High A recent cross (1997) of UCD Mixed Two autosomal dp-3, sc Poor 3M/5F Semen Yes Abbott Diplopodia-3 (dp-3) mutants display moderate preaxial Scaleless-High with UCD recessives: one polydactyly, dwarfing, exposed viscera, occasional cleft Diplopodia-3 X 003 embryonic lethal (dp3), palate, and shortened upper beak; homozygous one semi-viable (sc). scaleless mutants lack spurs, scales and most feathers. UCD Eudiplopodia/Limbless Mildly inbred, including some UCD SCWL Two autosomal eu, ll Poor 10M/10F Semen Yes Abbott See UCD Eudiplopodia and UCD Limbless descriptions. 003; crossed with UCD recessive embryonic Scaleless-High and -Low in 1996 lethals. UCD Limbless/Stumpy Ancestral background includes SCWL Two autosomal ll, stu Poor 4M/4F Semen Yes Abbott See UCD Limbless and UCD Stumpy descriptions. leukosis-free stocks kept at U recessive embryonic California-Davis in the 1980s lethals. UCD Silkie cross Derived from UCD Silkie; in 1995 Mixed Silkie Five autosomal dom. Cr, Fm, h, Poor 4M/7F No Yes Abbott UCD Silkie crossed to UCD-003 or UCD Scaleless-low to crossed with both UCD 003 and UCD (Cr,Po,Pt,Fm,Mb), one id, Mb, Po, decrease inbreeding and enhance egg production, then Scaleless-Low to increase vigor; sex-linked rec. (id), Pt, sc repeatedly back-crossed to UCD Silkie (see UCD-Silkie backcrossed repeatedly to UCD two autosomal rec. for desciption of mutations). Silkie (h,sc).

Chicken genetic stocks Appendix 2 Table 2.1 13 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Mutant-Gene pool (cont.) UCD Talpid-2/Wingless-2 Mildly inbred, including some UCD SCWL Two autosomal ta-2, wg-2 Poor 10M/10F Semen Yes Abbott See UCD Talpid-2 and UCD Wingless-2 descriptions. 003; crossed with UCD recessive embryonic Scaleless-High and -Low in 1996 lethals.

Mutant-Immunological defect Arkansas Smyth Line B101 Acquired from J. Smyth at U Brown Leghorn, Multifactorial with Good 10M/20F No With Erf Selected for high expression of delayed Massachusetts-Amherst in 1996; synthetic variable expressivity. collaboration amelanogenesis (autoimmune vitiligo: increasing also known as DAM line (delayed amount of white feathers with each molt) also: blindness amelanogenesis) and thyroiditis; amelanosis now seen >85% of offspring. Arkansas Smyth Line B102 Acquired from J. Smyth at U Brown Leghorn, Multifactorial with Good 10M/20F No With Erf Selected for high expression of delayed Massachusetts-Amherst in 1998; synthetic variable expressivity. collaboration amelanogenesis (autoimmune vitiligo: increasing also known as DAM line (delayed amount of white feathers with each molt) also: blindness amelanogenesis) and thyroiditis; amelanosis now seen >85% of offspring. Cornell Obese (B-13) Derived from Cornell C Strain, SCWL Multifactorial, with as B13 Poor 40M/120F No Yes Marsh MHC B13; affected birds develop spontaneous selected for MHC haplotype B13; many as five major autoimmune thyroiditis and, in females, a persistant right closed flock for over 30 years; genes. Mullerian duct. pedigreed annual reproduction UCD 200 Mutation first reported at Oregon SCWL At least two recessive sd Poor 10M/12F No Yes Abplanalp Inbreeding coefficient (F)>0.80; develops autoimmune State U in 1961 genes and scleroderma (progressive systemic sclerosis), with multifactorial modifiers. necrosis and sloughing of the combs and wattles (self-dubbing), polyarthritis, and some visceral lesions. UMass Smyth Line Also know as the DAM line (for Brown Leghorn, Multifactorial with Dispersal 200 No Yes Smyth Delayed amelanosis (DAM) homozygotes display a delayed amelanogenesis); mutation synthetic variable expressivity. in 1998 gradual loss of feather pigment with successive molts originally found in the UMass Brown (an autoimmune condition mimicking human vitiligo), Line with some retinal dystrophy and autoimmune thyroiditis.

Mutant-Neurological defect Saskatchewan Epileptiform seizures Synthetic strain, mostly Fayoumi, Mixed Fayoumi Autosomal recessive epi Good 100M/170F No With Classen Homozygotes afflicted with seizures of varying severity derived from Agriculture Canada semi-viable mutation collaboration thoughout life of bird, but good viability with extra care; (CFAR) stocks in 1963 with incomplete used as disease model in pharmacological and penetrance. physiological research. UNL Paroxysm Acquired from R. Cole at Cornell U in SCWL Sex-linked recessive. px Fair: Hatch, 5M No With Beck Post-hatch lethal mutation, causing seizures, slow the 1960s regional, collaboration growth and eventual death of hemizygous females. misc. Wisconsin Pirouette Kept in Wisconsin Leghorn genetic SCWL Autosomal recessive pir Fair: 6M/12F No With Bitgood Homozgyous chicks expressing this neurological background semi-viable. institutional collaboration mutation will spin in circles for short periods.

Chicken genetic stocks Appendix 2 Table 2.1 14 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Mutant-Physiological defect Athens-Canadian Dwarfs Derived from Athens-Canadian Commercial Sex-linked recessive. dw Good 25M/50F No Yes Burke Sex-linked dwarf mutation in Athens-Canadian Randombred meat sire cross background. Cornell Sex-linked Dwarf Derived from the old Kemper SCWL SCWL Sex-linked recessive. Dw, B15 Fair 120F No With Marsh Homozygous males and hemizygous females are strain, which is also was ancestral collaboration reduced in body size; mutants are characterized by low to Cornell K; pedigreed yearly serum T3 levels and expression of a defective form of reproduction the growth hormone receptor; MHC: B15. Ohio Low-score Normal Derived from Storrs Muscular Mixed SCWL Not yet defined. Good 50M/50F No With Velleman Affected birds show intermediate to low exhaustion Dystrophy after an outcross with collaboration scores when subjected to the “flip test” used to identify commercial SCWL in 1970s muscular dystrophy homozygotes; such expression is associated with an altered extra-cellular matrix organization. Ohio Muscular Dystrophy Mutation first reported in 1956 at U Mixed Autosomal recessive. am Good 50M/50F No With Velleman Homozygotes develop joint stiffness and muscle California-Davis; acquired from U collaboration weakness; breast and other muscle replaced by fat and Connecticut-Storrs in 1997; kept as connective tissue. homozygotes Storrs Crooked-neck Dwarf Mutation discovered in New Mixed New Autosomal recessive cn Poor 5M/22F No Yes Pierro Homozygotes are edemic and dwarfed, with crooked, Hampshire-type chicken stock in Hampshire embryonic lethal. fragile necks, thin amuscular legs, and no voluntary 1945; acquired from U muscle contractions. California-Davis in 1950s Storrs Muscular Dystrophy Mutation first reported in 1956 at U Mixed SCWL Autosomal recessive. am Poor 5M/15F No Yes Pierro Homozygotes develop joint stiffness and muscle California-Davis; acquired 1958; kept weakness; breast and other muscle replaced by fat and as homozygotes connective tissue. UCD 077 Imported from Switzerland in 1987; SCWL Multifactorial B19 Poor 5M/6F No Yes Abplanalp Inbreeding coeffiecient (F)>0.95; MHC: B19; high blood full-sib inbreeding since 1968 lipid levels. UCD 413 Derived from commercial meat stock New Hampshire Autosomal recessive. am Fair 15M/20F No Yes Wilson Muscular dystrophy homozygotes develop joint stiffness displaying muscular dystrophy; and pectoral muscle weakness starting about 4 weeks closed flock since 1972 post-hatch, a condition produced by the replacement of these muscles by fat and connective tissue; some wing reduction defects not related to MD also seen. UCD Crooked-neck Dwarf Acquired from U Connecticut-Storrs Mixed SCWL Autosomal recessive cn Fair 15M/20F No With Abbott Homozygotes are edemic and dwarfed, with crooked, in 1991; crossed to UCD 003 several embryonic lethal. permission fragile necks, thin amuscular legs, and no voluntary times since 1996 muscle contractions. UCD Riboflavin Transfer Deficient Out-crossed to UCD 003 in 1996; SCWL Autosomal recessive, rd Poor 5M/5F Semen Yes Abbott Homozygotes can only make defective riboflavin binding acquired from Pennsylvania State U maternal-effect lethal. protein; birds are viable, but such hens cannot put in 1985 enough riboflavin into their egg albumen to support an embryo beyond 16 days of incubation; such embryos are dwarfed and hemorrhagic.

Chicken genetic stocks Appendix 2 Table 2.1 15 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Mutant-Physiological defect (cont.) UCD-Cornell Autosomal Dwarf Mutation first reported in Cornell K SCWL Autosomal recessive. adw Poor 25M/50F No With Delany Homozygotes’ body size reduced by 30% , recognizable Strain in 1973; transferred to U collaboration by six to eight weeks; avg weight of female is 1173 g, California-Davis in 1998 egg weight 57.7g, 245 eggs/cycle, generally good viability but poor hatchability. UDel Riboflavin Transfer Deficient Acquired from E. Buss at SCWL Autosomal recessive, rd Poor 10M/50F No Yes White Homozygotes can only make defective riboflavin binding Pennsylvania State U maternal-effect lethal. protein; birds are viable, but such hens cannot put enough riboflavin into their egg albumen to support an embryo beyond 16 days of incubation; such embryos die dwarfed and hemorrhagic.

Mutant-Reproductive defect Arkansas Sd Line Mutation first reported in the 1960s at Delaware X Autosomal recessive, sdg or sd Good 25M/150F No No Kirby Males homozygous for sperm degeneration have Ohio State in Delaware breed; SCWL sex-limited. defective sperm due to efferent duct malfunction. out-crossed with SCWL from a single male in 1980s Wisconsin Double Oviduct Line Rhode Island Incompletely penetrant Rov Fair: 4M/15F No With Bitgood Both right and left oviduct form in most females of this Red with multifactorial institutional collaboration line. modifiers. Wisconsin Restricted Ovulator Kept in Wisconsin Leghorn genetic SCWL Sex-linked recessive. ro Fair: 6M No With Bitgood Hemizygous females lay few if any eggs, have high background institutional collaboration blood lipids, and produce no offspring; males do not appear to be affected.

Mutant-Uncategorized ISU S1-19H Derived from two inbred Hy-Line SCWL B19, Good 4M/24F No With Lamont Inbreeding coefficient (F)>0.5; MHC: B19; IrGAThigh strains in 1964 IrGAThigh collaboration allele linked to MHC. ISU S1-19L Derived from two inbred Hy-Line SCWL B19, Good 4M/24F No With Lamont Inbreeding coefficient (F)>0.5; MHC: B19; IrGATlow strains in 1964 IrGATlow collaboration allele linked to MHC. ISU S1-1H Derived from two inbred Hy-Line SCWL B1, Good 3M/30F No With Lamont Inbreeding coefficient (F)>0.5; MHC: B1; IrGAThigh strains in 1964 IrGAThigh collaboration allele linked to MHC. ISU S1-1L Derived from two inbred Hy-Line SCWL B1, Good 3M/30F No With Lamont Inbreeding coefficient (F)>0.5; MHC: B1; IrGATlow strains in 1964 IrGATlow collaboration allele linked to MHC. Storrs Rose Comb Mutation long known in exhibition Mixed Rose Autosomal dominant. R Combined see: Storrs No Yes Pierro Homozygotes and heterozygotes have a broad comb, stock; introduced into Storrs Creeper comb WL with Storrs Creeper covered with papillae, and a single spike at the back; in 1960s Creeper has been associated with male infertility.

Chicken genetic stocks Appendix 2 Table 2.1 16 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Mutant-Uncategorized (cont.) UCD Crest/Hemoglobin-D Mutant form of hemoglobin reported SCWL Linked autosomal Cr, HbD No live 0 Semen With Abbott HbD is a hemoglobin variant, found in both adult and linked to mutant crest allele, found at dominant (Cr) and birds permission embryonic hemoglobin, which is linked to the mutant U California-Davis codominant (HbD). crest allele; Crest causes a tuft of long feathers to form on the head. UCD Multiplex Comb Causes conformational faults in Mixed SCWL Multifactorial. No live 0 Semen With Abbott Modifies the single-comb shape by causing points comb shape of single-comb birds permission (fleshy projections) to form along accessory comb axes exhibition chickens (up to five); these are usually smaller than the primary points of the single comb. Wisconsin Sex-linked Skin Color Kept in Wisconsin Leghorn genetic SCWL Sex-linked recessive. y Fair: 6M/12F No With Bitgood Homozygous or hemizygous mutant birds cannot deposit background institutional collaboration yellow pigment in the skin.

Pure breed Arkansas Giant Jungle Fowl Imported from Southeast Asia in Giant Jungle Good 9M/45F No Yes Anthony Naturally highly resistant to Rous sarcoma virus; 1950 (one male and five females); Fowl probably moderately inbred (foundation flock of 6 birds in kept as closed flock 1950). Guelph Silkie Derived from exhibition stock; Silkie Five autosomal Cr, Fm, h, Poor 20M/20F No With Etches Breed with five major mutations: Cr (long feathers on foundation was one pair; inbreeding dominants id, Mb, Po, permission crown of head), Po (one or more extra preaxial toes), Pt minimized (about 35% in 1995) (Cr,Po,Pt,Fm,Mb), one Pt (legs and toes feathered), Fm (dark pigment in skin, sex-link recessive (id), internal organs), Mb (long feathers under chin), and h one autosomal (feather defect: no hooklets). recessive (h). NCSU Barred Plymouth Rock Kept as closed flock used in Barred Plymouth Fair 4M/40F No Yes Christensen research and teaching Rock NCSU Rhode Island Red Kept as closed flock used in Rhode Island Fair 4M/40F No Yes Christensen research and teaching Red Ottawa New Hampshire New Hampshire No live 0 Blastodisc cells With Etches birds permission Saskatchewan Barred Plymouth Rock Acquried in 1920s Barred Plymouth Good 20M/50F No With Classen Used as a slow-growing chicken model in cardiac and Rock collaboration digestive physiology research, and as source of eggs with many blood and meat spots. Saskatchewan Brown Leghorn A strain of Danish Brown Leghorn Brown Leghorn Good 20M/50F No With Classen Used as a slow-growing chicken model in cardiac and acquired from Scattered Acres collaboration digestive physiology research, and as source of fertile Hatchery in Hanover, Ontario in 1965 eggs for use in research. UBC-Minnesota Rhode Island Red Acquired from U Minnesota-St. Paul; Rhode Island Poor 8M/40F No Yes Cheng From a moderately inbred (F approx. 0.6) flock of kept as closed flock for over 20 Red Rhode Island Red. Body weight 4.5 lb. generations; back-cross parent population for UBC RC

Chicken genetic stocks Appendix 2 Table 2.1 17 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Pure breed (cont.) UCD Silkie Descended from six exhibition birds Silkie Five autosomal dom. Cr, Fm, h,Fair 3M/3F No Yes Abbott Breed with five major mutations: Cr (long feathers on acquired from a hobby-breeder in (Cr,Po,Pt,Fm,Mb), one id, Mb, Po, crown of head), Po (one or more extra preaxial toes), Pt central California in 1994 (4M/2F) sex-linked rec. (id), Pt (legs and toes feathered), Fm (dark pigment in skin, one autosomal rec. (h). internal organs), Mb (long feathers under chin), and h (feather defect: no hooklets). UI-Urbana Columbian Non-exhibition (meat) variety; kept at Columbian Good 50M/600F No With Parsons Meat type, white/black feathers, slow growth, long legs, U Illinois-Urbana as closed flock collaboration narrow breast; very mild selection for body size. for over 30 years UI-Urbana New Hampshire Non-exhibition (meat) variety; at U New Hampshire Good 50M/200F No With Parsons Meat type, moderate growth, good conformation; new Illinois-Urbana for over 30 years; collaboration bloodlines introduced approx. 1993 to increase body kept as closed flock except for weight. outcross in 1993 UMass Light Brown Leghorn Serves as control for UMass Smyth Light Brown Dispersal 15M/35F No Yes Smyth Light-brown Leghorn chicken that has never shown Line (no occurance of delayed Leghorn in 1998 signs of delayed amelanogenesis. amelanogenesis)

Randombred Arkansas Brown Line B101 Acquired from J. Smyth at U Brown Leghorn eb Good 10M/20F No With Erf MHC-matched control/parental line for Arkansas Smyth Massachusetts-Amherst in 1996; collaboration line B101. subline of ancestral parent stock for Smyth Line Arkansas Brown Line B102 Acquired from J. Smyth at U Brown Leghorn, eb Good 10M/20F No With Erf MHC-matched control/parental line for Arkansas Smyth Massachusetts-Amherst in 1998; synthetic collaboration line B102. subline of ancestral parent stock for Smyth Line Arkansas Light Brown Leghorn B101 Acquired from J. Smyth at U Light Brown Good 10M/20F No With Erf MHC-matched control for Arkansas Smyth line B101; Massachusetts-Amherst in 1996 Leghorn collaboration does not develop delayed amelanogenesis (autoimmune vitiligo). Arkansas Randombred Formed by crossing commercial Commercial Good 16M/48F No Yes Anthony Randombred meat bird control from multiple parental meat (broiler) parent lines (seven meat sire cross strain cross. male lines and eight female lines)

Athens Randombred Synthetic line integrating Commercial Good 30M/150F No Yes Burke Randombred control/standard; foundation males from commercial and UGA Experiment meat sire cross commercial meat-type (WPR, WCornish, NH); foundation Station meat-type stocks, started in females from egg-production selected RIR, BPR, WPR, 1956 NH, SCWL and Cornish from Southern Regional Experiment Stations. Athens-Canadian Randombred Acquired from the Canadian Dept of Commercial R, P Good 60M/180F No Yes Burke Randombred control/standard segregating for single, Agriculture in 1958; includes White meat sire cross rose, and pea comb, with dominant white, some red Wyandotte and three synthetic meat and black feather color occurring. strains

Chicken genetic stocks Appendix 2 Table 2.1 18 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Randombred (cont.) Cornell C Specials (B13) MHC-matched to Cornell Obese; SCWL B13 Poor 8M/42F No Yes Marsh Control line for Cornell Obese; MHC B13; also can kept as closed flock for over 30 produce a persistant right Mullerian duct (often leading to years; derived from Cornell C Strain the formation of two oviducts) in affected females. NCSU-Cornell K Strain Derived from Cornell K-strain SCWL B15 Good 40M/100F No Yes Qureshi MHC: B15. Ottawa 10 No selection since 1973; derived SCWL No live 0 Blastodisc cells With Etches Control/standard maintained without selection since from a combination of North birds permission 1973. American commercial egg-layer stocks Ottawa 20 Formed by combining nine Commercial No live 0 Blastodisc cells With Etches Pedigreed randombred meat (broiler) reference stock from commercial broiler sire stocks in meat sire cross birds permission commercial sire lines. 1979 Ottawa 30 Formed by crossing nine Commercial No live 0 Blastodisc cells With Etches Pedigreed randombred meat (broiler) reference stock from commercial broiler dam stocks in meat sire cross birds permission commercial dam lines. 1979 Ottawa 5 No selection since 1950 SCWL No live 0 Blastodisc cells With Etches Control/standard maintained without selection since birds permission 1950. Ottawa 7 Derived from four commercial SCWL No live 0 Blastodisc cells With Etches Control/standard maintained without selection since egg-layer stocks and kept without birds permission 1958. selection since 1958; originally known as Kentville Control Strain 7 UCD 412 Kept as closed flock since 1972 New Hampshire Fair 15M/20F No Yes Wilson Control/standard for UCD-413 (muscular dystrophy). UMass Brown Line Source of delayed amelanogenesis Brown Leghorn, Autosomal recessive. eb Dispersal 90 No Yes Smyth Brown homozygotes are solid brown as chicks; adult mutation; serves as MHC-matched synthetic in 1998 males are wild-type, females are stippled dark brown; control for UMass Smyth Line serves as MHC-matched controls for UMass Smyth Line. Wisconsin Leghorn Kept as closed flock for over 30 SCWL Fair: 20M/180F No With Bitgood Closed population of Single-comb White Leghorns. generations; used as genetic institutional collaboration background for several mutant stocks at U Wisconsin-Madison Wisconsin Leghorn line UW-6X From cross of commercial SCWL Poor Few No With Bitgood Closed randombred/control population of 1950s origin egg-layers (Spruceleigh X HN) in collaboration egg-type commercial Single-comb White Leghorns. 1950s; kept as closed flock for over 20 years; almost extinct, only a single, low production female in 1998 Wisconsin New Hampshire Kept as closed flock for over 30 New Hampshire Fair: 20M/180F No With Bitgood Closed randombred/control population of purebred New generations; used as genetic institutional collaboration Hampshire chickens. background for several mutant stocks at U Wisconsin-Madison

Chicken genetic stocks Appendix 2 Table 2.1 19 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Selected-Behavioral trait Purdue KGB Derived from a seven-way, wide SCWL Fair 100M/100F No With Muir Selected for non-aggressive behavior and resistance to commercial cross at the North collaboration stress (“Kinder, Gentler Bird”). Central Regional Poultry Laboratory in 1972 Purdue MBB Derived from Purdue KGB SCWL Fair 150M/250F No With Muir Selected for more aggressive behavior (“Mean, Bad collaboration Bird”).

Selected-Egg trait Cornell K Strain Kept as closed flock since 1954; SCWL B15 Poor 165 No Yes, fee Dietert MHC: B15; resistant to leukosis complex (particularly selected to optimize egg production, Marek’s disease) by selection after natural exposure to egg size, body weight, other the viruses; good egg production characteristics. economic egg traits until 1971, then randombred with minimal selection Guelph Barred Plymouth Rock Derived from commercial stock Barred Plymouth Good 30M/130F No With Etches Commercial stock selected for egg production. acquired in 1991 Rock permission Guelph Commercial Leghorn Line Derived from commercial stock SCWL Good 30M/130F No With Etches Commercial stock selected for egg production. acquired in 1991 permission Ottawa 1 Derived from Ottawa 5 in 1950; SCWL No live 0 Blastodisc cells With Etches Selected for high egg production and related traits. divided into Ottawa 1 and 3 in 1971 birds permission

Ottawa 2 Derived from seven Canadian ROP SCWL No live 0 Blastodisc cells With Etches Selected for high egg production and related traits. (egg-type) stocks in 1951; divided in birds permission 1969 into Ottawa 2 and 4 Ottawa 3 Established from Ottawa 5 in 1950; SCWL No live 0 Blastodisc cells With Etches Selected for high egg production and related traits. divided into Ottawa 1 and 3 in 1971 birds permission Ottawa 4 Derived from seven Canadian ROP SCWL No live 0 Blastodisc cells With Etches Selected for high egg production and related traits. (egg-type) stocks in 1951; divided in birds permission 1969 into Ottawa 2 and 4 Ottawa 8 Derived from Ottawa 7 in 1969 SCWL No live 0 Blastodisc cells With Etches Selected for high egg production and related traits. birds permission Ottawa 9 Derived from Ottawa 7 in 1969 SCWL No live 0 Blastodisc cells With Etches Selected for high egg production and related traits. birds permission UCD 058 SCWL Poor 5M/6F No Yes Abplanalp Inbreeding coefficient (F)>=0.8; selected for increased egg production. UCD 082 SCWL Poor 5M/6F No Yes Abplanalp Inbreeding coefficient (F)>0.76; selected for egg production with relaxed selection in recent generations.

Chicken genetic stocks Appendix 2 Table 2.1 20 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Selected-Growth trait Auburn Tibial Dyschondroplasia-High Derived from a commercial meat sire Commercial Good 15M/70F No Yes Berry One of two strains that were developed from a line acquired in 1988 meat sire line commercial meat sire line by divergent selection for tibial dyschondroplasia; incidence is 95% for birds in this line after 11 generations of selection. Auburn Tibial Dyschondroplasia-Low Derived from a commercial meat sire Commercial Good 15M/70F No Yes Berry One of two strains that were developed from a line acquired in 1988 meat sire line commercial meat sire line by divergent selection for tibial dyschondroplasia; incidence is 6% for birds in this line after 11 generations of selection. Ottawa 21 Derived from Ottawa 20 Commercial No live 0 Blastodisc cells With Etches Selected for high body weight and low fat. meat sire cross birds permission Ottawa 23 Derived from Ottawa 20 Commercial No live 0 Blastodisc cells With Etches Selected for high body weight and feed efficiency. meat sire cross birds permission Ottawa 25 Derived from Ottawa 20 Commercial No live 0 Blastodisc cells With Etches Selected for high body weight, low fat, and feed meat sire cross birds permission efficiency. Ottawa 31 Derived from Ottawa 30 Commercial No live 0 Blastodisc cells With Etches Selected for high body weight, feed efficiency, and egg meat sire cross birds permission production. PSU-Athens RB 14-42H (HiK) Derived from Athens-Canadian Commercial Good: Exp. 20M/60F No With Barbato Selected for maximum growth between 14 and 42 days Randombred from U Georgia-Athens meat stock X Sta. & collaboration from a starting population of 350. egg selected USDA female lines PSU-Athens RB 14-42L (LoK) Derived from Athens-Canadian Commercial Good: Exp. 20M/60F No With Barbato Selected for minimum growth between 14 and 42 days Randombred from U Georgia-Athens meat stock X Sta. & collaboration from a starting population of 350. egg selected USDA female lines PSU-Athens RB 14H Derived from Athens-Canadian Commercial Good: Exp. 20M/60F Semen, Germ With Barbato Over nine generations selected for maximum growth Randombred from U Georgia-Athens meat stock X Sta. & cells collaboration between zero and 14 days from a starting population of egg selected USDA 350. female lines PSU-Athens RB 14L Derived from Athens-Canadian Commercial Good: Exp. 20M/60F Semen, Germ With Barbato Over nine generations selected for minimum growth Randombred from U Georgia-Athens meat stock X Sta. & cells collaboration between zero and 14 days from a starting population of egg selected USDA 350; very low fertility (25-30%). female lines PSU-Athens RB 42H Derived from Athens-Canadian Commercial Good: Exp. 20M/60F Semen, Germ With Barbato Over nine generations selected for maximum growth Randombred from U Georgia-Athens meat stock X Sta. & cells collaboration between zero and 42 days from a starting population of egg selected USDA 350. female lines PSU-Athens RB 42L Derived from Athens-Canadian Commercial Good 20M/60F Semen, Germ With Barbato Over nine generations selected for minimum growth Randombred from U Georgia-Athens meat stock X cells collaboration between zero and 42 days from a starting population of egg selected 350. female lines

Chicken genetic stocks Appendix 2 Table 2.1 21 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Selected-Growth trait (cont.) Virginia Body Weight-High Formed by crossing seven inbred White Plymouth Poor 100M/100F No With Siegel Selected 40 generations for high 8-week body weight. lines kept at Virginia State in 1957 Rock collaboration Virginia Body Weight-Low Formed by crossing seven inbred White Plymouth Poor 100M/100F No With Siegel Selected 35 generations for low 8-week body weight. lines kept at Virginia State in 1957 Rock collaboration

Selected-Immune trait Arkansas Progressor Derived from SCWL maintained at U SCWL Good 9M/45F No Yes Erf Selected 20 generations for tumor growth (progression) Arkansas since approximately 1945; following formation with exposure to Rous sarcoma thought to be highly inbred; also virus. known as Arkansas Rous Sarcoma Progression Arkansas Regressor Derived from F-1 and F-2 progeny of SCWL X Giant Good 9M/45F No Yes Erf Selected 20 generations for tumor regression following crosses of SCWL and Giant Jungle Jungle Fowl formation with exposure to Rous sarcoma virus. Fowl; also known as Arkansas Rous Sarcoma Regression Athens AR Derived from a cross of Athens SCWL Good 36M/36F No Yes Burke Selected for resistance to aflatoxin. AR2.5 and AR3.0 in 1997 Auburn R Kept as closed flock since 1948 SCWL see Good 180 No With Ewald Resistant to coccidiosis; MHC: B3; other erythrocyte description collaboration alloantigens: A/E2, C2, D3, H1, I2, K2, P3, “Q”2. Auburn S Kept as closed flock since 1952 SCWL see Good 200 No With Ewald Susceptible to coccidiosis; MHC: B5; other erythrocyte description collaboration alloantigens: A/E2, C3, D2, H1, I2, K3, P2, “Q”1. Cornell S13 Derived from Cornell S Strain; SCWL B13 Good 28M/106F No Yes, fee Schat MHC: B13; highy susceptible to Marek’s disease virus; specific pathogen-free free of most avian viruses. Ottawa 2R Derived from Ottawa-2 and-4; also SCWL No live 0 Blastodisc cells With Etches Selected for resistance to Marek’s disease virus. referred to as Ottawa R2 birds permission Ottawa 3R Derived from Ottawa-1 and-3; also SCWL No live 0 Blastodisc cells With Etches Selected for resistance to Marek’s disease virus. referred to as Ottawa R3 birds permission Ottawa 8R Derived from Ottawa 8 and-9; also SCWL No live 0 Blastodisc cells With Etches Selected for resistance to Marek’s disease virus. referred to as Ottawa R8 birds permission Virginia Antibody Line-High Derived from a Cornell randombred SCWL Poor 100M/100F No With Siegel Selected over 20 generations for high antibody response SCWL, starting in 1977 collaboration to sheep red blood cells. Virginia Antibody Line-Low Derived from a Cornell randombred SCWL Poor 100M/100F No With Siegel Selected over 20 generations for low antibody response SCWL, starting in 1977 collaboration to sheep red blood cells.

Selected-Physiological trait Arkansas Ascites Resistant Pedigreed commercial synthetic Commercial Good 16M/48F No No Anthony Selected three generations for resistance to ascites stocks meat sire cross under high altitude simulation; family selection. Chicken genetic stocks Appendix 2 Table 2.1 22 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Chicken (cont.) Selected-Physiological trait (cont.) Arkansas Ascites Susceptible Pedigreed commercial synthetic Commercial Good 16M/48F No No Anthony Selected three generations for susceptibility to ascites stocks meat sire cross under high altitude simulation; family selection.

Transgenic ADOL Trans-ALVE6 SCWL ALVE6 Good: N/A No Yes Bacon Homozygous for the alv-6 transgene; expresses env USDA glycoprotein of ALV subgroup A; resists infection with ALV subgroup A. Ottawa TR SCWL ALVE6 No live 0 Blastodisc cells With Etches Has incorporated the alv-6 transgene. birds permission

Uncategorized Ottawa 6 Not reported No live 0 Blastodisc cells With Etches Not reported. birds permission Ottawa 80 Not reported No live 0 Blastodisc cells With Etches Not reported. birds permission Ottawa 90 Not reported No live 0 Blastodisc cells With Etches Not reported. birds permission Ottawa N3 Not reported No live 0 Blastodisc cells With Etches Not reported. birds permission Ottawa N4 Not reported No live 0 Blastodisc cells With Etches Not reported. birds permission Ottawa N8 Not reported No live 0 Blastodisc cells With Etches Not reported. birds permission

Chicken genetic stocks Appendix 2 Table 2.1 23 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Japanese quail Inbred UBC I Inbred starting in 1992, with Poor 8M/16F No Yes Cheng Full-sibling inbreeding for four generations, starting in relaxation of inbreeding for the last 1992; relaxed inbreeding pressure in 1996 (crossing half few years sibs or less closely related birds).

Mutant-Color, eggshell UBC CE Acquired from U Nagoya (Japan) in Autosomal recessive. ce Combined see: UBC C-CE No Yes Cheng Females homozygous for celadon lay blue-shelled eggs. 1988; combined with UBC C in 1995 with UBC C in 1995 UBC WE Cross of U Nagoya (Japan) WE and Autosomal recessive. we Combined see: UBC W-WE No Yes Cheng Females homozygous for white-egg lay white-shelled U Saskatchewan stock; combined with UBC eggs. with UBC W in 1995 W in 1998

Mutant-Color, feather Arkansas White Mutation reported in Arkansas Autosomal recessive. Poor 36M/36F No Anthony Homozygotes have pure white feathers with dark eyes, randombred Japanese quail different from English White. Arkansas English White Acquired from the Quail Resource Autosomal recessive. wh Good 36M/36F No Anthony Homozygotes have dark eyes and mostly white feathers Center with spashes of wild-type color. UBC BH Acquired from U Nagoya (Japan) in Autosomal dominant. Bh Poor 6M/12F No Yes Cheng Black-at-hatch homozygotes die by the sixth day of 1988; frequently backcrossed to incubation; heterozygotes are viable, but have only faint UBC A remnants of the wild-type yellow stripes at hatch. UBC C-CE Cinnamon mutation reported in UBC Autosomal recessives. cin, ce Poor 24M/48F No Yes Cheng Cinnamon homozygotes have bright orange-brown M in 1978; celadon mutation feathers instead of medium brown, and eyes are red in acquired from U Nagoya (Japan) in the chick; females homozygous for celadon lay 1988; combined 1995 blue-shelled eggs. UBC D Acquired in 1979, then combined Two allelic sex-linked alD, al Poor 24M/48F No Yes Cheng Dark-eyed dilute homozygotes have dark eyes and with UBC AL (from U Saskatchewan) recessives. diluted feather color; homozygotes have unpigmented in 1984 retinas and nearly white feathers; albino hemi- and homozygotes are nearly white. UBC F-SB Fawn mutation from a breeder near Autosomal dominant Yf, sb Poor 24M/48F No Yes Cheng Fawn heterozygotes have fawn-colored feathers, but Yf Vancouver, BC in 1987; combined Yf is lethal in is lethal in the homozygotes; short-barb homozygotes with UBC SB homozygotes; sb is an have feather barbs approximately 75% shorter than autosomal recessive. normal. UBC H Back-crossed to UBC A each Autosomal incomplete E Poor 6M/12F No Yes Cheng Extended brown homozygotes and, to a lesser extent, generation dominant. heterozygotes, have extended distribution of black and dark brown pigment in the feathers, with both sexes appearing the same.

Japanese quail genetic stocks Appendix 2 Table 2.1 24 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Japanese quail (cont.) Mutant-Color, feather (cont.) UBC RH Acquired from Virginia Polytechnic Autosomal recessive. erh Combined see: UBC No Yes Cheng Redhead homozygotes have distinctly red head feathers Inst. in 1977; combined with UBC with UBC RF-RH (same as pansy); ruffled homozygotes have curved, bent RF in 1995 RF in 1995 or ruffled feathers. UBC SI Acquired from U Nagoya (Japan) in Autosomal incomplete B Poor 6M/12F No Yes Cheng Silver homozygotes have white feathers and a centrally 1988; back-crossed to UBC A every dominant. depigmented retina (ring-retina); heterozygotes have generation greyish feathers, and may have a few white primaries. UBC W-WE Mutation wh from flock near Autosomal recessives. wh, we Poor 24M/48F No Yes Cheng Recessive white homozygotes have white feathers and Vancouver, BC (1976); we from a dark eyes; heterozygotes have white in ventral feather cross of stocks from U Nagoya and tracts and face, with a mixture of dark and white feathers U Saskatchewan; combined 1995 on the back; those homozygous for we lay white eggs. UBC WB Mutation reported in UBC A in 1975; Autosomal recessive. wb Combined see: UBC No Yes Cheng White-breasted mutants have white feathers on face, combined with UBC PC in 1995 with UBC PC-WB ventral neck, breast, primaries and most secondaries. PC in 1995 UBC Y Mutation reported in UBC D in 1983; Autosomal dominant, Y Poor 6M/12F No Yes Cheng Yellow heterozygotes have yellow (golden) feathers with back-crossed to UBC A every lethal in homozygotes. restricted black pigment distribution; the mutation is generation lethal in homozygous form.

Mutant-Developmental defect-Skin/feather UBC DF-MDF Mutations reported in UBC W in 1979 Autosomal dominant Df, mdf Poor 24M/48F No Yes Cheng Two mutations acting in concert to produce defective (Df) and recessive feathers: short, sparse down at hatch, and defective (mdf) with variable barbs in later feathers; the Df dominant mutation is lethal expressivity. in homozygotes. UBC PC-WB Pc mutation reported in UBC W in Autosomal recessives. pc, wb Poor 24M/48F No Yes Cheng Porcupine mutants reproduce poorly and have feathers 1979; wb mutation reported in UBC A that resemble porcupine quills (the vanes do not uncoil); in 1975; combined 1995 white-breasted mutants have white feathers on face, ventral neck, and breast; wing flight feathers (primaries and most secondaries) are also white. UBC RF-RH Rf mutation reported in UBC B in Autosomal recessives. rf, erh Poor 24M/48F No Yes Cheng Ruffled homozygotes have curved, bent or ruffled 1983; redhead (erh) from Virginia feathers (rf mutation not yet reported in the literature). Poly. Inst. in 1977; combined 1995 UBC RT Mutation reported in UBC A in 1977; Autosomal recessive. rt Combined see: UBC M No Yes Cheng Rough-textured homozygotes have feathers that appear combined with UBC M in 1989 with UBC matted and rough, and the females produce fewer viable M in 1989 embryos. UBC SB Mutation reported in UBC A in 1982; Autosomal recessive. sb Combined see: UBC F-SB No Yes Cheng Short distal barb mutants show fusion in the distal barbs pooled with UBC F with UBC F of contour feathers during feather growth; barbs are about 1/4 normal length, most visible in the contour feathers of the back.

Japanese quail genetic stocks Appendix 2 Table 2.1 25 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Japanese quail (cont.) Mutant-Developmental defect-Skin/feather (cont.) UBC SP Mutation found in UBC AL in 1988; Autosomal recessive. sp Combined see: UBC B No Yes Cheng Spade homozygotes have defective feathers (sp combined with UBC B in 1996 with UBC B mutation not yet reported in the literature). in 1997

Mutant-Gene pool Wisconsin Japanese Quail Acquired from U Autosomal recessive. wh, we Good: 150M/350F No Yes Wentworth Homozygous wh birds have white feathers; homozygous Massachusetts-Amherst in 1969 NASA we females lay chalk-white eggs.

Mutant-Uncategorized UBC H5 Mutation reported in UBC WILD in Incomplete dominant. Poor 48M/96F No Yes Cheng Mutation causes H5 histones to form dimers in vitro. 1992; crossed with UBC A in 1997

Randombred Arkansas RBC Acquired from Eastern Shore as a Good 36M/36F No Anthony Randombred control strain from Eastern Shore randombred control in 1990 Randombred. Athens Control Quail Kept as closed flock since 1963 Good 120M/120F No Yes Burke Randombred control, with white egg shell mutation in the gene pool, propagated by random pair-matings. Louisiana Randombred Quail Kept at Louisiana State as closed flock Good 60M/120F No Yes Satterlee Unselected, randombred population with some color for over 20 years mutations (tuxedo, redhead, white egg). Ohio R1 Derived from a cross of Athens Poor 36M/36F No Yes Nestor Propagated using 36 pairs each generation. Randombred, Athens white egg, and Wisconsin stock; kept as closed flock for 38 generations UBC A Derived from a cross of UCD Poor 48M/96F No Yes Cheng Randombred flock. Randombred quail and quail stock from Korea; kept as closed flock for over 70 generations UBC B Acquired from U Alberta in 1977, sp Poor 24M/48F No Yes Cheng Exceptionally nervous randombred; spade homozygotes combined with UBC SP (spade have defective feathers. mutation, affecting feathers) by 1998 UBC M UBC M from a commercial (Marsh Autosomal recessive. rt Poor 24M/48F No Yes Cheng Rough-textured homozygotes have feathers that appear Farms) strain in 1975; combined matted and rough, and the females produce fewer viable with UBC RT in 1989 embryos (rt mutation not yet reported in the literature); UBC M have the extended brown allele, and are slightly heavier than UBC A. UBC N Acquired from U Nagoya (Japan) in Poor 24M/48F No Yes Cheng Very docile randombred. 1988

Japanese quail genetic stocks Appendix 2 Table 2.1 26 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Japanese quail (cont.) Randombred (cont.) UBC NC Acquired from NCSU-randombred Poor 24M/48F No Yes Cheng Randombred that has proven to be very sensitive to quail in 1990 changes in photoperiod. UBC S Acquired from U Saskatchewan in Poor 24M/48F No Yes Cheng 1983 UBC WILD Foundation stock consisted of 12 Poor 48M/96F No Yes Cheng feral birds caught in Hawaii in 1985 UCD Randombred Quail Derived from stock imported from Good 200+ No Yes Wilson Wild-type feather color pattern, unselected, randomly Japan and Taiwan (1950s and 1972) grouped in colony cages (2M/4F); reproduced every six to eight months. UMaryland Randombred Quail Acquired from U Wisconsin/USDA in Good 100 No With Ottinger the 1970s; kept as closed flock for collaboration approximately 20 years UNL Wild-type Coturnix Acquired from U Georgia-Athens Fair: Hatch, 30-60 pairs No With Beck regional, collaboration misc.

Selected-Behavioral trait Purdue Coturnix KGB Derived from Athens Control quail (U Good: 10,000 birds No With Muir Selected for non-aggressive behavior starting in 1988. Georgia-Athens) Industry collaboration

Selected-Growth trait Arkansas H10 Derived from Arkansas RBC Good 36M/36F No Anthony Selected 18 generations for high 10-day body weight. Arkansas H17 Derived from Arkansas RBC Good 36M/36F No Anthony Selected 18 generations for high 17-day body weight. Arkansas H28 Derived from Arkansas RBC Good 36M/36F No Anthony Selected 18 generations for high 28-day body weight. Arkansas H40 Derived from Arkansas RBC Good 36M/36F No Anthony Selected 18 generations for high 40-day body weight. Arkansas HL Good 36M/36F No Anthony Selected for high early body weight gain (10-17 days), low later body weight gain (17-28 days). Arkansas LH Good 36M/36F No Anthony Selected for low early body weight gain (10-17 days), high later body weight gain (17-28 days). Athens 52 Derived from a cross of Athens 51 Good 36M/36F No Yes Burke High body weight selected. and 53 (both selected 38 generations for high 4-week body weight) Athens 54 Derived from a cross of two stocks, Good 36M/36F No Yes Burke Low body weight selected. both selected 38 generations for low 4-week body weight Japanese quail genetic stocks Appendix 2 Table 2.1 27 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Japanese quail (cont.) Selected-Growth trait Athens 56 Derived from a cross of Athens P-, Good 36M/36F No Yes Burke Intermediate body weight stock resulting from a cross of T-, and S-lines long-term selected high and low body weight stocks. Athens P-line Derived from Athens Control quail Good 60M/60F No Yes Burke Selected 100 generations for high 4-week body weight on a 28% protein diet; at 70 generations, the adult size was over 150% above the control-standard population. Athens T-line Derived from Athens Control quail Good 60M/60F No Yes Burke Selected 100 generations for high 4-week body weight while under a low protein and thiouracil stress diet; resists growth depression on diets with up to 0.2% thiouracil. Ohio HW Derived from Ohio R1 Poor 48M/48F No Yes Nestor Inbreeding coefficient (F)=0.417; selected 30 generations for increased 4-week body weight. Ohio HW-HP Derived from Ohio HW Poor 36M/36F No Yes Nestor Inbreeding coefficient (F)=0.375; selected for male increased 4-week body weight, for female increased plasma phosphorus (indicator of yolk precursors). Ohio HW-LP Derived from Ohio HW Poor 36M/36F No Yes Nestor Inbreeding coefficient (F)=0.359; selected for male increased 4-week body weight, for female decreased plasma phosphorus two weeks after start of lay. Ohio LW Derived from Ohio R1 Poor 48M/48F No Yes Nestor Inbreeding coefficient (F)=0.357; selected 30 generations for decreased 4-week body weight. UBC G-QM UBC G derived from a commercial Poor 24M/48F No Yes Cheng Selected for average female body weight of 280 g at 6 strain (Marsh Farms); combined with weeks. UBC QM in 1992 UBC QF Acquired from Deschambault in 1990 Poor 48M/96F No Yes Cheng Selected for average female body weight of 280 g at 6 weeks. UBC QM Acquired from Deschambault in Combined see: UBC G-QM No No Cheng Selected for average male body weight of 280 g at 6 1990; combined with UBC G in 1992 with UBC weeks. G in 1992

Selected-Immune trait Athens AR3.0 Good 36M/36F No Yes Burke Selected for resistance to aflatoxin.

Selected-Physiological trait Athens H-PCHOL Derived from Athens Control quail Good 30M/30F No Yes Burke Selected for high blood plasma cholesterol for 37 generations; currently relaxed selection. Japanese quail genetic stocks Appendix 2 Table 2.1 28 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Japanese quail (cont.) Selected-Physiological trait (cont.) Athens L-PCHOL Derived from Athens Control quail Good 30M/30F No Yes Burke Selected for low blood plasma cholesterol for 37 generations; currently relaxed selection. Louisiana High Stress Response Derived from Louisiana Randombred Good 60M/120F No Yes Satterlee Selected over ten years for high blood corticosteroid Quail levels in response to stress. Louisiana Low Stress Response Derived from Louisiana Randombred Good 60M/120F No Yes Satterlee Selected over ten years for low blood corticosteroid Quail levels in response to stress. Ohio HP Derived from Ohio R1 Poor 36M/36F No Yes Nestor Inbreeding coefficient (F)=0.36; selected 30 generations for increased plasma phosphorus in the female two weeks after start of lay. Ohio LP Derived from Ohio R1 Poor 36M/36F No Yes Nestor Inbreeding coefficient (F)=0.394; selected 30 generations for decreasing levels of plasma phosphorus in the female two weeks after start of lay. UBC RES Acquired from NCSU in 1988 Poor 24M/48F No Yes Cheng Selected for resistance to atherosclerosis when fed high cholesterol diets. UBC SUS Acquired from NCSU in 1988 Poor 48M/96F No Yes Cheng Selected for susceptibility to atherosclerosis when fed high cholesterol diets.

Japanese quail genetic stocks Appendix 2 Table 2.1 29 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Turkey Mutant-Developmental defect-Eye UMass Glaucoma Naturally mating, exhibition-type Slate ga Dispersal 10M/25F No Yes Smyth Glaucoma homozygotes tend to develop glaucoma and turkey; in the process of transfer to in 1998 become blind. private curator.

Mutant-Reproductive defect Guelph Parthenogenetic Turkey Originally developed at USDA Beltsville Small multifactorial Poor 10M/30F No Yes Etches Selected for spontaneous development of 40% laboratories in Beltsville, MD, by White unfertilized eggs (parthenogenetic development), with Olsen in the 1970s 0.5% of developing embryos (all male) hatching.

Pure breed NCSU Black Spanish Acquired from Ohio State U in 1980; Black Spanish Fair 5M/10F No Yes Christensen kept as closed flock used in research and teaching NCSU Bronze Acquired from Ohio State U in 1980; Bronze Fair 5M/15F No Yes Christensen kept as closed flock used in research and teaching NCSU Slate Acquired from Ohio State U in 1980; Slate Fair 5M/15F No Yes Christensen kept as closed flock used in research and teaching Saskatchewan Bronze Turkey Acquired from Ridley (a breeder in Bronze Good 30M/80F No With Classen Resembles commercial turkeys from the 1940s (carcass Saskatoon area) in the 1980s; collaboration and production characteristics) and is able to breed resembles old commercial stocks naturally; used in cardiac, digestive, and reproductive physiology teaching and research. Wisconsin Midget White Developed by J. Smyth (U Midget White Good 120 No Yes Wentworth Midget white turkey, males=12 lb, females=8lb. Massacusetts); acquired in 1972 and kept as closed flock

Randombred NADC Turkey Originally from USDA Beltsville Beltsville Small Good 70-90 No Yes Rimler National Animal disease Center research stock. turkey stocks; kept as closed flock White for over 30 years; recently sent to Southeast Poultry Res. Lab. NCSU Ohio-RBC1 Acquired from Ohio State U in 1980; Large White Good 10M/60F No Yes Christensen kept as closed flock NCSU Ohio-RBC2 Acquired from Ohio State U in 1980; Large White Good 10M/60F No Yes Christensen kept as closed flock Ohio RBC1 Derived from a cross of four Large White Poor 36M/36F No Yes Nestor Inbreeding coefficient (F) approximately 0.148. commercial turkey strains in 1957 Ohio RBC2 Derived from a cross of two Large White Poor 36M/36F No Yes Nestor Inbreeding coefficient (F) approximately 0.12. commercial turkey strains in 1966

Turkey genetic stocks Appendix 2 Table 2.1 30 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Turkey (cont.) Randombred (cont.) Ohio RBC3 Derived from a cross of Ohio F Line Large White Poor 36M/36F No Yes Nestor Inbreeding coefficient (F) approximately 0.033. with commercial turkey strains in 1986 Wisconsin Broad-breasted Bronze Derived from Trylor Bronze of Broad-breasted Good 30M/200F Semen, PGC Yes Wentworth Old commercial-type turkey. Jerome Organization in N. Wisc.; Bronze kept as closed flock since 1969 Wisconsin Broad-breasted White Derived from Nicholas X Ralston Broad-breasted Good 30M/200F Semen, PGC Yes Wentworth Old commercial-type turkey. synthetic meat cross developed at White Washington State U; kept as closed flock since 1969

Selected-Egg trait NCSU Ohio-E Derived from Ohio-E; kept as Large White Good 10M/60F No Yes Christensen Selected for increased egg production. closed flock Ohio E Line Derived from Ohio RBC1 Large White Poor 72M/72F No Yes Nestor Inbreeding coefficient (F)=0.478; selected 38 generations for increased egg production.

Selected-Growth trait NCSU Ohio-F Derived from Ohio-F; kept as Large White Good 10M/60F No Yes Christensen Selected for increased body weight at 16 weeks. closed flock Ohio F Line Derived from Ohio RBC2 Large White Poor 36M/72F No Yes Nestor Inbreeding coefficient (F)=0.26; selected 30 generations for increased 16-week body weight. Ohio FL Line Derived from Ohio F line Large White Poor 36M/54F No Yes Nestor Inbreeding coefficient (F)=0.274; selected 17 generations for increased shank width.

Turkey genetic stocks Appendix 2 Table 2.1 31 Table 2.1 Stock information Category Genetic Allele Number Cryo- Stock name and description Origin and history Breed characteristics symbol Status of birds preserv. Available Curator Waterfowl/Gamebird Bloodtype-Gene pool NIU Bobwhites Acquired from Mississippi Northern see Fair 50+ No With Briles Various erythrocyte alloantigens in quail. State U in 1992 Bobwhite description collaboration NIU Pheasants Acquired from state gamebird Ring-necked see Fair 50+ No With Briles Population segregating for a variety of MHC B hatcheries in Wisconsin and Pheasant description collaboration haplotypes. Illinois in 1986

Pure breed ADOL Pekin Duck Kept as closed flock since Pekin Duck Good: 8M/35F No Yes Bacon Specific pathogen free, probably moderately inbred, the 1960s USDA reproduced 2X/year. Cornell White Pekin Specific pathogen-free Pekin Duck Good 9M/39F No Yes, fee Schat Commercial duck stock. NCSU Brown China Kept as closed flock; used in Brown Chinese Fair 10M/15F No Yes Christensen research and teaching Goose NCSU Pilgrim Kept as closed flock; used in Pilgrim Goose Fair 10M/15F No Yes Christensen research and teaching Saskatchewan Pilgrim Goose Acquired from Agriculture-Canada Pilgrim Goose Good 9M/18F No With Classen Goose breed with sexually dimorphic colors; used in (CFAR) in 1965 collaboration teaching bird handling in agriculture and veterinary medicine classes. Saskatchewan Rouen Duck Acquired from Miller Hatcheries in Rouen Duck Good 12M/24F No With Classen Used in teaching bird handling in agriculture and Saskatoon in 1965 collaboration veterinary medicine classes.

Waterfowl/Gamebird genetic stocks Appendix 2 Table 2.1 32 Table 2.2. Stocks listed by country, state or province, institution, and curator. Country—State/Province Institution Country—State/Province Institution Species/Category/Stock name Species/Category/Stock name CANADA—BC University of British Columbia CANADA—ON University of Guelph Curator: Kimberly Cheng Curator: Robert J. Etches Chicken Chicken Mutant-Developmental defect-Eye Chromosomal variant UBC RC Ottawa B-19/B-19 M13 Cryo. only Mutant-Gene pool Ottawa B-21/B-21 M13 Cryo. only UBC-Minnesota Marker Inbred Pure breed Ottawa GF Cryo. only UBC-Minnesota Rhode Island Red Ottawa GH Cryo. only Japanese quail Ottawa M2 Cryo. only Inbred Ottawa WG Cryo. only UBC I Ottawa XP Cryo. only Mutant-Color, eggshell Pure breed UBC CE Guelph Silkie UBC WE Ottawa New Hampshire Cryo. only Mutant-Color, feather Randombred UBC BH Ottawa 10 Cryo. only UBC C-CE Ottawa 20 Cryo. only UBC D Ottawa 30 Cryo. only UBC F-SB Ottawa 5 Cryo. only UBC H Ottawa 7 Cryo. only UBC RH Selected-Egg trait UBC SI Guelph Barred Plymouth Rock UBC W-WE Guelph Commercial Leghorn Line UBC WB Ottawa 1 Cryo. only UBC Y Ottawa 2 Cryo. only Mutant-Developmental defect-Skin/feather Ottawa 3 Cryo. only UBC DF-MDF Ottawa 4 Cryo. only UBC PC-WB Ottawa 8 Cryo. only UBC RF-RH Ottawa 9 Cryo. only UBC RT Selected-Growth trait UBC SB Ottawa 21 Cryo. only UBC SP Ottawa 23 Cryo. only Mutant-Uncategorized Ottawa 25 Cryo. only UBC H5 Ottawa 31 Cryo. only Randombred Selected-Immune trait UBC A Ottawa 2R Cryo. only UBC B Ottawa 3R Cryo. only UBC M Ottawa 8R Cryo. only UBC N Transgenic UBC NC Ottawa TR Cryo. only UBC S Uncategorized UBC WILD Ottawa 6 Cryo. only Selected-Growth trait Ottawa 80 Cryo. only UBC G-QM Ottawa 90 Cryo. only UBC QF Ottawa N3 Cryo. only UBC QM Ottawa N4 Cryo. only Selected-Physiological trait Ottawa N8 Cryo. only UBC RES Turkey UBC SUS Mutant-Reproductive defect Guelph Parthenogenetic Turkey

Appendix 2 Table 2.2 1 Table 2.2. Stocks listed by country, state or province, institution, and curator. Country—State/Province Institution Country—State/Province Institution Species/Category/Stock name Species/Category/Stock name CANADA—SK University of Saskatchewan USA—AR University of Arkansas–Fayetteville Curator: Henry L. Classen Curator: N.B. Anthony Chicken Selected-Growth trait Mutant-Neurological defect Arkansas H10 Saskatchewan Epileptiform seizures Arkansas H17 Pure breed Arkansas H28 Saskatchewan Barred Plymouth Rock Arkansas H40 Saskatchewan Brown Leghorn Arkansas HL Turkey Arkansas LH Pure breed USA—AR University of Arkansas–Fayetteville Saskatchewan Bronze Turkey Curator: Gisela Erf Waterfowl/Gamebird Chicken Pure breed Mutant-Immunological defect Saskatchewan Pilgrim Goose Arkansas Smyth Line B101 Saskatchewan Rouen Duck Arkansas Smyth Line B102 USA—AL Auburn University Randombred Curator: Wallace Berry Other contact: Gayner R. McDaniel Arkansas Brown Line B101 Chicken Arkansas Brown Line B102 Selected-Growth trait Arkansas Light Brown Leghorn B101 Auburn Tibial Dyschondroplasia-High Selected-Immune trait Auburn Tibial Dyschondroplasia-Low Arkansas Progressor USA—AL Auburn University Arkansas Regressor Curator: Sandra Ewald USA—AR University of Arkansas–Fayetteville Chicken Curator: John Kirby Bloodtype-Gene pool Chicken Auburn DAX Mutant-Reproductive defect Bloodtype-MHC Arkansas Sd Line Auburn M USA—CA University of California–Davis Auburn N Curator: Ursula K. Abbott Other contact: J.M. Pisenti Auburn RM Chicken Auburn RMH Mutant-Developmental defect-Face/limb Auburn RN UCD Cleft Primary Palate/Scaleless Selected-Immune trait UCD Coloboma X 003 Auburn R UCD Diplopodia-1 X 003 Auburn S UCD Diplopodia-3 X 003 USA—AR University of Arkansas–Fayetteville UCD Donald-duck Beak/Scaleless Curator: N.B. Anthony UCD Eudiplopodia X 003 Chicken UCD Limbless X 003 Pure breed UCD Polydactyly X 003 Arkansas Giant Jungle Fowl UCD Stumpy X 003 Randombred UCD Talpid-2 X 003 Arkansas Randombred UCD Wing-reduced X 003 Selected-Physiological trait UCD Wingless-2 X 331 Arkansas Ascites Resistant Mutant-Developmental defect-Skin/feather Arkansas Ascites Susceptible UCD Ichthyosis X 003 Japanese quail UCD Naked-neck Cryo. only Mutant-Color, feather UCD Scaleless-High Arkansas English White UCD Scaleless-Low Arkansas White Mutant-Developmental defect-Spine/tail Randombred UCD Scoliosis Cryo. only Arkansas RBC

Appendix 2 Table 2.2 2 Table 2.2. Stocks listed by country, state or province, institution, and curator. Country—State/Province Institution Country—State/Province Institution Species/Category/Stock name Species/Category/Stock name USA—CA University of California–Davis USA—CA University of California–Davis Curator: Ursula K. Abbott Other contact: J.M. Pisenti Curator: Barry Wilson Mutant-Gene pool Chicken UCD Diplopodia-3/Scaleless High Mutant-Physiological defect UCD Eudiplopodia/Limbless UCD 413 UCD Limbless/Stumpy Randombred UCD Silkie cross UCD 412 UCD Talpid-2/Wingless-2 Japanese quail Mutant-Physiological defect Randombred UCD Crooked-neck Dwarf UCD Randombred Quail UCD Riboflavin Transfer Deficient USA—CT University of Connecticut Mutant-Uncategorized Curator: Louis J. Pierro UCD Crest/Hemoglobin-D Cryo. only Chicken UCD Multiplex Comb Cryo. only Mutant-Developmental defect-Face/limb Pure breed Storrs Chondrodystrophy UCD Silkie Storrs Creeper USA—CA University of California–Davis Storrs Diplopodia-3 Curator: Hans Abplanalp Storrs Diplopodia-5 Chicken Storrs Limbless Bloodtype-MHC-Inbred Storrs Micromelia-Abbott UCD 003 Storrs Micromelia-Hays UCD 253 Storrs Nanomelia UCD 254 Storrs Perocephaly UCD 312 Storrs Polydactyly UCD 313 Cryo. only Storrs Talpid-2 UCD 330 Storrs Wingless-2 UCD 331 Mutant-Developmental defect-Skin/feather UCD 335 Storrs Ottawa Naked UCD 336 Storrs Ptilopody UCD 342 Storrs Scaleless UCD 361 Mutant-Developmental defect-Spine/tail UCD 380 Storrs Dominant Rumplessness UCD 386 Storrs Recessive Rumpless UCD 387 Mutant-Physiological defect Mutant-Immunological defect Storrs Crooked-neck Dwarf UCD 200 Storrs Muscular Dystrophy Mutant-Physiological defect Mutant-Uncategorized UCD 077 Storrs Rose Comb Selected-Egg trait USA—DE University of Delaware UCD 058 Curator: Harold B. White III UCD 082 Chicken USA—CA University of California–Davis Mutant-Physiological defect Curator: Mary E. Delany UDel Riboflavin Transfer Deficient Chicken USA—GA University of Georgia Chromosomal variant Curator: William H. Burke UCD-Cornell Mono-PNU Chicken UCD-Cornell Trisomic Mutant-Physiological defect Inbred Athens-Canadian Dwarfs UCD 001 Randombred Mutant-Physiological defect Athens Randombred UCD-Cornell Autosomal Dwarf Athens-Canadian Randombred

Appendix 2 Table 2.2 3 Table 2.2. Stocks listed by country, state or province, institution, and curator. Country—State/Province Institution Country—State/Province Institution Species/Category/Stock name Species/Category/Stock name USA—GA University of Georgia USA—IL Northern Illinois University Curator: William H. Burke Curator: W. Elwood Briles Selected-Immune trait Chicken Athens AR Bloodtype-Gene pool Japanese quail NIU B haplotypes Randombred NIU B-haplotype Recombinants Athens Control Quail NIU Male Breeder Alloantigen Reservoir Selected-Growth trait NIU Segregating Male Breeder Line Athens 52 Bloodtype-MHC Athens 54 NIU Female Breeder Parent Stock B19 Athens 56 NIU Female Breeder Parent Stock B2 Athens P-line NIU Female Breeder Parent Stock B5 Athens T-line Waterfowl/Gamebird Selected-Immune trait Bloodtype-Gene pool Athens AR3.0 NIU Bobwhites Selected-Physiological trait NIU Pheasants Athens H-PCHOL USA—IL University of Illinois–Urbana Athens L-PCHOL Curator: Carl Parsons Other contact: Bob Leeper USA—IA Iowa State University Chicken Curator: Susan J. Lamont Pure breed Chicken UI-Urbana Columbian Bloodtype-MHC-Inbred UI-Urbana New Hampshire ISU 19-13 USA—IN Purdue University ISU 19-15.1 Curator: W.M. Muir ISU 8-15.1 Chicken ISU G-B1 Selected-Behavioral trait ISU G-B2 Purdue KGB ISU GH-1 Purdue MBB ISU GH-13 Japanese quail ISU GH-15.1 Selected-Behavioral trait ISU HN-12 Purdue Coturnix KGB ISU HN-15 ISU M15.2 USA—LA Louisiana State University–Baton Rouge ISU M5.1 Curator: Daniel G. Satterlee ISU Sp21.2 Japanese quail Mutant-Uncategorized Randombred ISU S1-19H Louisiana Randombred Quail ISU S1-19L Selected-Physiological trait ISU S1-1H Louisiana High Stress Response ISU S1-1L Louisiana Low Stress Response USA—IA National Animal Disease Center USA—MA University of Massachusetts–Amherst Curator: Richard Rimler Curator: J. Robert Smyth Jr Turkey Chicken Randombred Mutant-Developmental defect-Eye NADC Turkey UMass Pink Eye Mutant-Immunological defect UMass Smyth Line Pure breed UMass Light Brown Leghorn Randombred UMass Brown Line

Appendix 2 Table 2.2 4 Table 2.2. Stocks listed by country, state or province, institution, and curator. Country—State/Province Institution Country—State/Province Institution Species/Category/Stock name Species/Category/Stock name USA—MA University of Massachusetts–Amherst USA—MI USDA-ARS-Avian Disease and Oncology Laboratory Curator: J. Robert Smyth Jr Curator: Larry D. Bacon Other contact: Laura Parks Turkey Inbred Mutant-Developmental defect-Eye ADOL 6C.7A ReCon UMass Glaucoma ADOL 6C.7B ReCon USA—MD University of Maryland–College Park ADOL 6C.7C ReCon Curator: Mary Ann Ottinger ADOL 6C.7D ReCon ADOL 6C.7F ReCon Japanese quail ADOL 6C.7G ReCon Randombred ADOL 6C.7I ReCon UMaryland Randombred Quail ADOL 6C.7J ReCon USA—MI USDA-ARS-Avian Disease and Oncology Laboratory ADOL 6C.7K ReCon Curator: Larry D. Bacon Other contact: Laura Parks ADOL 6C.7L ReCon Chicken ADOL 6C.7M ReCon Bloodtype-MHC ADOL 6C.7N ReCon RPRL-Cornell JM-N ADOL 6C.7P ReCon RPRL-Cornell JM-P ADOL 6C.7R ReCon Bloodtype-MHC-Inbred ADOL 6C.7S ReCon RPRL 15.15-5 ADOL 6C.7T ReCon RPRL 15.6-2 ADOL 6C.7V ReCon RPRL 15.7-2 ADOL 6C.7W ReCon RPRL 15.C-12 ADOL 6C.7X ReCon RPRL 15.N-21 Transgenic RPRL 15.P-13 ADOL Trans-ALVE6 RPRL 15.P-19 Waterfowl/Gamebird RPRL 15I5 Pure breed RPRL 7I1 ADOL Pekin Duck RPRL Line 0 USA—NC North Carolina State University–Raleigh Endogenous virus RPRL 15B1 Curator: Vern L. Christensen Endogenous virus-Inbred Chicken RPRL 100B Pure breed NCSU Barred Plymouth Rock RPRL 6I3 NCSU Rhode Island Red RPRL 7I2 RPRL Reaseheath Line C Turkey Pure breed NCSU Black Spanish NCSU Bronze NCSU Slate Randombred NCSU Ohio-RBC1 NCSU Ohio-RBC2 Selected-Egg trait NCSU Ohio-E Selected-Growth trait NCSU Ohio-F Waterfowl/Gamebird Pure breed NCSU Brown China NCSU Pilgrim

Appendix 2 Table 2.2 5 Table 2.2. Stocks listed by country, state or province, institution, and curator. Country—State/Province Institution Country—State/Province Institution Species/Category/Stock name Species/Category/Stock name USA—NC North Carolina State University–Raleigh USA—NY Cornell University Curator: Muquarrab Qureshi Curator: K.A. Schat Chicken Chicken Bloodtype-MHC-Inbred Bloodtype-MHC NCSU GB-1 Cornell N2a NCSU GB-2 Cornell P2a Randombred Selected-Immune trait NCSU-Cornell K Strain Cornell S13 USA—NE University of Nebraska–Lincoln Waterfowl/Gamebird Curator: Mary Beck Pure breed Cornell White Pekin Chicken Mutant-Neurological defect USA—OH Ohio State University–OARDC UNL Paroxysm Curator: Karl E. Nestor Japanese quail Japanese quail Randombred Randombred UNL Wild-type Coturnix Ohio R1 USA—NH University of New Hampshire Selected-Growth trait Curator: Robert Taylor Jr Ohio HW Ohio HW-HP Chicken Ohio HW-LP Bloodtype-Gene pool Ohio LW UNH 105 Selected-Physiological trait Bloodtype-MHC Ohio HP UNH 192 Ohio LP Bloodtype-MHC-Inbred UNH 6.15-5 Turkey UNH 6.6-2 Randombred Ohio RBC1 UNH-UCD 003 Ohio RBC2 UNH-UCD 003.R1 Ohio RBC3 UNH-UCD 003.R2 UNH-UCD 003.R3 Selected-Egg trait Ohio E Line UNH-UCD 003.R4 UNH-UCD 003.R5 Selected-Growth trait Ohio F Line UNH-UCD 003.R6 Ohio FL Line UNH-UCD 386 UNH-UCD 387 USA—OH Ohio State University–OARDC UNH-UCD 3C.1 Curator: Sandra G. Velleman USA—NY Cornell University Chicken Curator: Rodney R. Dietert Mutant-Physiological defect Ohio Low-score Normal Chicken Ohio Muscular Dystrophy Selected-Egg trait Cornell K Strain USA—OR Oregon State University–Corvallis USA—NY Cornell University Curator: Thomas F. Savage Curator: James Marsh Chicken Mutant-Gene pool Chicken OSU Dwarf Leghorn Mutant-Immunological defect Cornell Obese (B-13) Mutant-Physiological defect Cornell Sex-linked Dwarf Randombred Cornell C Specials (B13)

Appendix 2 Table 2.2 6 Table 2.2. Stocks listed by country, state or province, institution, and curator. Country—State/Province Institution Country—State/Province Institution Species/Category/Stock name Species/Category/Stock name USA—PA Pennsylvania State University USA—WI University of Wisconsin–Madison Curator: Guy F. Barbato Curator: Bernard C. Wentworth Chicken Japanese quail Selected-Growth trait Mutant-Gene pool PSU-Athens RB 14-42H (HiK) Wisconsin Japanese Quail PSU-Athens RB 14-42L (LoK) Turkey PSU-Athens RB 14H Pure breed PSU-Athens RB 14L Wisconsin Midget White PSU-Athens RB 42H Randombred PSU-Athens RB 42L Wisconsin Broad-breasted Bronze USA—VA Virginia Polytechnic Institute and State University Wisconsin Broad-breasted White Curator: Paul B. Siegel Other contact: E. Ann Dunnington Chicken Selected-Growth trait Virginia Body Weight-High Virginia Body Weight-Low Selected-Immune trait Virginia Antibody Line-High Virginia Antibody Line-Low USA—WI University of Wisconsin–Madison Curator: James J. Bitgood Other contact: John F. Fallon Chicken Chromosomal variant Wisconsin Chromosomal Rearrangements Inbred Wisconsin Ancona Wisconsin Leghorn line UW-Sp2 Mutant-Color, feather Wisconsin Autosomal Albino Mutant-Developmental defect-Eye Wisconsin Blind/Cataract Wisconsin Pink-eye Wisconsin Pop-eye Mutant-Developmental defect-Face/limb Wisconsin Ametapodia Wisconsin Limbless Wisconsin Talpid-2 Wisconsin Wingless-2 Mutant-Developmental defect-Skin/feather Wisconsin Tardy Feathering Mutant-Neurological defect Wisconsin Pirouette Mutant-Reproductive defect Wisconsin Double Oviduct Line Wisconsin Restricted Ovulator Mutant-Uncategorized Wisconsin Sex-linked Skin Color Randombred Wisconsin Leghorn Wisconsin Leghorn line UW-6X Wisconsin New Hampshire

Appendix 2 Table 2.2 7

Table 2.3. Curator contact information. Ursula K. Abbott James J. Bitgood Rodney R. Dietert Dept. of Animal Science Dept. of Animal Sciences Dept. of Microbiology/Immunology University of California 1675 Observatory Dr. Rice Hall One Shields Avenue University of Wisconsin Cornell University Davis CA 95616 USA Madison WI 53706 USA Ithaca NY 14853 USA Tel: (530) 752-7325 Tel: (608) 263-4300 Tel: (607) 253-4015 Alt tel: 752-1300 FAX: (608) 262-5157 FAX: (607) 253-3369 FAX: (530) 752-8960 [email protected] [email protected] [email protected] W. Elwood Briles E. Ann Dunnington Hans Abplanalp Dept. of Biological Sciences Dept. of Animal/Poultry Sciences Dept. of Animal Science Northern Illinois University Virginia Polytechnic Institute and State University of California Dekalb IL 60115-2861 USA University One Shields Avenue Tel: (815) 753-0433 Blacksburg VA 24061-0306 USA Davis CA 95616 USA FAX: (815) 753-0461 Tel: (540) 231-9179 Tel: (530) 752-1300 FAX: (540) 231-3713 William H. Burke FAX: (530) 752-8960 Dept. of Poultry Science Gisela Erf N.B. Anthony 120 Livestock-Poultry Bldg. Dept. of Poultry Science Dept. of Poultry Science University of Georgia Center for Poultry Science Center for Poultry Science Athens GA 30602-2772 USA University of Arkansas University of Arkansas Tel: (706) 542-1358 Fayetteville AR 72701 USA Fayetteville AR 72701 USA FAX: (706) 542-1827 Tel: (501) 575-8664 Tel: (501) 575-4833 [email protected] FAX: (501) 575-3026 FAX: (501) 575-3026 [email protected] Kimberly Cheng Larry D. Bacon Dept. of Animal Science Robert J. Etches Avian Disease and Oncology Laboratory University of British Columbia Origen Therapeutics 3606 East Mount Hope Road Vancouver BC V6T 1Z4 CANADA 651 Gateway Blvd., Ste. 980 East Lansing MI 48823 USA Tel: (604) 822-2480 South San Francisco, CA 94080 USA Tel: (517) 337-6828 FAX: (604) 822-4400 Tel: (650) 827-0200 FAX: (517) 337-6776 [email protected] FAX: (650) 827-0300 [email protected] [email protected] Vern L. Christensen Guy F. Barbato Dept. of Poultry Science Sandra Ewald Dept. of Poultry Science North Carolina State University Dept. of Poultry Science Pennsylvania State University Box 7608 236 Animal Sciences Bldg. University Park PA 16802 USA Raleigh NC 27695-7608 USA Auburn University Tel: (814) 865-4481 Tel: (919) 515-5385 Auburn University AL 36859 USA FAX: (814) 865-5691 Alt tel: 515-2626 Tel: (334) 844-2647 [email protected] FAX: (919) 515-2625 Alt tel: 844-2722 [email protected] FAX: (334) 844-2652 Mary Beck [email protected] Dept. of Animal Science Henry L. Classen University of Nebraska Dept. of Animal/Poultry Science John F. Fallon Lincoln NE 68583 USA University of Saskatchewan Dept. of Anatomy Tel: (402) 472-6439 Saskatoon SK S7N 5B5 CANADA 1300 University Ave. FAX: (402) 472-6362 Tel: (306) 966-6600 University of Wisconsin [email protected] Alt tel: 966-4128 Madison WI 53706-1532 USA FAX: (306) 966-4560 Tel: (608) 262-3775 Wallace Berry [email protected] FAX: (608) 262-2327 Dept. of Poultry Science Auburn University Mary E. Delany John Kirby Auburn University AL 36849 USA Dept. of Animal Science Dept. of Poultry Science Tel: (334) 844-2600 University of California Center for Poultry Science FAX: (334) 844-2641 One Shields Avenue University of Arkansas Davis CA 95616 USA Fayetteville AR 72701 USA Tel: (530) 754-9343 Tel: (501) 575-8623 Alt tel: 752-1300 FAX: (501) 575-3026 FAX: (530) 752-8960 [email protected] [email protected]

Appendix 2 Table 2.3 1 Table 2.3. Curator contact information. Susan J. Lamont Louis J. Pierro Paul B. Siegel Dept. of Animal Science Storrs Agr. Exp. Sta. Dept. of Animal/Poultry Sciences 201 Kildee Hall University of Connecticut Virginia Polytechnic Institute and State Iowa State University 1376 Storrs Rd. University Ames IA 50011-3150 USA Storrs CT 06269-4010 USA Blacksburg VA 24061-0306 USA Tel: (515) 294-4100 Tel: (860) 486-0334 Tel: (540) 231-6472 FAX: (515) 294-2401 FAX: (860) 486-4375 FAX: (540) 231-3713 [email protected] [email protected] [email protected] Bob Leeper Jacqueline M. Pisenti J. Robert Smyth Jr 284 Animal Science Laboratory Genetic Resources Conservation Program Veterinary/Animal Science University of Illinois University of California 307 Stockbridge Hall 1207 W. Gregory Dr. One Shields Avenue University of Massachusetts Urbana IL 61801 USA Davis CA 95616 USA Amherst MA 01002 USA FAX: (217) 333-7861 Tel: (530) 754-8508 Tel: (413) 545-2137 James Marsh FAX: (530) 754-8505 FAX: (413) 545-6326 [email protected] Dept. of Microbiology/Immunology C5-103 Robert Taylor Jr College of Veterinary Medicine Muquarrab Qureshi Dept. of Animal/Nutr. Science Ithaca NY 14853 USA Dept. of Poultry Science Kendall Hall Tel: (607) 253-4010 North Carolina State University University of New Hampshire FAX: (607) 253-3384 Box 7608 Durham NH 03824 USA [email protected] Raleigh NC 27695-7608 USA Tel: (603) 862-2130 W.M. Muir Tel: (919) 515-5388 FAX: (603) 862-3758 Dept. of Animal Science FAX: (919) 515-2625 [email protected] Purdue University [email protected] Sandra G. Velleman West Lafayette IN 479071151 USA Richard Rimler Dept. of Animal Science Tel: (765) 494-8032 National Animal Disease Center Ohio State University/OARDC FAX: (765) 494-9346 MWA/USDA 1680 Madison Ave. [email protected] P.O. Box 70 Wooster OH 44691-4096 USA Karl E. Nestor Ames IA 50010 USA Tel: (330) 263-3905 Dept. of Animal Sciences Tel: (515) 239-8534 FAX: (330) 263-3949 Ohio Agricultural Reasearch and Alt tel: 239-8255 [email protected] Development Ctr. FAX: (515) 239-8458 Ohio State University Bernard C. Wentworth Wooster OH 44691 USA Daniel G. Satterlee Dept. of Poultry Science Tel: (330) 263-3757 Dept. of Poultry Science 1675 Observatory Dr., Rm. 260 FAX: (330) 263-3949 Louisiana State University University of Wisconsin [email protected] 206 Clyde Ingram Hall Madison WI 53706-1284 USA Baton Rouge LA 70803 USA Tel: (608) 262-8945 Mary Ann Ottinger Tel: (504) 388-4406 FAX: (608) 262-6005 Dept. of Poultry Science FAX: (504) 388-1259 [email protected] University of Maryland [email protected] College Park MD 20742 USA Harold B. White III Tel: (301) 405-5780 Thomas F. Savage Dept. of Chemistry/Biochemistry FAX: (301) 314-9059 Dept. of Animal Science University of Delaware [email protected] Withycombe Hall 112 Newark DE 19716 USA Oregon State University Tel: (302) 831-2908 Laura Parks Corvallis OR 97331-6702 USA FAX: (302) 831-6335 Avian Disease and Oncology Laboratory Tel: (541) 737-5066 [email protected] 3606 East Mount Hope Road FAX: (541) 737-4174 East Lansing MI 48823 USA Barry Wilson [email protected] Tel: (517) 337-6828 Dept. of Animal Science FAX: (517) 337-6776 K.A. Schat University of California [email protected] Dept. of Microbiology/Immunology One Shields Avenue College of Veterinary Medicine Davis CA 95616 USA Carl Parsons Cornell University Dept. of Animal Sciences Tel: (530) 752-3519 Ithaca NY 14853-6401 USA 284 Animal Science Laboratory FAX: (530) 752-8960 Tel: (607) 253-3365 [email protected] 1207 W. Gregory Dr. FAX: (607) 253-3369 Urbana IL 61801 USA [email protected] Tel: (217) 333-8774 FAX: (217) 333-7861 Appendix 2 Table 2.3 2 Top right: Wild-type Japanese quail (UCD Randombred Quail) used in a wide range of experimental studies. Female (right) and male (left). Photograph courtesy of J. Clark, University of California– Davis) Center left: Fawn mutation in the Japanese quail (UBC F-SB). (Photograph courtesy of K. Cheng, University of British Columbia) Center right: Male giant Japanese quail (UBC G-QM). More than double the size of unselected quail, this line was developed by intensive selection for increased six-week body size in the females. (Photograph courtesy of K. Cheng, University of British Columbia) Right: Modern commercial Large White turkeys. (Photograph courtesy of R.A. Ernst, University of California–Davis.)