Protecting Food Animal Gene Pools for Future Generations a Paper in the Series on the Need for Agricultural Innovation to Sustainably Feed the World by 2050

Number 65 Issue Paper September 2019 Protecting Food Animal Gene Pools for Future Generations A paper in the series on The Need for Agricultural Innovation to Sustainably Feed the World by 2050

Using different preservation techniques, breeds such as the Mulefoot hog, Buckeye chicken, San Clementine goat, Gulf Coast sheep, and Narragansett turkey can be preserved to ensure genetic diversity in livestock and poultry around the world. (Photo collage by Megan Wickham. Photos courtesy of the USDA, Wikimedia Commons, and Curtis Youngs.)

ing. The number of breeds has declined urgent need to develop and maintain Abstract as farming practices have focused on a an intensive program of sampling and The world’s population is expected to small number of high-producing breeds evaluation of the existing gene pools. reach more than 9 billion by 2050, creat- to meet low-cost market demands. In Genetic diversity can be preserved ing a grand societal challenge: ramping fact, up to 25% of global livestock through living populations or cryopre- up agricultural productivity to feed the breeds are either at risk of being lost, or served for future use. Living populations globe. Livestock and poultry products have already been lost. In the face of the can adapt to changes in the natural or are keys to the world supply of protein, mounting depletion in genetic diversity production environment, provide value but genetic diversity of livestock is fad- among livestock species, there is an in research, and contribute to specialty

This material is based upon work supported by the U.S. Department of Agriculture’s (USDA) Agricultural Research Service (ARS) and Animal and Plant Health Inspection Service (APHIS) Agreement No. 59-0202-5-002. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of USDA–ARS, USDA–APHIS, any other USDA agency, or the USDA. CAST Issue Paper 65 Task Force Members

Authors Dr. Robert L. Taylor, Jr., Division of Dr. Terry Stewart, College of Agri- Animal and Nutritional Sciences, West culture, Purdue University, West Dr. Julie A. Long (Chair), Animal Virginia University, Morgantown, West Lafayette, Indiana Bio-sciences & Biotechnology Virginia Dr. Terrence R. Tiersch, Aquatic Laboratory, U.S. Department of Dr. Fred Silversides, Chilliwack, British Germplasm and Genetic Resources Agriculture–Agricultural Research Columbia, Canada Center, School of Renewable Service, Beltsville, Maryland Dr. Curtis R. Youngs, Department of Natural Resources, Louisiana State Dr. Harvey Blackburn, National Animal Science, Iowa State University, University Agricultural Center, Animal Germplasm Program, U.S. Ames, Iowa Baton Rouge, Louisiana Department of Agriculture–Agricul- tural Research Service, Ft. Collins, Colorado Reviewers CAST Liaison Dr. Robert Evans, Elanco Animal Dr. Alison Martin, The Livestock Dr. Janet E. Fulton, Hy-Line Interna- Conservancy, Pittsboro, North tional, West Des Moines, Iowa Health, Harrisonburg, Virginia Carolina

markets. Cryopreservation offers rare 2014), will be largely nourished. Ani- there is a global contraction in genetic and major breeds a benefit—whether to mals are an important source of human diversity” (USDA-NGRAC 2018). The reconstitute lost bloodlines or to serve as dietary protein, supplying one-third of the contraction is more evident when moving a safety net in case of catastrophic loss protein consumed in the world, as well beyond the handful of productive breeds, of a diminished population. This paper as micronutrients vital for infant brain where up to 20% of livestock and 79% of addresses several important challenges development. poultry breeds are classified as “at risk” regarding the effective protection of The United States has one of the most for extinction (FAO 2007). remaining livestock and poultry genetic vibrant livestock sectors in the world. Two examples of American breeds that diversity: (1) characterizing the animal Livestock breeders produce the genetic are considered rare, but that possess eco- populations to identify unique attributes resources necessary to address domes- nomically important traits, are the Gulf that will influence the collection and tic consumption and supply genetic Coast sheep and the Narragansett turkey. conservation of breeds; (2) improving resources to the world. For example, in The Gulf Coast sheep breed is resistant cryopreservation technology for a variety 2017 the United States exported approxi- to internal parasites, foot rot, and other of germplasm and cell types that targets mately $175 million of bull semen for use common sheep diseases; however, there biological differences impeding success in other countries compared to domes- are fewer than 200 pedigree registra- among species; (3) expanding the con- tic sales of approximately $22 million tions1 per year in the United States and an tent, accessibility and cross-talk among (https://www.naab-css.org/semen-sales). estimated global population of less than databases housing breed and genetic The productivity of the U.S. livestock 2,000 individuals. Parasitism is widely resource information; and (4) developing sector, however, is based upon ready recognized as the most important health private-public partnerships among rare access to and use of highly specialized issue of sheep and goats, and the costs of breed associations/curators, agricultural genetic resources, and there is cause for prevention, treatment, and lost produc- universities, federal agencies and non- concern at multiple levels. The highly tion worldwide are proposed to be tens of governmental organizations to ensure specialized livestock industries in North billions of dollars (Roeber et al. 2013); the long-term operational continuity of America are dominated by a small num- thus, genetic resistance to parasites is germplasm repositories. ber of productive breeds for which there an important prevention strategy. The is a concomitant downward trend in the Narragansett turkey, named for the bay effective number of breeding animals and in Rhode Island where it was developed Introduction a general contraction of genetic diversity, in the 1800s, not only is one of the oldest Seven domesticated species (cattle, particularly in the commercial dairy and turkey breeds but also possesses genes sheep, goats, pigs, chickens, turkeys, and poultry breeds. This problem has been ducks) account for most of the world’s noted in the recent National Genetics Re- 1 Registration identifies an animal as the product livestock and poultry food production sources Advisory Council’s Animal Ge- of a known sire and dam, born on a known date. (FAO 2019). It is from this handful of netic Resources summary, where it was Among livestock, primarily breeding animals have stated that “all livestock and poultry spe- their pedigrees registered with associations that track domesticated species that the world’s each breed; thus, annual registrations are a strong population, expected to reach 9.6 billion cies and breeds share a common genetic indicator of breeding population size and are used in less than 35 years (Searchinger et al. resource problem to varying degrees: by conservation organizations in most countries.

2 COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY for important economic traits—such as was the first animal to be sequenced for be administered by the ARS. The NAGP early maturation, egg production, meat the construction of the bovine genome repository currently houses cryopreserved quality, and disposition—and has broader (The Bovine Genome Sequencing and germplasm from the major livestock genetic variation than commercial turkey Analysis Consortium et al. 2009), due to (cattle, goat, sheep, and pig), and poultry lines (Aslam et al. 2012; Kamara et al. the uniformity of this unique stock after (chicken and turkey) species, as well as 2007). There are no more than seven pri- 75 years of selective breeding. As another major aquatic species. This collection mary Narragansett breeding flocks in the example, the University of Nebraska includes a number of rare and minor United States, and the estimated global developed a unique line of pigs with su- breeds such as the Gulf Coast sheep but population is less than 5,000. perior reproductive qualities for ovulation lacks many of the other minor breeds Although the rare livestock and poul- rate and embryonic survival (Johnson et (e.g., Narragansett turkey). There are try breeds are currently not major contrib- al. 1999) which not only helped elucidate additional gaps in the germplasm collec- utors to modern U.S. agriculture, one can the molecular basis of ovarian physiology tion for other rare and minor breeds for examine the recent outbreaks of highly in swine (Caetano et al. 2004), but also all of the major livestock species. In the pathogenic avian influenza in the United could be sought by swine producers in face of the mounting depletion of genetic States (or outbreak of African swine fever the future, similar to the Line 1 Hereford. diversity among livestock species, there in China) and realize that over-reliance The Avian Disease and Oncology Labora- is an urgent need to expand the sampling on a few highly-productive breeds could tory of the ARS maintains more than 30 program, sustain the preservation effort, endanger the global food supply if these lines of layer chickens, some of which and evaluate the remaining livestock and productive breeds are highly susceptible have been developed with resistance to poultry gene pools. to a new pathogen. The 2015 outbreak Marek’s disease, a highly contagious National germplasm repositories are of avian influenza cost the layer chicken, viral disease-causing lymphoma in chick- the responsibility of national govern- broiler chicken, and turkey industries ens (Chang et al. 2010; Mitra et al. 2012). ments. Accordingly, 128 countries have in the United States an estimated $3.3 These unique populations take substan- established gene banks (FAO 2015) and billion. The United Nation’s Convention tial time and resources to develop and we estimate that samples from more than on Biological Diversity and its Nagoya provide invaluable answers to many basic 100,000 animals have been collected to Protocol (https://www.cbd.int/abs/about/), biological questions. Their elimination is date (Paiva, McManus, and Blackburn which provides countries a mechanism to a major cause for concern as they are not 2016). Limited finances, combined with regulate exchanges of genetic resources, easily replaced. Unfortunately, the long- low priority in national livestock policies, are signals of countries viewing livestock term value of these populations is often were cited as the most common factors genetic resources from a new perspective. not realized until after they are gone. A hindering the establishment and operation As a result, genetic resources from out- case in point was a research broiler line of germplasm repositories. side the United States may become more selected in the 1980s for the duration of The objectives of this paper are: difficult to obtain. This, in turn, increases fertility after insemination with cryopre- 1. Identify and define what types of the need to conserve and manage exist- served/thawed semen (Ansah and Buck- traditional livestock resources (e.g., ing U.S. livestock and poultry genetic land 1983; Ansah, Seugura, and Buckland commercial lines, minor breeds, resources. 1985; Bentley, Ansah and Buckland research strains, transgenic stocks) In addition to rare or minor live- 1984) but that is now gone. With today’s should be considered for long-term stock breeds, there are unique research genomic tools, these genetic traits would germplasm preservation; lines at U.S. research and educational have been invaluable for addressing the 2. Describe the state-of-the-art pres- institutions that contain valuable pheno- challenges associated with poultry semen ervation methodologies for those types for various traits and have served cryopreservation (Long 2006), and for animal genetic resources with special as important research models for the increasing the understanding of cryo- emphasis on gaps in knowledge and livestock and biomedical communities. preservation at the cellular level. application; For example, the Agricultural Research Long-term preservation of semen and 3. Describe the existing operations for Service (ARS) of the U.S. Department embryos in a deep-frozen state provides livestock animal germplasm preserva- of Agriculture (USDA) developed Line a measure of insurance against the loss tion within the United States; 1 Hereford cattle in the late 1940s which of genetic diversity, whether among or 4. Identify the resources needed to de- was selected for certain characteristics, within specialized lines, breeds or spe- velop a highly efficient and fully opti- including exceptionally fast growth and cies. A CAST (1984) Task Force Report mized national germplasm repository, weight gain. It was not possible to predict succinctly made the case for develop- including (a) a contemporary com- at that time that, in the 1970s, the Line 1 ing a national germplasm repository in prehensive census of existing breeds Hereford genetics would be responsible the United States. The USDA-ARS’s and strains in the United States, (b) a for transforming the commercial Here- National Animal Germplasm Program strategic plan for prioritizing germ- ford breed as producers sought to address (NAGP) was formed in 1999 as a result plasm collection, and (c) research consumer preferences for leaner beef. of 1990 Farm Bill, which called for the programs targeted to improve gamete Thirty years later, a cow from the Line 1 Secretary of Agriculture to develop a and tissue storage and use for poultry, Hereford population, “Dominette 01449”, National Genetic Resources Program to small ruminant, swine, and other

COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY 3 species in which cryopreservation is less than optimum; and Major centers of livestock domestication as inferred from archaeological and 5. Frame a realistic plan to develop the molecular genetic evidence necessary resources to maintain the long-term operational continuity of a highly efficient and fully optimized national germplasm repository.

Genetic Diversity of Today’s Livestock Breeds Domestication and the Rise of Animal Agriculture Domestication of livestock and poultry began about 12,000 years ago and changed human culture and ecol- Figure 1. Domestication centers are: (1) turkey; (2) guinea pig, llama, alpaca, ogy profoundly (Larson et al. 2014). Muscovy duck; (3) rabbit; (4) donkey; (5) taurine cattle, pig, goat, sheep; The exact sequence of events leading to (6) dromedary, (7) zebu cattle, river buffalo; (8) Bactrian camel; (9) horse; domestication probably varied by species. (10) reindeer; (11) yak; (12) pig; (13) chicken; (14) swamp buffalo; (15) Figure 1 shows the primary locations of Bali cattle. Source: FAO 2015. p. 10. Reproduced with permission. domestication events for agriculturally relevant species. strengthened behavioral and phenotypic herd and across herds to each other, and Early domestications provided a changes in these livestock and poultry breeding only “the best to the best” as regular supply of meat, first for settled species. a strategy to improve herds. The result- communities and later in conjunction ing “improved” breeds such as Leicester with nomadic pastoralists. Domesticated Signatures of Selection: Longwool sheep and Shorthorn cattle sheep and goats provided fiber and milk soon spread across the world to influence in addition to meat. As the first draft Shaping Breeds for Optimal livestock populations in many countries. animals, cattle represented a significant Food Production More importantly, the principles used by development for agriculture. The diver- Livestock and poultry have long been English breeders were rapidly adopted sity of pigs and cattle indicates several selected to suit needs and desires of by other breeders interested in livestock domestication events (e.g., taurine vs. humans. Over time, differences emerged genetic improvement. Furthermore, these zebu cattle) and regionally different in livestock populations of different principles inspired Austrian monk Gregor husbandry practices (Larson et al. 2007; regions due to combinations of distinct Mendel to conduct his foundational work McCann et al. 2014). Poultry likewise foundation animals, genetic isolation, in plant genetics (Wood and Orel 2001). underwent multiple domestication events genetic drift, and selection. These influ- Driven by the industrial revolution, the in various centers of human development. ences explain most differences among mid-to-late 1800s saw a dramatic upsurge Chickens were domesticated in Southeast livestock populations. Prior to humans, of deliberate breed development and stan- Asia; domestication of ducks followed natural selection assured that populations dardization. Livestock exhibition grew to 2,000–3,000 years later. Turkeys, origi- were adapted to various local environ- be a passion. At the same time, the open- nally found only on the American conti- mental conditions. Subsequent selection ing of trade routes to the Far East brought nent, were first domesticated in Mexico by humans resulted in breeds suited for novel breeds to Europe and America, and and later by the Pueblo cultures of North specific roles, such as milk production or breeders experimented with those breeds. America. draft power. The result of these combined These experiments led to new genetic Domesticated species share common selection influences was an intricate combinations and subsequent breed behavioral traits that lent themselves to patchwork of populations that varied development. Breed standardization and co-existence with humans. Simple mating from region to region. development left their marks on Ameri- strategies and plasticity in food require- Genetic selection of livestock as we can agriculture as a few of the newer ments made them compatible to human know it today did not become routine breeds replaced many distinct older local ecologies. These attributes made them until the 18th century in England and types of livestock (Leavitt 1933; Lemmer easy to manage and reproduce and pro- northern Europe (Wood and Orel 2001). 1947). For example, muscular Hereford vided human caretakers with animals for Breeders established and documented and Angus cattle became specialty beef food production. Both unintentional and the fundamental concepts of measuring breeds, and eventually replaced most of intentional selection for domestication production, comparing animals within a the dual-purpose Shorthorns and “native”

4 COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY cattle of Spanish origin, especially as production systems that cannot always be intensification of livestock production stockyards grew increasingly important predicted. For example, U.S. swine farm- and a new array of disease and parasite to fatten cattle in the final weeks before ers in the 1920s probably did not envision preventions and treatments diminished slaughter. the transition from lard-type hogs to lean the value of environmental adaptation Mechanization and social changes meat hogs. and enabled larger, faster growing breeds led to further shifts and consolidation Whereas much of the world is focus- to capture the agricultural market. Yet, in livestock agriculture. Tractors and ing on least-cost production of livestock emergence of multi-resistant parasites, trucks replaced draft animals. Trains products, a new two-tier approach to inbreeding in dominant livestock breeds and refrigeration made it possible to consumer demand for livestock products (such as Holstein dairy cattle), and ever- transport livestock and food over previ- is emerging within the United States and changing environmental stressors and ously unimaginable distances. Economic Europe. While the larger tier focuses on production requirements emphasize the shifts in the 1930s and 1940s caused the large-scale, least-cost production, newer need to conserve animal genetic resourc- U.S. government to invest in research and smaller niche markets desire locally es with adaptive potential. to improve animal productivity. Farms raised food products, such as eggs from Poultry losses are more difficult to as- became ever larger because of enhanced pasture-raised chickens and meats from sess; 50% or more of the genetic diversity efficiency needs, and grocery stores cre- slow-growing animals raised in less in- in ancestral chicken breeds is lacking in ated consumer demand for large supplies tensive production systems. These niche commercial pure lines (Muir et al. 2008). of uniform, low-cost products. markets provide an entry into the mar- Nonindustrial turkey breeds have been hit Selection of livestock and poultry ketplace for a much wider array of breed especially hard, with almost no produc- for improved production made this new types, and new opportunities are opening tion-oriented breeding occurring until the intensive form of agriculture possible. to breeders of less common or rare breed 1990s. Historic sheep breeds adapted to Breeds became specialized—no longer animals (e.g., meat from the Berkshire Florida and the Gulf Coast conditions are would one type of chicken be used for breed of pig for high value charcute- now greatly reduced from their previous- egg and meat production or one breed of rie dishes that can fit these alternative ly high numbers (Dohner 2001). These cattle for meat, milk, and draft. Specialty consumer requirements). Demands from are sheep adapted to survive humid con- breeds were developed for improved the niche market consumers are being ditions and heavy internal parasite loads, yields. New husbandry methods were de- met primarily by small farmers. Signifi- traits that would be difficult to reestablish veloped that allowed more animals to be cant efforts are needed to increase those if those breeds are lost. In fact, most produced using less land and feed (Cap- farmers’ access to and use of genetic, similarly adapted strains of Spanish goats per, Cady, and Bauman 2009; Pelletier, reproductive, and information technolo- previously found in the southeastern Ibaruru and Xin 2014). Specific breeds gies appropriate to the markets that they United States are now extinct and their excelled in these ever-more concentrated are supplying. adaptation to humid subtropical environ- livestock production systems, whereas ments has been lost. In the Southwest, other breeds were deemed inferior. Then and Now: What Has the Navajo-Churro sheep was saved from Today, breed improvement and selec- Been Lost extinction only by the active engage- tion are global as well as local, spurred Agricultural books of the early 20th ment of several breeders (see Textbox 1). by growing demand for livestock prod- century featured a dozen breeds per Well-planned efforts to preserve existing ucts in conjunction with income growth species from which the farmer could livestock and poultry genetic resources (FAO 2007). Highly specialized breeds or choose, in addition to locally available and to characterize their adaptations, pro- new composite breeds (formed by mating breeds. Locally adapted Spanish cattle ductivity, and their genomes can prevent two or more different breeds) are selected that were once the mainstay of beef such losses in the future. for productivity and other economically production in California are now extinct. Intensification of global animal valuable traits. Genetic change is now be- While three other cattle breeds that share agriculture has depleted the historical ing accelerated by sophisticated statisti- a Spanish origin still exist in the United numbers of breeds to a relatively few cal analyses, ultrasound measurements States (Texas Longhorn, Pineywoods, breeds selected for high-production traits of body composition, genomic analyses, and Florida Cracker), their numbers are to meet low-cost market demands. Devel- and assisted reproductive technologies. drastically reduced from the hundreds of opment of these specialized breeds has The United States is a leader in providing thousands that once roamed Texas and been facilitated by intensive management genetic resources on a global scale (FAO the Deep South (Simon 2006; Sponen- systems such as enhanced nutritional 2007; Gollin, Van Dusen, and Blackburn berg and Olson 1992). The vast array regimens, indoor rearing (some spe- 2009), and U.S. husbandry methods of Linebacked cattle from the northeast cies), and improved health care. Modern have been exported concurrently with United States has declined to a single line examples of breeds that are markedly germplasm resources. At the same time, saved from 12 animals (genetic variation different from their ancestors, despite the local and regional breed populations have is lost through bottlenecks such as this). breed name remaining the same, include contracted, and losses in these breeds Hog breeds like the Mulefoot came very swine breeds such as Duroc, Hampshire, represent losses of unique genetic varia- close to extinction but now are the target Chester White, and Yorkshire, which tions with potential value for future food of conservation programs. In each case, substantially changed from their original

COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY 5 Textbox 1. Preventing Extinction of a Breed: The Navajo Sheep Project this trend, requiring breeding companies to shift selection criteria for production in less-intensive environments, more similar Navajo-Churro sheep are a distinctive to the historical breeds. breed descended from Churra sheep One of the ways genetic diversity of from Spain. They have been part livestock and poultry can be represented of the Navajo, Hispanic, and Anglo cultures in the Southwest United is in breeds; therefore, breed disappear- States for more than 400 years. The ance means a loss of easily used genetic fleece type, with its durability and diversity (Bixby et al. 1994; FAO 2007). mixture of short fine fibers and longer Moreover, because many breeds are coarse fibers, is superbly suited to the closely tied to the history of specific com- textiles produced in the local region, munities and locations, breed losses also famous throughout the United States represent losses of the cultural landscape. for their unique qualities and cultural Although disappearance of a few breeds relevance. Navajo sheep numbered more than 550,000 in 1930; however, the may not entail a complete loss of genes breed nearly became extinct from the 1950s to 1970s following severe drought, government stock reduction programs, and crossbreeding programs. By 1977, that are shared within a species, loss of fewer than 500 head of traditional-type Navajo sheep remained. The launching several breeds reduces genetic variation of the Navajo Sheep Project prevented total extinction. This and other conserva- and increases the theoretical likelihood tion programs saved this unique breed. In 1986, a registry system was launched of permanently losing specific genes and through the efforts of individual breeders and non-governmental organizations, gene combinations that often define a and ongoing inspection of each generation assures that breed type remains breed. Putting a value to the loss of these traditional. Census numbers are now close to 3,000 head, and the breed can genetic variants is always incomplete be found widely throughout the United States (Maiwashe and Blackburn 2004). because one cannot predict whether Adapted from Sponenberg and Taylor (2009). these genes or gene combinations will be needed for future environments, production changes, or biomedical research. conformations due to shifts in consumer ity and productive lifespan are being felt This is especially true in light of the dietary preferences (i.e., desire for lean even as milk production per cow con- “genomics era” where all of the major meat). Nevertheless, the Hampshire, tinues to increase. Effective population livestock species now have a reference Yorkshire and, in particular, Duroc are sizes in Holstein and Jersey dairy cattle genome sequence, and comparisons of among the most genetically diverse pig dropped to 39 and 30 animals, respec- DNA sequences of breeds with different populations in the United States, and tively (Weigel 2001), and the existence phenotypes could provide much needed this diversity should allow for plasticity of only two Y chromosome lineages in information to drive selection forward within these breeds as agriculture and the Holstein, suggest only two sire lines for specific traits (e.g., sheep breeds with consumer demands continue to evolve are present for the breed (Yue, Dechow, known resistance to parasites). With (Faria et al. 2019). and Liu 2015). Genetic contraction also the loss of many therapeutics for use In general, across livestock and has occurred in swine breeds, where in animal production systems, genetic poultry species, performance for some composite populations of pig breeds have resistance to disease has more relevance traits (foraging, climate adaptation, resulted in smaller purebred populations today than ever before. Additionally, mothering ability, longevity, and fertility) (Welsh et al. 2010). The entire U.S. sheep newly developed gene-editing methods has decreased in some breeds because industry has contracted over the last six would allow the introduction of desirable of selection pressures and elements of decades, reducing numbers for all breeds. variants identified in minor breeds into intensified production systems. Although Goats have escaped many losses, and more mainstream breeds. It is critical that the pace of modernizing animal agri- although numbers are greatly reduced genetic resources be conserved to main- culture has slowed somewhat, existing for San Clemente, Angora, and Span- tain as many options as possible to meet a breeds are still undergoing contraction. ish goats, they remain as viable locally wide variety of future needs that are often Beef breeds such as Limousine, Gelb- adapted breed resources (do Prado Paim unknown at present, vieh, and Salers have shown a reduction et al. 2019). For chickens, the culmina- in purebred registration numbers because tion of intensive production systems has they are being crossbred to be competi- led to the development and use of very Protecting Remaining tive in commercial production systems. distinct, specialized strains that have been Food Animal Gene The dairy industry in the United States selected for traits linked to commercial relies almost entirely upon the Holstein production, such as reduced broodiness to Pools in North America breed, and inbreeding in Holstein cattle is provide a more continuous production of accelerating in the United States (Dairy eggs. Consumer preference (e.g., produc- On-farm Conservation: The Cattle Reproduction Council 2019); the tion of cage-free eggs, reduced use of an- Value of Live Populations effects of inbreeding on reduced fertil- tibiotics) is now causing some reversal in Farm animal populations consist of

6 COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY living individuals, and there are advan- or recipient animal can be from a readily female gametes (oocytes), embryos, tages of keeping genetic material in this available commercial line or breed, more embryonic cells, gonadal tissue, pri- form. Living populations are advanta- effort will be required to reconstitute the mordial germ cells (PGC), and somatic geous because they can adapt to changes lost line if the recipient animals are ge- tissues. There are two main approaches in the natural or production environment, netically divergent. For example, if there to cryopreservation of cells or tissues: such as the emergence of new disease are no living females from a research slow “equilibrium” cooling and ultra-fast challenges, alterations of husbandry prac- poultry line, multiple breedings known as “non-equilibrium” cooling, known as tices, changes in consumer preferences “backcrosses” are required to restore the vitrification (see Textbox 2; Youngs et al. and climate change (FAO 2010). As line with commercially available hens. 2010; Youngs 2011). The goal of slow- populations respond genetically to their For example, five to seven backcrosses cooling procedures is to prevent cell dam- environment, producers in turn main- would yield 96.9 to 99.2% of the original age caused by ice crystal formation by retain or develop knowledge concerning line’s genome, at which point the recon- moving intracellular water (e.g., cellular husbandry and use, including unexpected stituted line will still contain up to 3.12% dehydration) via diffusion across the cell discoveries such as human disease mod- of the genetics of the unrelated recipient membrane. Slow cooling has been used els (Torres et al. 2010). hens. Importantly, living animals are also extensively for sperm and other cells, but Live populations of animals can con- necessary to verify the effectiveness of it cannot be used with equal efficiency tribute a part or all of the cost of support- cryopreservation techniques. Verification for other tissues and organs (Liu, Cheng, ing themselves through the production includes the routine evaluation of cryo- and Silversides 2013a) because tissues of meat, milk, eggs, or fiber (or simply preserved material and the validation of and organs contain a wide variety of cell through their cultural value), but annual techniques for specific lines because there types that often have different character- expenditures are greater than for main- is well-documented variation among istics (Mazur 1970). A slow-cooling pro- tenance of the same genetic resources in species, lines, and individuals in the tocol that results in high survival of one a cryopreserved form. Living animals ability of biological material to survive cell type may lead to the death of other in a conservation program can be used cryopreservation, as well as from a wide types of cells in that same tissue. Vitrifi- to develop specialty markets to support variety of non-biological sources includ- cation procedures, on the other hand, turn economies in rural areas, and their char- ing research techniques (Bacon et al. water inside the cell to a solid without acteristics can be integrated immediately 1986; Blesbois et al. 2007; Kishida et al. allowing ice crystals to form (Liu, Cheng, into a production system (Sponenberg, 2015; Long et al. 2014; Windsor 1997;). and Silversides, 2013a). The ultra-rapid Beranger, and Martin 2014). This verification should include the final cooling of biological materials converts Living populations provide value proof of success, the production of viable intracellular and extracellular aqueous in research because the physical traits and healthy live animals, and not just the components to a glass-like state almost (phenotypes) can be observed and stud- identification of fertility or pregnancy instantaneously. Irrespective of the ied. Highly inbred and selected research rates. Moreover, living animals also are cryopreservation method, cryobiologists lines have contributed to basic scientific needed as a resource for research to de- have calculated that cells and tissues may knowledge in agriculture, medicine, velop new and/or more effective methods be stored indefinitely at the temperature physiology, and genetics. Such stocks of cryopreservation. of liquid nitrogen (-196°C). For example, have been subjected to long-term selec- The possibility of using and study- cryopreserved ram semen has maintained tion, and in some cases reconstituting ing living animals in various production its fertilizing ability for 35 years (Sal- these stocks from cryopreserved mate- environments and for research means that amon et al. 2004). rial would require both a relatively high maintaining living populations is nearly level of expertise and cost. Unfortunately, always the preferred conservation strat- Male Genetic Material: many of the specialty research lines are egy if financial concerns are removed. Spermatozoa unable to generate enough income to be Most countries have adopted conserva- Cryopreservation of spermatozoa economically self-sufficient and thus their tion strategies that include living popula- (hereafter, sperm) has taken place for continued existence is often vulnerable to tions, primarily through public-private decades, and substantial efforts have been short-term budget considerations. partnerships. In cases where a particular made toward developing protocols, pri- Maintenance of living populations species, breed or line cannot be cryopre- marily because of the relative ease of se- is complementary to a cryopreservation served, maintenance of living populations men collection. The discovery that glyc- program, where the genetics of breeds is the only preservation strategy currently erol could protect rooster sperm against and lines are conserved in frozen form. available. damage caused by cold temperatures Cryopreservation offers rare and major (Polge, Smith, and Parks 1949) paved breeds a benefit—whether to reconstitute the way for semen cryopreservation lost bloodlines or to serve as a safety net Ex Situ Preservation: Current procedures for a wide range of species, in case of catastrophic loss of a dimin- Methods of Cryopreservation including livestock, companion animals, ished population. Reconstitution of Genetic material from livestock and aquatic species, and humans. The great- cryopreserved genetic material requires poultry can be cryopreserved in several est progress in commercial use of sperm live animals as hosts and, while the host forms: male gametes (spermatozoa), cyropreservation has been achieved

COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY 7 Textbox 2. Embryo Cryopreservation Methods: Slow Cooling Versus Vitrification

The Water/Ice Problem: Preimplantation embryos from mammalian livestock species consist of approximately 80% Figure 2. A straw such as this one can water. This high water be used for long-term content represents a cryopreservation of semen. significant obstacle to the successful preservation of embryos at for cattle, but numerous successes have subzero temperatures been reported in the scientific literature because water turns for sheep and goats. In sheep, one of into ice crystals when the historical challenges with frozen- cooled below 0°C (32°F). Ice crystals that thawed semen was the inability to obtain form inside the cells of high pregnancy rates following cervical an embryo cause sig- insemination because of the difficulty in nificant damage to the passing through the ewe’s cervix (Sal- cells, usually leading to amon and Maxwell 1995a,b). The use death of the embryo. of laparoscopic artificial insemination, where semen is placed directly into the Two Methods of uterus via a fiber optical endoscope, has Freezing: improved conception rates from cryopre- To reduce the likeli- served semen to as high as 80% (Cseh, hood of ice crystals Faigl, and Amridis 2012). This insemina- forming inside the cells tion method is used extensively for sheep of an embryo, embryos must be dehydrated in some countries outside of North Amer- prior to cooling. De- ica; however, the U.S. sheep industry hydration is accom- perceives the use of cryopreserved semen plished by placing as having a minimal benefit-cost ratio, embryos into a solution where the improved conception rate is a containing a compound marginal benefit compared to the added that draws water out of cost of laparascopic insemination. As a the embryo. As illustrated in the top graph, the slow-cooling equilibrium method result, it is used only in very elite flocks. consists of a 10-minute equilibrium period, followed by a gradual cooling period Goat semen has been cryopreserved for for nearly an hour, and then a final 10-minute equilibrium period. In contrast, the bottom graph illustrates ultra-rapid, nonequilibrium cooling (vitrification) and several decades, and there have been that involves placement of the embryo in a very small volume of the dehydrating reports of acceptable pregnancy rates of solution directly into liquid nitrogen (-196°C [-320°F]) or into liquid nitrogen vapor 70 to 76% (Bispo et al. 2011). (-180°C [-292°F]) for a few seconds before plunging into liquid nitrogen. North American swine producers routinely use fresh semen that has been chilled (not frozen) for artificial insemination (Flowers 2015). The commercial by the dairy and beef cattle industries, sperm, and the rate of cell survival after swine industry has not yet embraced the where semen cryopreservation has been freezing and thawing is not critical so use of frozen semen because it typically optimized, standardized, and automated long as a sufficiently large number of yields lower pregnancy rates and reduced for commercial production. The National functional sperm cells are deposited into litter sizes. Boar sperm are sensitive to a Association of Animal Breeders (NAAB) the female at the time of insemination. phenomenon known as cold shock, have indicates that more than 23.1 million For example, even when fewer than 20% low tolerance to osmotic stress, and there units (i.e., straws) of cryopreserved dairy of thawed bovine sperm cells are alive, are dramatic differences among boars in cattle semen and more than 2.5 million fertility rates as high as 68% are routinely the ability of sperm to survive the freeze/ units of cryopreserved beef cattle semen observed (Vishwanath 2003). thaw procedure (Benson et al. 2012). Use were sold by the NAAB members during Semen cryopreservation procedures of a nonsurgical intrauterine artificial in- 2017. A typical straw of bovine semen for other domestic mammalian livestock semination method (Kraeling and Webel (Figure 2) contains many millions of species are not as well developed as those 2015) could enable more widespread use

8 COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY of thawed boar semen, especially when any species using only thawed semen embryos. Numerous efforts to cryopre- used in conjunction with methods to con- requires multiple generations of back- serve oocytes (Arav 2014; Dinnyes, Liu, trol the time of ovulation in sows. crossing to reduce the "contaminating" and Nedambale 2007; Hwang and Hochi Although the first live chick was DNA from the recipient female, and for 2014; Mullen and Fahy 2012; Somfai, produced from thawed rooster semen in birds this cost is compounded by the need Kikuchi, and Nagai 2012; Zhou and Li the 1940s (Shaffner, Henderson, and Card for concentrated semen to overcome the 2013) highlight the need for substantial 1941), semen freezing technology has issues of fertility (Silversides et al. 2012). improvements in methodology. Although subsequently developed more success- Despite the limitations of cryopreserv- a limited number of healthy mammalian fully for other animal groups than for ing semen for birds, that technique is the offspring have been produced using poultry. Bird sperm physiology and the basis of several significant avian cryo- vitrified oocytes, it is not yet a routine requirements for fertilization are different conservation programs in the absence procedure. Comparable results for poultry from those of mammals (Liu, Cheng, and of other technologies (Blackburn 2006; oocytes have not been achieved for rea- Silversides 2013a; Long 2006). Sperm Blesbois et al. 2007; Woelders, Zuidberg, sons described above. must be able to be stored in the sperm and Hiemstra 2006). storage ducts in the lower end of the hen Embryos and embryonic cells oviduct and subsequently released to co- Female Genetic Material Cryopreservation of embryos from incide with hen ovulation. Cryopreserved Oocytes domestic mammalian livestock species rooster semen may retain less than 2% Oocytes are not as accessible as sperm has been possible for several decades. of the fertilizing ability of fresh semen because the female gonad (ovary) resides The first reports of live offspring after the (Wishart 1985). Lower fertility rates of within the internal body cavity, and transfer of cryopreserved cattle, sheep frozen/thawed semen, combined with surgical procedures are often required to and goat embryos (Bilton and Moore inconsistent results, have greatly hindered recover oocytes. Avian oocytes are even 1976; Willadsen et al. 1974; Wilmut and the use of cryopreserved semen by the less accessible than mammalian oocytes Rowson 1973) were published in the poultry industry. Cryopreserved chicken because the egg of the hen includes a 1970s and in the 1980s for pig embryos semen can yield fertility rates ranging large and fragile yolk, and non-fertilized (Hayashi et al. 1989). Cryopreservation from 0% to 90%; while the range for tur- avian oocytes degrade during the 23 procedures have become routine for most keys (0% – 65%) is lower (Blesbois et al. hours between ovulation and egg lay. domestic mammalian livestock species. 2007) and results often are not repeatable Oocytes are not as plentiful as sperm. This is particularly true for cattle, where (Long et al. 2014). High fertility is not For example, a cow has an average of more than 59% of embryos recovered needed for conservation and recovery of 133,000 oocytes at puberty (Erickson from live cattle and transferred globally avian lines (Blackburn, Silversides, and 1966), and this finite number will not in 2017 had been cryopreserved (Viana Purdy 2009; Blesbois et al. 2007), but increase during the cow’s lifetime. In 2018). Most embryo cryopreserva- there is variation among genetic lines in contrast, a bull produces 6.0–7.5 bil- tion methodologies were developed for the sperm’s ability to survive the freeze/ lion sperm per day (Senger 2012). The embryos recovered from live animals. thaw cycle (Ansah and Buckland 1982; mammalian oocyte is more difficult to Technology now permits the production Long et al. 2014) and some lines may cryopreserve than sperm, primarily due of embryos in the laboratory through in not be recoverable from cryopreserved to its larger size; nevertheless, mam- vitro fertilization, but survival of labo- semen. malian oocytes can be recovered, frozen, ratory-produced embryos is after trans- Another difference between avian and thawed, fertilized in vitro and resulting plantation can be 40% lower than in vivo- mammalian sperm is the sex chromo- embryos can be transplanted into the derived embryos (Farin and Farin 1995; some composition. In mammals, males uterus, with good success in some species Papadopoulos et al. 2002). Vitrification have an “XY” sex chromosome composi- (e.g., >50% pregnancy rate in cattle). For seems well-suited for cryopreservation tion, and individual sperm contain either poultry, an additional barrier to the use of embryos produced in the laboratory, an “X” or a “Y” chromosome, which of cryopreserved oocytes is that, while and it has been performed for many determines genetic sex of the embryos minimal embryonic development occurs years with animal-derived embryos from at the time of fertilization. In birds, the in the female reproductive tract (30,000 cattle, sheep, goats, and pigs (Kobayashi sex chromosomes are labeled as “W” and to 60,000 cells), most embryonic devel- et al. 1998, Massip et al. 1986; Schiewe, “Z”; females are “WZ” and males are opment is largely external (i.e., occurs Rall, and Wildt 1990; Yuswiati and Holtz “ZZ”, and the presence of a “Z” or “W” within a hard-shelled egg after the egg 1990;). Relatively high pregnancy rates chromosome in the oocyte determines is laid by the female). The complexity (60 to 80%) have been reported from genetic sex at the time of fertilization. of this developmental process limits the the transfer of thawed embryos for these Stored semen lacks the female “W” ability to reintroduce a fertilized avian species and such pregnancies proceed chromosome and maternal mitochondrial oocyte into a hard-shelled egg. normally thereafter. DNA which, from a practical perspective, Without question, the technology to One advantage of using cryopreserved are necessary to maintain the complete cryopreserve oocytes from domestic embryos (versus sperm or oocytes) is genetic complement of avian genetic mammalian livestock species is far less cost saving during the reconstitution lines. Recovering a line or breed from developed than that for sperm and for process because the embryo represents a

COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY 9 “complete” genetic package of the breed with the subsequent development and immature chickens followed by implan- (Gandini et al. 2007). Moreover, embryos production of fertile gametes. Gonadal tation of donor ovarian tissue into the from a rare breed can be transferred to transplantation has been successful in a normal anatomical location, enabled the uterus of a common-breed female number of mammalian species—includ- transplanted tissues to survive and surrogate to accelerate the production of ing humans (Comizzoli and Wildt 2014; resume development in recipients of the purebred progeny of the rare breed. The Silber 2012)—and also can be used for same age (Song and Silversides 2006). same result can be obtained with semen functional recovery of cryopreserved Further work in Japanese quail demon- only if insemination occurs with a rare avian gonadal tissue (Silversides and strated that ovarian tissue from adults breed female (which may not always be Liu 2012). Harvesting of gonadal tissue could be recovered in chicks (Liu, Cheng, available); otherwise multiple generations could prove vital to enabling the rescue and Silversides 2015). An important as- of backcrossing are needed to reconsti- of genetic material from animals that die pect of gonadal transplantation is the use tute “pure” populations. Reconstituting a unexpectedly. of immunosuppressants to prevent rejec- mammalian breed only with semen also Cryopreservation of gonadal mate- tion of the donor tissue. These techniques suffers from the lack of capturing the rial could become a primary approach to have been used to produce donor-derived maternal genetic contribution of mito- cryopreservation of poultry germplasm offspring from the transplantation of chondrial DNA that is strictly maternally because of the difficulties of cryopreserv- fresh ovarian tissue from chickens (Song inherited. ing poultry sperm, oocytes, and embryos and Silversides 2007a), ducks (Song et As for avian species, bird embryos (Textbox 3). Surgical ovariectomy of al. 2012), and Japanese quail (Liu et al. cannot be cryopreserved because of the structure of the embryo in relation to the Textbox 3. Overview of Ovary Cryopreservation and Transplantation in the Chicken yolk, the number of embryonic cells present when the egg is laid, and the size and structure of the egg itself. Although avian The Unlike mammals where the Y embryos cannot be cryopreserved, avian Decider chromosome from males deter- embryonic cells can be isolated, grown mines genetic sex, the genetic sex in culture, cryopreserved, and used to of birds is determined by the W produce germline chimeras (Naito 2003; chromosome from females; thus, Petitte 2006). In principle, these embry- females are needed for 100% onic cells could be used for cryopreser- recovery of a line. vation; however, the technology was developed primarily to provide access to germplasm for the genetic manipulation of poultry (van de Lavoir et al. 2006; Li Recovering oocytes for cryopreservation from and Lu 2010) which requires much lower mature ovaries (shown on the left) is not an option efficiencies than those needed for genetic for birds; however, immature ovarian tissue (which conservation. Several steps of the process contains a large pool of premature oocytes) can of cryopreservation and reconstitution be frozen whole and subsequently transplanted of avian embryonic cells work well, but into recipient birds. the procedures needed are complex, and more than 25 years of intensive investigation by researchers around the world have not produced a technique for reconstitution that is sufficient for use in a cryopreservation program (Silversides and Liu 2012).

Gonadal material Donor (day old) Needle-in-straw vitrification* Recipient (day-old) During embryonic development, primordial germ cells that will eventually The ovary is recovered from a day-old chick, frozen using a process known as produce the next generation of sperm and vitrification, sealed in a specialized straw, and stored in liquid nitrogen (-196 oocytes migrate to and establish them- °C). The recipient bird is ovarectomized prior to transplantation of the donor ovary. Immunosuppressants are administered for up to two months to prevent selves within the gonads. These immature rejection of the donor ovary. For quails, the optimal age for ovary recovery and gonads can be surgically removed, cryo- transplantation is one week after hatch; while the optimal age for the turkey has preserved and, after thawing, transplanted not yet been determined. to recipient animals. Both of these *Adapted from Liu et al., 2012 processes allow conservation of the germ (Song and Silversides 2007; Song and Silversides 2008) cells in their natural microenvironment

10 COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY 2010; Song and Silversides 2008a). mammalian livestock species, and further and within-breed levels. Information For avian testicular tissue, transplan- refinements in methodology will enable is needed at the pedigree and genomic tation to a site other than the normal more consistent and repeatable results to levels to select animals or groups of anatomical location of the testes is be obtained. animals to fill these gaps. Prioritizing required because the male gonad is more conservation within breeds must also intrinsically associated with the repro- Categorizing and Prioritizing consider bloodlines and pedigrees to ductive tract than the ovary and, to date, acquire the needed genetic diversity. For this limitation has not been overcome. A Animal Populations for Cryo- breeds that are critically endangered, transplant location under the skin on the conservation or that suffer inbreeding due to a small back of the chicken can support testicular Despite the losses described above, number of founders, individual animals growth (Silversides, Robertson and Liu there is still tremendous biological may represent extremely rare diversity 2013a) and live, donor-derived offspring diversity among agriculturally important needed for breed survival. Similar situa- have been produced by sperm recovered food animal species in North America. tions exist within commercially important from transplanted testicles, although A strong need exists to characterize this populations (e.g., Line 1 Herefords and this sperm was fresh, not cryopreserved remaining biological diversity to identify Wye Plantation Angus) that have made (Song and Silversides 2007b). uniqueness that will influence the collec- important contributions to the Hereford tion and conservation of breeds. Main- and Angus breeds at varying points in Primordial germ cells and somatic taining the diversity of livestock breeds time due to the selection strategies used cells is important to enable animal production within those populations. Precise genetic editing (via CRISPR/ systems to adapt to changing production Genomic technologies aid in quan- Cas9 or similar enzyme systems) is environments caused by factors such tification of diversity and allelic com- becoming more and more feasible in as climate change and urbanization of binations for economically important livestock to produce animals with desired farmlands (ERFP 2014), as well as to production and adaptation traits. Ge- traits such as a lack of horns or resistance address changing consumer demands nomic information would enable better to disease (Tait-Burkard et al. 2018). (e.g., niche markets). Any loss of existing prioritization of which samples to be As these gene editing techniques are animal genetic resources could hamper cryopreserved. This is particularly true more widely used, new opportunities are future efforts to feed the world. The FAO when one considers the number of ongo- becoming available for the use of cryo- has estimated that 17% of the world’s ing genome-wide association studies that preserved chicken primordial germ cells. remaining livestock and poultry breeds are identifying polymorphisms associ- These cells can be injected into early age are at risk of extinction (FAO 2015), so ated with performance traits such as meat embryos (2.5 days old) and will migrate action is needed now. quality (Sanchez et al. 2014) and milk to the gonads to become the eventual In North America, the critical impor- production (Fang et al. 2017). Genomic oocytes. Recently, gene-editing technol- tance of characterizing and cryopreserv- information will also safeguard against ogy was used to create sterile hens that ing livestock genetic animal resources the unintentional narrowing of genetic do not lay eggs but are otherwise healthy has been recognized by the U.S. Depart- diversity among North American live- (Taylor et al. 2017). The next step would ment of Agriculture, Agriculture and stock populations that could occur as a be to transplant primordial germ cells Agri-Food Canada, and The Livestock result of intense genetic selection for one from a rare breed into the sterile hen, al- Conservancy. While Canadian and U.S. or a handful of traits. Nevertheless, an though this methodology has not yet been conservation policies dictate cryopreser- over-reliance on genomic technologies developed. If successful, this approach vation efforts for all breeds, the cryo- may be problematic because it assumes a could overcome some of the limitations preservation program and in-situ efforts perfect understanding of the traits needed with cryopreservation in birds. in Brazil have focused solely on heritage for the future. Somatic cells (such as skin cells) breeds. In the United States, prioritization A range of genetic diversity stud- can be cryopreserved, usually with- for germplasm collection has considered ies have been completed for livestock out difficulty, and contain a complete among-breed and within-breed genetic and chicken breeds that have provided complement of genetic information. For variability, societal values (especially important insights regarding the genetic some mammalian species (e.g., cattle, regarding heritage breeds), genomic variability within species; however, many sheep, goats, pigs), these cells can be information, pedigrees, and geographic of these performed prior to 2010 used the used to produce offspring by somatic location. This approach has enabled the now outdated technology of microsatel- cell nuclear transfer (a.k.a. cloning); this current germplasm collection to acquire a lite markers. The development of single is not currently an option for birds. The broad array of genetic resources. Evalu- nucleotide polymorphism (SNP) marker major advantages of somatic cells over ation of the number of samples per breed panels and whole genome sequencing al- germinal tissue are their greater avail- and the relatedness of those samples lows for a fuller understanding of genetic ability, greater ease for cryopreservation, among animals within the breed readily variability within and among breeds. and the possibility to introduce selected reveals new priorities for collection. For example, these genomic tools enable genetic modifications. Healthy offspring Collection gaps exist in the U.S. identification of breeds or subpopula- have been produced in a multitude of cryopreservation program at the breed tions within breeds that are best suited for

COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY 11 specific environments and could iden- breeders typically lack infrastructure to conservation will take place on an ad hoc tify productive roles for minor and rare collect production data and to perform basis as opportunities become available. breeds. Quantifying the existing genetic the needed genetic analyses. One such diversity will assist with informed deci- mechanism could be a public-private Germplasm Repositories: sions on what populations should receive partnership where researchers conduct priority. controlled research studies (with ap- Existing Government and propriate federal funding) necessary to Private facilities Challenges characterize the rare breeds. The USDA-ARS established the There are several important challenges Once sufficient characterization has NAGP in 1999, and thereby began devel- regarding the characterization of animal been accomplished, the task of pri- opment of livestock, poultry and aquatic populations for cryopreservation. Firstly, oritization will become easier. Priority gene banking for species of agricultural a common agreement of basic data to be must be given to populations with (1) importance. The role of the U.S. Gov- gathered across breeds within a species important unique genetic attributes (e.g., ernment in maintaining collections of must be identified, in a manner analogous disease and parasite resistance, surviv- genetic diversity for agricultural purposes to the Dairy Herd Improvement Associa- ability, adaptability), (2) rare alleles and has been acknowledged by the global tion standardized production record keep- divergent genetics, and (3) outstanding community. In 2007, 109 nations (including systems, which facilitated significant genetic performance for production traits. ing the United States) adopted the Inter- improvement in milk production. Animals within populations probably will laken Declaration and the Global Plan of Secondly, financial support (in all not embody all of these priorities. It is Action for Animal Genetic Resources. breeds except those with large numbers important to preserve breeds with unique The Global Plan of Action details key of animals) is needed to develop and genetic traits, even though they may be priorities needed to advance the conser- better use breed-specific genetic improve- less productive under current agricul- vation and utilization of genetic resources ment technologies, as well as to identify tural production systems. The poultry (FAO 2007; 2015). As of 2014, 128 unique genetic traits or alleles that may industry provides a good example of countries have established gene banks aid in adaptation, disease resistance, this, as global breeding companies have for animal genetic resources. A collec- survival, and other biologically important developed strains that perform well in the tion summary for five of these countries traits. tropics and for free-range production sys- appears in Table 1. Thirdly, research must be supported tems (Aviagen 2019) These same animals Since its initiation, the NAGP has to develop viable and affordable cryo- would be less productive in U.S. broiler developed into the world’s largest and preservation techniques for species that houses, but without a broad array of most comprehensive repository for farm cannot be adequately prioritized until foundational genetics, these new strains animal genetic resources (Danchin- robust methods are in place. Heightened could not have been developed. Burge, Hiemstra, and Blackburn 2011; research efforts are needed to overcome Characterization of breeds and indi- Paiva, McManus, and Blackburn 2014). this present limitation to cryopreservation viduals for conservation is a challeng- Currently, the collection contains more efforts. Additionally, applied research ing task, and much remains to be done. than 1,000,000 samples (98% is cryopre- should be directed at approaches that can Nevertheless, conservation should move served semen) from 54,790 animals that be efficiently scaled up for commercial forward with a focus on breeds at greatest represent 169 breeds and 349 subpopula- use including throughput, quality man- risk of extinction. The framework pro- tions (USDA 2019a). The breeds and spe- agement, labeling and storage systems vided by The Livestock Conservancy’s cial populations in the collection consist (Torres and Tiersch 2018). Conservation Priority List is the most of commercially important breeds, rare Finally, enhanced partnerships among commonly used reference for on-farm breeds, and research populations. Of the agricultural universities, federal govern- conservation, whereas the goal of the collected breeds, 46% have reached the ment laboratories (e.g., the U.S. Animal NAGP is to preserve genetic materials minimum collection goals in terms of Genomics and Improvement Laboratory), from all livestock and poultry breeds. Re- number of animals and samples; while and breed associations are needed to source constraints also dictate that some 36% of the breeds on the Livestock Con- facilitate more rapid characterization of North American food animal populations. Table 1. Gene bank semen collection sizes for selected countries in 2014. For many of the major breeds (across species), long-standing and productive Country Species Breeds Animals Number doses partnerships already exist; however, Brazil 12 25 416 71,867 these relationships need to be encouraged and expanded where appropriate. Such Canada 9 31 3,077 261,083 partnerships generally do not exist for France 9 181 4,337 352,068 minor (rare) breeds, and a mechanism Netherlands 7 59 5,691 309,088 to build, strengthen and maintain these relationships is needed. This is especially United States 38 149 16,397 709,657 important because rare and minor animal From: Paiva, McManus, and Blackburn (2014)

12 COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY servancy’s priority list (of rare breeds) cryopreserved semen and embryos from collection longevity. At the corporate have reached minimum germplasm col- 68 animals representing 11 breeds, which level, where storage and space costs are lection goals, underscoring the fact that was subsequently donated to the NAGP. issues, samples are often destroyed when germplasm collection must be a continual Within the private sector, two types of they are no longer deemed to have market process. cryopreserved germplasm collections value. For public collections universi- Prior to the establishment of the exist: (1) major companies who sell se- ties often dispose of the collection once NAGP there was no organized U.S. men and embryos to producers; and (2) the faculty member using the collection governmental collection of cryopreserved individual breeders who develop their retires. germplasm. The Livestock Conservancy own collections. These private and public Germplasm collection longevity is had a small collection consisting of collections share a common weak point— particularly an issue after changes in company ownership. Among private Textbox 4. Importance of Assisted Reproductive Technology for Gene Bank Use breeders and university faculty members, lifetime collections have been destroyed when administrators perceived Assisted reproductive technologies (ART) for livestock and poultry have been the collections as too costly to maintain. developed with varying degrees of success. Factors contributing to this vari- Fortunately, some research-oriented ability may include the cryopreservation processes, varying degrees of field collections have been donated to the expertise, and biological differences that exist among breeds or management NAGP upon retirement of the scientists, practices. For example, weaning age differs substantially between indoor swine including important lines of Holstein and operations vs. outdoor rearing systems. Such difference could impair the effec- Hereford cattle. Additionally, more than tiveness of breeding sows at the time of first estrus after weaning.The following 3,5000 samples from private and com- details two experiences with ART and swine. mercial collections have been donated to The Success: Purdue University developed and maintained a line of pigs ho- the NAGP. These private sector donations mozygous for genes controlling meat quality (napole and halothane conditions). have formed the backbone of germ- Thinking the research use of the line was complete, the decision was made plasm collection and are quite valuable to cryopreserve boar semen for storage at the NAGP and dispose of the line. because they: (1) provide a snapshot of Three years later, Purdue University needed to rebuild the population after re- breed performance at specific points in ceiving extramural funding. University researchers inseminated Yorkshire sows with the thawed semen from the NAGP collection and obtained a 100% preg- time; (2) are often from some of the most nancy rate. This was documented in more than 10 publications, and a second influential males among the breeds; and population of the pigs was established at another university. (3) increase the genetic variability of the collection. As a case in point, ABS The Failure: Large Black pig breeders in the United States imported cryopre- Global donated to the NAGP more than served semen from the United Kingdom to broaden the breed’s genetic base. 40 years’ (1960–2005) of cryopreserved Working across four herds with faculty from three different universities, the pregnancy rate after insemination was zero. semen from dairy and beef bulls (more than 200,000 units of semen from more Lesson learned: The team involved in the Large Black project hypothesized than 5,000 bulls). that protocols developed for intensively managed production systems, and for The dual purposes of developing certain breeds, did not transfer well into other production settings for pigs of national animal genetic resource collec- other breeds. If this is indeed the case, rare breed producers may not be able tions are to: (1) secure genetic variability to use typical ART for production purposes; as a result, this limits their ability to use a diverse set of genetic resources and lowers production levels. A research from a wide range of genetic resources study is now exploring this hypothesis. The research community has an impor- in perpetuity, and (2) provide genetic tant role to play in understanding and modifying technologies for producers from resources to regenerate populations or all sectors of the livestock industry. introduce genetic variability into breeds when needed. Moreover, germplasm can serve industry, research and policy needs (Blackburn et al. 2014). To date, samples from more than 6,000 animals have been released from the NAGP repository. These samples have been used to regenerate populations that were no longer in existence introduce genetic variability into rare breeds, perform reproductive studies, and conduct wide-range genomic studies (see Textbox 4). A recent example Large Black pig (left, ARS photo) and Purdue University napole and halo- of a germplasm release followed the thane piglets (right, photo courtesy of Terry Stewart). finding that current Holstein bulls used in artificial insemination descend from

COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY 13 1.0 0.9 0.8 0.7

0.6 ● Beef (23/46; 50%) 0.5 ● Chicken (16/28; 57%)

Collection Goal Index 0.4 ● Dairy (6/13; 46%) 0.3 ● Goat (3/14; 21%) 0.2 ● Pig (11/25; 44%) 0.1 ● Sheep (17/35; 49%) 0.0

Figure 4. Status of breed collections (each dot represents a breed) by species based upon a collection goal based on the amount of germplasm and Figure 3. Holstein bull calves, born number of animals in the collection. An index value of 1.0 indicates that from frozen semen stored at the minimum collection goal of a breed has been met. In parentheses are the NAGP repository, have the number of breeds meeting minimum collection goals/ number of unique Y chromosomes breeds per species group (Blackburn 2018). missing from the current population. of the NAGP collection for this pur- breeds and 336 research and industry- pose. Three factors that can contribute based populations. Although a broad only two paternal lines, suggesting only to achieving this goal are: (1) raising array of genetic resources used by the two Y chromosome variants are present awareness within the research commu- livestock and poultry industries has been in the population (Yue, Dechow, and Liu nity that the collection is available for captured, the NAGP collection is not a 2014). Fortunately, the NAGP collection use, (2) making funding sources aware complete representation of the available contained samples from bulls with two of the potential use so they can encour- breeds and genetic lines. There is a strong additional paternal lines. Samples from age the research community to provide and urgent need to enhance the NAGP these bulls were used to produce bull and use this material, and (3) funding the collection, especially for poultry. calves with the intention of incorporating cost of reconstituting a population. The Having a breed represented in the lost Y chromosomal materials back into cost challenge is significant as animals NAGP collection may not be sufficient the Holstein breed (Figure 3). In addition, must be raised to reproductive age and to reestablish the breed in the event of a the progeny are being used in efforts to multiple generations may be necessary to catastrophic loss in the industry. For each re-sequence the bovine Y chromosome reconstitute a specific population. breed, a “minimum collection goal” can and evaluate fertility aspects of bull se- be calculated as the minimum number of men at Pennsylvania State University and animals that would be needed to recon- nhancing the ational a commercial bull stud. E N stitute the breed in the event of a total Collection of Cryo- industry loss. Currently, only 47% of the Challenges preserved enetic breeds in the NAGP collection have met Use of the NAGP’s germplasm collec- G a minimum collection goal to reestablish tion by various stakeholder groups could Resources the breed (Figure 4). This situation places be expanded if research populations were many breeds at risk. curated with sufficient germplasm to Prioritizing Germplasm There are three main priorities for reconstitute populations on demand for Collection Efforts enhancement of the NAGP collection. specific projects. The plant community Gene banks have been established One main priority is to add new breeds to has had a long history of using germ- across the globe to protect livestock and the NAGP collection, even if the number plasm collections for such purposes. This poultry industries from loss of genetic of animals falls short of the minimum tradition, however, does not exist within diversity that could subsequently hinder collection goal for the breed. A second the livestock research community. Given their capacity to adapt to new environ- main priority is to complete the exist- the challenges within public institutions mental or market pressures. The U.S. ing breed collections, encompassing all in maintaining livestock populations, the livestock and poultry germplasm col- breeds available. Given that 70 to 80% opportunity exists to promote greater use lection at the NAGP encompasses 169 of the genetic variation of a species is

14 COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY 3000 Future Directions Livestock breeds have never been 2000 naturally occurring populations; they have been constructed by livestock producers 1000 to meet the needs they or society deem important. In conserving breeds and subpopulations it is noteworthy to recall that, 0 for centuries, breeds and subpopulations have been developed, recombined, and -1000 discarded as conditions dictated. Charles Darwin noted that livestock “breeders ha- -2000 Repository bitually speak of an animal’s organization Lower St. Dev. as something plastic which they model -3000 December 2014 Milk PTA Upper St. Dev. as they please” (Wood and Orel 2001). He also observed that the Berkshire pig Min -4000 of the 1780s was quite different from that Max of 1810 (Wilkinson et al. 2013), suggest- -5000 Bull Breed Avg. ing breed development has always been a dynamic process. -6000 When assessing breeds and their 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 conservation, two points are important to note: (1) breeds are a subpopulation of Figure 5. The Predicted Transmitting Ability (PTA) is a measure of the sire’s a species; and (2) as breeds evolve their genetic influence on the daughter’s ability to produce milk over time. genetic structure tends to become more In this graph, the PTA of semen from living bulls used for artificial similar due to genetic drift and selection. insemination (purple line) approximates the average PTA of semen from However, when viewed in total (i.e., a the NAGP repository (green line), demonstrating that the germplasm pooling of all breeds within a species) collection encompasses the variability of the in-situ population. The many species appear to have retained dashed lines represent one standard deviation above (blue) and below (red) the repository PTA mean; while the dotted lines represent the much genetic variation; for example, repository minimum (red dots) and maximum (blue dots) PTAs (from total genetic diversity of sheep and goat Blackburn, 2018). breeds near the center of domestication in Turkey and in the United States remain similar (Blackburn et al. 2011; Carvalho attributed to individual animal differ- The third main priority is to refresh et al. 2015; do Prado Paim et al. 2019). It ences (Blackburn et al. 2011; Lawson NAGP breed collections to ensure that is important to keep in mind that breeds et al. 2007; Peter et al. 2007), selection changes in allelic frequencies (which represent an array of allelic combinations of animals within a breed is critical to may have resulted from intense genetic in an easy-to-use form, and this may be establish a functional germplasm reposi- selection or widespread loss) have been their major value. Therefore, conservation tory. Guidelines for identifying animals captured. This need particularly applies at the breed level can be useful to incor- for germplasm acquisition have been to major breeds that are making genetic porate large segments of a genome into developed (FAO 2012) and are being changes more quickly than rare or minor another breed by combining two breeds. used in the United States. Animals are breeds. When germplasm collections Within this context, the following points selected based on genetic relationship encompass high-performing and low- provide a basis for further enhancement to other animals within the breed and performing animals, a substantial range of germplasm collections: collection, phenotypic information, and of genetic variation has been captured 1. Continue germplasm collection for computational or molecular genetic infor- (Figure 5). Moreover, it shows that a major and minor breeds of livestock, mation when available (Blackburn 2012; highly productive dairy bull collected in targeting current collection gaps; FAO 2012; Smith 1984;). In situations 1980 remained above breed average for 2. Increase collection of breeds with involving rare breeds, collecting samples approximately 15 years (until 1995; three contracting census numbers, including across geographic regions has and can to four generations). Similar trends have those not on the Livestock Conservan- be employed (Maiwashie and Blackburn been computed for pig breeds and sup- cy’s list of endangered breeds (e.g., 2004). Furthermore, by sampling across port the concept of refreshing the collec- Salers, Senepol, and Santa Gertrudis ecosystems a broader range of genetic tions frequently. Furthermore, genomic cattle; Columbia and Targhee sheep); diversity can be acquired, as shown by a approaches are accelerating genetic 3. Maintain an expanded germplasm fine structure genomic analysis of cattle change by shortening generation length; collection. Experience to date with (Blackburn et al. 2017) and pigs (Faria et therefore, refreshing the collection every U.S. plant and animal germplasm al. 2019). three generations would be prudent. collections suggests the larger the

COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY 15 germplasm collection, the more useful tings are needed, incorporating enhanced ably these techniques could be developed it is (particularly in view of advances methods of estrus synchronization, semen for cryopreservation of other agricultur- made with genomics). Germplasm thawing, and semen dosage. For these ally important mammalian species, but collection use for the Holstein Y chro- techniques to be successfully applied to research is needed to confirm that. For mosome study and by the American reconstitute breeds, such techniques must birds, the feasibility of transplanting Angus Association demonstrated the also work when semen quality or quantity avian gonads has been demonstrated need for and advantages of large, is compromised. For breeds with less for chickens, Japanese quail, and ducks comprehensive germplasm collec- than 200 animals (small population size), (Silversides and Liu 2012); however, the tions; research on cryopreservation of sperm methods have not been replicated suc- 4. Incorporate new tools such as obtained from the epididymis or seminif- cessfully by other groups (Liptoi et al. geographic information systems erous tubules of deceased animals would 2013) and have not been developed for into collection activities to support be beneficial. Avian semen can be cryo- turkeys. acquisition of alleles that can confer preserved (Silversides and Liu 2012), but Cryopreservation of preimplantation an ability to perform under various fertility from cryopreserved avian semen embryos is one strategy for conserv- environmental stressors (e.g., heat is highly variable. The ability of avian se- ing mammalian germplasm, and it is stress, heavy internal parasite load) men to withstand cryopreservation is not considered advantageous because each only species-specific but also line specific embryo represents a complete individual (Long et al. 2014; Silversides and Liu that needs only a surrogate uterus to be Targeted Cryopreservation 2012), and fertility from cryopreserved reconstituted; however, there is a greater Research for Species in Need semen for many avian species or lines is cost associated with the collection of em- Major differences exist in the effi- either not sufficiently high for cryopreser- bryos compared with semen (FAO 2012; cacy of cryopreservation procedures not vation or has not been investigated. Gandini et al. 2007). Cryopreserved em- only among the major domestic species Several reviews have been published bryos are used extensively by the cattle (cattle, swine, sheep, goats, chickens, and regarding the cryopreservation of oocytes industries and, although similar technolo- turkeys) but also among the types of cells from cattle, sheep, and pigs (Hwang and gies are available for other species, they or tissue (e.g., sperm, oocytes, gonads, or Hochi, 2014; Mullen and Fahy 2012; are not yet optimized for widespread embryos). Sperm are the most accessible Somfai, Kikuchi, and Nagai 2012; Zhou commercial use. gamete and remain the predominant cryo- and Li 2013). In general, the develop- preserved cell type; however, extreme mental competence of cryopreserved Priority Research Areas differences exist in the viability of frozen/ oocytes lags far behind that observed §§Spermatozoa thawed sperm not only among species but with either cryopreserved semen or úúCattle - Despite commercial success, also within animals of the same species. embryos. Oocytes are different than there is still tremendous opportunity Today the bovine is the only farm animal sperm or preimplantation embryos with to improve cryopreservation proce- species for which cryopreservation of respect to cryopreservation: the oocyte dures because approximately 50% of sperm is commercially routine. The suc- is a larger cell, its membrane does not frozen bovine sperm fail to survive cess of semen cryopreservation in sheep permit easy movement of water in and the freeze/thaw cycle. This is an im- and goats is lower than that of cattle, out of the cell, it possesses a compara- portant conservation issue when the but better than swine. Among the major tively high lipid content, and its internal number of living males of a particu- mammalian food animal species, the pig skeletal structure is more susceptible to lar breed or species is limited. poses the greatest challenge for semen chilling damage (Arav 2014). As is the úúSwine – Boar sperm are extremely cryopreservation. case with the male, it is feasible to collect sensitive to temperatures below Potential targets for improving gametes from recently deceased females. 15°C. One publication has shown cryopreservation technologies for all The ovaries contain tens of thousands of promising results with thawed boar mammalian livestock species include the immature oocytes at the time of puberty semen (73% pregnancy rate and prevention of (1) premature acrosome and, through the use of in vitro oocyte an average of 10.8 fetal piglets per reaction, (2) DNA fragmentation, and (3) maturation, in vitro fertilization, and in sow; Spencer et al. 2010); however, damage to the sperm plasma membrane vitro culture technologies, it is possible additional research is needed to con- (Holt and Penfold 2014). The biologi- to produce live offspring from a recently firm these findings. Use of thawed cal basis for male-to-male differences deceased female. This approach could boar sperm is further complicated by in post-thaw survival of cryopreserved prove highly valuable when females of a the relative inability to effectively sperm also needs to be better understood rare breed die unexpectedly. synchronize estrus in sows to allow to reduce the number of males that are Gonadal transplantation has been dem- precise timing of insemination rela- “discarded” due to poor post-thaw sperm onstrated for several mammalian species, tive to multiple ovulations. Research survival. Likewise, robust processes for including mice (Sztin et al. 1998), rats to develop effective timed artificial successful artificial insemination of swine (Dorsch et al. 2004), sheep (Gosden et al. insemination protocols is needed. and small ruminants using cryopreserved 1994), rabbits (Almodin et al. 2004), and úúSmall ruminants - The sperm plasma semen in a variety of production set- humans (Donnez et al. 2004). Presum- membrane of the ram is relatively

16 COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY fragile, and ovine sperm are sensi- that optimization of the techniques is Germplasm Repository tive to cold shock. Use of thawed species-specific. The production of ram semen is hindered due to the offspring from transplanted ovaries is Infrastructure: Information anatomical nature of the ewe’s straightforward because the normal re- System Development cervix which requires intrauterine productive apparatus is still being used In the broadest sense, collections of deposition of thawed semen to attain to produce an egg. However, the tes- animal genetic resources are an accu- acceptable pregnancy rates. Buck ticles cannot be replaced in their nor- mulation of information. Examples of semen contains an enzyme known as mal position, and the exudate from the this information on a specific animal phospholipase A that prevents use of transplant that contains sperm must be can include what the animal looked like egg-yolk based semen extenders un- harvested and used for insemination. (via photographs), where the animal was less the seminal plasma is removed; Techniques and timing of insemination raised, under what conditions the animal however, removal of seminal plasma have not been optimized for chickens was raised, how it performed for various thus far has proven detrimental to or quail and have not been investi- traits of interest, what was its genetic goat sperm. Research is needed to gated for other avian species, but they composition and pedigree, what type and develop methodologies to overcome are expected to be dependent on the how many samples are in the repository, ram sperm plasma membrane fragil- anatomical, physiological, and perhaps and how the samples were cryopreserved. ity and buck semen extenders that even behavioral reproductive specifici- Equally important is how accessible do not require removal of seminal ties of each species. this broader information is to an array plasm before freezing. §§Embryos and embryonic cells. Cryo- of users from research laboratories and úúPoultry - The morphology of avian preserved in vivo-derived embryos industry. sperm is very different from that of from ruminant livestock species (cat- Of the three components of gene bank- mammalian sperm and requires pro- tle, sheep, and goats) typically yield ing—genetic diversity, cryobiology, and tocols specific to birds. To date, the 60 to 75% pregnancy rates; however, information systems—information sys- ideal conditions for cryopreservation in vitro produced (IVP) embryos from tems are critically important and should are under development with some those same species (cryopreserved not be overlooked. For large and substan- recent advances (Thélie et al. 2019). with the same method) typically yield tial collections like the NAGP collection, Extremely rapid cooling (vitrifica- a pregnancy rate of only 25 to 50% information systems are indispensable tion) of sperm does not require the (Youngs 2011). With the exponential for users to view the collection and make same degree of pre-freezing cellular growth of IVP technology in cattle, decisions about which samples will serve dehydration and may be an effective these differences must be resolved. their research or reconstitution purposes. method of preserving the ability of For porcine embryos, the greatest Since 2005, the Animal-Genetic sperm to fertilize avian eggs (Liu research needs include development Resources Information Network (Animal- et al. 2013). Research is needed to of more field-practical methods for GRIN) has been the primary vehicle for identify genetic factors causing line embryo cryopreservation that do not storing information about animals in and individual differences in freez- require handling of embryos indi- the NAGP’s collection. A second ver- ing semen so that these limitations vidually during vitrification and more sion of the database, launched in 2016, may be overcome. robust/embryo tolerant methods of was a joint effort between Agrifoods §§Oocytes. The technology for cryo- warming. Although avian eggs and Canada, the Brazilian research organiza- preservation of oocytes has substan- embryos cannot be cryopreserved, the tion EMBRAPA, and the NAGP. The tial opportunity for improvement. potential cryopreservation of primor- unique feature of this updated version is To preserve fertility of oocytes after dial germ cells has seen some suc- that it allows all three countries to view cryopreservation, methods must be cess (Taylor et al. 2017) and warrants information about genetic resources in developed that will maintain structure further investigation. each country. and subsequent function of the internal §§Somatic cells. Skin cells can be easily Animal-GRIN (https://nrrc.ars. cellular structures (e.g., cortical gran- harvested, making them readily avail- usda.gov/A-GRIN/database_collabora- ules, microtubules, and mitochondria) able for cryopreservation. Technolo- tion_page_dev) is publicly accessible, during freezing and thawing. There is gies for reproduction of animals from dynamic, and searchable (Irwin, Wessel, also a need to investigate procedures somatic cells are now well established and Blackburn 2012). Descriptors in the to modify the pre-freeze cholesterol for cattle and horses, and to a lesser database encompass animal identification, and lipid content of oocytes and their extent for swine. Development of so- germplasm or tissue type, phenotypes, membranes to achieve higher survival matic cell nuclear transfer techniques genetic information, pedigree informa- rates. for all agricultural mammals, and tion, environment, and management. §§Gonadal material. Gonadal trans- for cell types other than fibroblasts, Tools have been developed for: donating plantation and immunosuppression could greatly facilitate conservation of and requesting germplasm or genotypes; procedures could be expected to be genetic resources. comparing genetic relationships between similar for a variety of avian spe- animals of the same breed; collection cies, but anatomical differences mean completeness for a breed or line; pedigree

COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY 17 trees and viewing changes in the collec- database where they can be made breed requires a complete package of tion. available for the community after the tools (e.g., synchronization of estrus, In addition to the features mentioned initial project has been completed to sperm cryopreservation, artificial above, the NAGP has developed a genom- capitalize on investments made in insemination techniques). Further ics component of Animal-GRIN that genotyping and to improve long term research on ART and cryopreserva- facilitates storage of genomic informa- archiving of data. tion methodologies are particularly tion pertaining to farm animal genetic needed for species where the success resources. Currently 2,083 animals from The Insurance Policy: of reconstitution from cryopreserved 41 breeds of cattle, sheep, goats, and pigs materials remains low. Each species have single-nucleotide polymorphism Long-term Operational needs techniques sufficiently robust genotypes in the genomic portion of the Continuity of Repositories to be applied to diverse future needs, database. Depending upon species, the Genetic resources are inextricably including the possibility that cryo- size of test panels per animal range from linked to food security and the livestock preserved materials may be needed 50,000 to 770,000 SNPs. As the animals sector’s economic vitality. For these in populations on farms with little or represented in the repository are geno- reasons, operation of a national gene no access to today’s most commonly typed, the information can be stored and bank and genetic conservation program used technologies and infrastructure. be made publicly accessible. The con- for livestock and poultry is a federal 2. While the NAGP collection is the struction of the genomics element is an responsibility as authorized by Congress. most comprehensive collection of ani- opportunity to leverage previous invest- It is recognized that such activities are for mal germplasm in the world, there are ments in genotyping for future research the public good given their contribution still gaps to be filled for many breeds. activities and industry utilization of to food security, economic growth, and In addition, there are opportunities to genomic phenotypic and environmental the opportunity to engage and address the expand existing breed collections to information. It also represents a unique concerns of livestock producers (espe- increase their use in genomic studies. structure where animal samples, phe- cially small-scale farmers). Due to the Importantly, cryopreserved samples notypes, and genotypes can be obtained long-term nature and the food security need to have a demonstrated capacity through a single information platform. aspects of gene banking, it is best ad- for some level of fertility, preferably However, continuing to add informa- dressed by the federal government (e.g., live offspring, otherwise, the samples tion for the animals in the collection will USDA-ARS). have limited value. require further investments in genotyping. The NAGP is entering its 20th year 3. Storage of all types of information Nevertheless, there are opportunities to thanks to the long-term support provided (phenotypes, genotypes, production incorporate functionality for future needs: by the ARS. It mirrors, but lags behind, systems, environments) in Animal- 1. An increased understanding and quan- the more than 50 years that the ARS has GRIN Version 2 is an important tification of the interactions between operated its plant germplasm system. mechanism for increasing the use genetics, environment and manage- Initial costs for collecting and holding and value of the collection which in ment are highly desired by the agricul- cryopreserved samples may be high, but turn supports operational continuity. tural community. Adding geographic costs are minimal when amortized over Further development of database ca- information systems capabilities to 50 years versus maintaining live popula- pacities to accommodate geographic Animal-GRIN will become an impor- tions (FAO 2012; Silversides, Blackburn, information systems, and addition tant tool in this research (Blackburn et and Purdy. 2012; Smith 1984). Relatively of tools to facilitate accessibility and al. 2017). low and static funding levels for the data analysis are critical areas of 2. Photographic images of animals with NAGP program have created a challenge enhancement. samples in the database are being for sustained collection. Funds are needed acquired. Adding the potential capa- to allow collection of samples in the field bility of phenotyping animals (e.g., or for owners to transport their animals to Conclusions body weight) using these photographs, the NAGP laboratory for collection. Re- Humanity depends on a tiny fraction as that technology advances, would sources are also needed for validation of of global animal species that have been significantly increase the information viability of samples already collected and domesticated for production of food. It is about animals in the collection, espe- the development of workable cryopreser- readily apparent that we cannot continue cially for breeds where phenotypes are vation methodologies. to rely solely on a few breeds to provide not routinely measured. the genetic diversity that is integral to 3. Accessibility would be enhanced Strengthening the System sustaining food production for future by development of apps for mobile There are opportunities to strengthen generations, as we cannot predict what platforms, bringing the Animal-GRIN and expand the NAGP’s capacity and traits will become important in the face information into the field. support long-term continuity of the proof weather extremes, niche markets, and 4. The USDA-supported genotyping gram. These include the following: consumer-driven demands (Rexroad et al. results and, where feasible tissue sam- 1. Research to improve ART is sorely 2019). Failure to conserve animal genetic ples should be added to the genomics needed because reconstitution of a resources may cripple our capacity to

18 COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY identify traits of value for the future. Dis- tions, universities, and small/local whenever possible, for the potential to appearance of breeds is likely to induce farming operations, and should be led generate offspring (not just fertility) losses of entire genetic combinations, by USDA-ARS in partnership with and use data to inform the minimum and it is these combinations that stand to State Departments of Agriculture, collection score to provide the best serve as ready-made matches for breeders land-grant universities, the Livestock protection of genetic resources for fu- to use. By losing breeds we make finding Conservancy and the USDA-National ture use. There are no formal mecha- potential solutions to future production Agricultural Statistics Service. nisms in place for this type of testing, demands much more difficult, and recent 2. Engage private sector philanthropic yet it is an important component of history indicates that predicting future de- awareness and expand funding op- the success of ex situ conservation. mand is problematic. Conserving breeds portunities across the federal govern- 5. Expand investment in permanent saves these options and keeping them in ment for research to develop the most staffing and programmatic support of the agricultural landscape is a reminder effective cryopreservation strategies the NAGP to increase the procure- that these options exist. The most ef- for domesticated livestock and poul- ment, management and utilization fective conservation of these resources try species, including species-specific of genetic resources. More staff are ideally involves living animals as well as protocols for routine use with a high needed with technical expertise in the cryopreserved reservoirs of their genetic success rate for recovering the desired areas of cryopreservation, genetics, material. On-farm conservation and cryo- population. Improvement of cryo- assisted reproductive technology and preservation of animal germplasm are preservation efficacy for species with information technology; additional complementary strategies for conserva- low success should receive particular funding also should be provided to tion of genetic diversity in livestock and emphasis. Funding priorities should the NAGP and universities to sup- poultry. Each strategy mitigates a differ- be directed toward populations with port census and outreach activities, as ent array of specific risks to agrobiodiver- contracting census numbers, ex- well as evaluation of cryopreserved sity, and one strategy should not proceed treme phenotypes, proven research materials. These measures will help to at the expense of the other; concurrent or industrial benefit and/or potential ensure the long-term operation of the efforts are needed. An increased scope commercial value. Interagency work- NAGP and its critical role in protect- of intensified sampling, cataloging and ing groups (USDA-NIFA; USDA- ing genetic resources for the future. evaluation of the existing gene pools in ARS; National Science Foundation; livestock and poultry, concomitant with National Institutes of Health; US Fish more resources to fully develop cryo- and Wildlife Service) should lead this Literature Cited Adelson, D. L., Z. Qu; J. M. Raison, and S. L. Lim. preservation methodologies and discover effort and partner with the private 2014. Bovine genomics. Pp. 130–132. In D.J. novel, more efficient methodologies, are sector. Garrick and A. Ruvinsky (eds.) The Genet- paramount to meet the expected increases 3. Support the conservation of in situ ics of Cattle, 2nd Ed., CABI, Wallingford, Oxfordshire, United Kingdom. in human population in the face of un- populations, particularly for those Agriculture and Agri-Food Canada. 2007. Canadian known—but certain—global challenges. species such as poultry in which Animal Genetic Resources Program. http:// cryopreservation methods are sub- www.agr.gc.ca/eng/?id=1297780434818. (Ac- cessed June 3, 2009.) optimal, through funding opportuni- Almodin C.G., V. C. Minguetti-Câmara, H. Meister, Task Force ties related to maintaining important J. O. Ferreira, R. L. Franco, A. A. Cavalcante, genetic stocks for research, small M. R. Radaelli, A. S. Bahls, A. F. Moron, and ecommendations C. G. Murta. 2004. Recovery of fertility after R farms, urban development and/or grafting of cryopreserved germinative tissue 1. Commit resources (capital, person- sustainable agricultural practices. in female rabbits following radiotherapy. Hum nel, facility, information technology) Specific funds, not tied to a particular Reprod 19 (6): 1287–93. Ansah, G. A. and R. B. Buckland. 1983. Eight gen- necessary to characterize the genetic research project, should be available erations of selection for duration of fertility of diversity of existing livestock and for in situ conservation. If unique frozen-thawed semen in the chicken. Poult Sci poultry populations in the United livestock or poultry lines housed by 62 (8): 1529–38. Ansah, G. A., J. C. Segura and, R. B. Buckland. States, including both phenotypic and universities are to be discontinued, 1985. Semen production, sperm quality, and genotypic data, and enhance a cloud- such lines designated for elimination their heritabilities as influenced by selection based platform to house the data that must be offered to other institutions or for fertility of frozen-thawed semen in the chicken. Poult Sci 64 (9): 1801–3. is publicly accessible and interfaces individuals. Furthermore, guidelines Ansah, G. and R. Buckland. 1982. Genetic variation with the USDA-NAGP, Animal-Ge- should be developed that require ap- in fowl semen cholesterol and phospholipid netic Resources Information Network, propriate genetic material, preferably levels and the relationship of these lipids with fertility of frozen-thawed and fresh semen. and the Livestock Conservancy germplasm, gonads or embryos, to be Poult Sci 61:623–637. Program Priority listings. Expand archived at the USDA-NAGP prior Aslam, M. L, J. W. M. Bastiaansen, M. G. Elferink, the information network to accom- to de-population of the live animals. H.-J. Megens, R. P. M. A Crooijmans, L. A. Blomberg, R. C Fleischer, C. P. Van Tassell, modate environmental descriptors Acceptance of these guidelines could T. S. Sonstegard, S. G. Schroeder, M. A. in a geographic information system be made a requirement of receiving M Groenen, and J. A. Long. 2012. Whole format. This effort will require large- federal or state funds. genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo). scale coordination of breed associa- 4. Evaluate cryopreserved germplasm, BMC Genomics 13:391

COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY 19 Arav, A. 2014. Cryopreservation of oocytes and zin, J. Besnard, D. Gourichon, G. Coquerelle, 2164-15-625. embryos. Theriogenology 81 (1): 96–102 doi: P. Rault, and M. Tixier-Boichard. 2007. Se- The Bovine Genome Sequencing and Analysis 10.1016/j.theriogenology.2013.09.011. men cryopreservation for ex situ management Consortium, C. G. Elsik, R. L. Tellam, and Association of Zoos and Aquariums. 2015. Species of genetic diversity in chicken: Creation of the K. C. Worley. 2009. The Genome Sequence Survival Plan® Programs. https://www.aza. French avian cryobank. Poult Sci 86:555–564. of Taurine Cattle: A Window io Ruminant org/species-survival-plan-program/ (June 1, Bryan, M. 2014. American Guinea Hogs – Pedigree Biology And Evolution. Science.324 (5926): 2015) Analysis and Breeding Recommendations. Ac- 522–8. doi: 10.1126/science.1169588. Aviagen. 2019. Aviagen. http://en.aviagen.com. cessed at: http://www.livestockconservancy. Erickson, B. H. 1966. Development and senescence (Accessed 3 June 2019.) org/index.php/heritage/internal/pig-breeding. of the postnatal bovine ovary. J Anim Sci 25 Bacon, L. D., D. W. Salter, J. V. Motta. ��L. B. Crit- Caetano, A. R., R. K. Johnson, J. J. Ford, and D. (3): 800–805. tenden and F. X. Ogasawara. 1986. Cryo- Pomp. 2004. Microarray profiling for differen- European Regional Focal Point for Animal Genetic preservation of chicken semen of inbred or tial gene expression in ovaries and ovarian fol- Resources (ERF). 2014. SUBSIBREED - specialized strains. Poult Sci 65:1965–1971 licles of pigs selected for increased ovulation Overview and Assessment of Support Mea- Bakst, M. R. 1993. The anatomy of reproduction in rate. Genetics 168 (3): 1529–1537. sures for Endangered Livestock Breeds. 262 birds, with emphasis on poultry. Pp. 15–28. Capper, J.L., R.A. Cady, and D.E. Bauman. 2009. pp. Drago Kompan, Marija Klopčič, Elzbieta In R. J. Etches and A. M. Verrinder Gibbons The environmental impact of dairy produc- Martyniuk (eds.). European Regional Focal (eds). Manipulation of the Avian Genome. tion: 1944 compared with 2007. J Anim Sci 87 Point for Animal Genetic Resources. Bonn, CRC Press, Boca Raton, Florida. (6): 2160–2167 doi:10.2527/jas.2009-1781. Germany. Benson, J. D., E. J. Woods, E. M. Walters, and J. K. Carvalho, G. M. C., S. R. Paiva, A. M. Araújo, A. Fang, L., G. Sahana, G. Su, Ying Yu, S. Zhang, M. Critser. 2012. The cryobiology of spermato- Mariante, and H. D. Blackburn. 2015. Genetic S. Lund and P. Sørensen. 2017. Integrating zoa. Theriogenology 78:1682–1699. structure of goat breeds from Brazil and the Sequence-based GWAS and RNA-Seq Pro- Bentley L.G., G.A. Ansah, and R. B. Buckland. United States: Implications for conservation vides Novel Insights into the Genetic Basis of 1984. Seminal plasma proteins of a line of and breeding programs. J Anim Sci 93:4629– Mastitis and Milk Production in Dairy Cattle. chickens selected for fertility of frozen-thawed 4636. Sci Rep 7:45560, doi:10.1038/srep45560. semen and the control line. Poult Sci 63: Chang, S., J. R. Dunn, M. Heidari, L. F. Lee, J. Fang, M., G. Larson, H. S. Ribiero, N. Li, and 1444–5. Song, C. W. Ernst, Z. Ding, L. D. Bacon, and L. Andersson. 2009. Contrasting mode of Bilton, R.J. and N. W. Moore. 1976. In vitro culture, H. Zhang. 2010. Genetics and vaccine effi -- evolution at a coat color locus in wild and storage, and transfer of goat embryos. Aust J cacy: Host genetic variation affecting Marek‘s domestic pigs. PLoS Genet 5 (1): e1000341, Bio Sci 29:125–129. disease vaccine efficacy in White Leghorn doi:10.1371/journal.pgen.1000341 Bispo, C. A. S., G. Pugliesi, P. Galvão, M. T. chickens. Poult Sci 89 (10): 2083–2091. Faria, D. A., C. Wilson, S. Paiva. and H. D. Black- Rodrigues, P. G. Ker, B. Filgueiras, and G. R. Comizzoli, P. and D. E. Wildt. 2014. Mammalian burn. 2019. Assessing Sus scrofa diversity Carvalho. 2011. Effect of low and high egg fertility preservation through cryobiology: among continental United States, and Pacific yolk concentrations in the semen extender for value of classical comparative studies and the islands populations using molecular markers goat semen cryopreservation. Small Rumi- need for new preservation options. Reprod from a gene banks collection Sci Rep 9:3173. nant Res 100:54–58. doi:10.1016/j.smallr- Fertil Dev 26:91–98. Farin P. W. and C. E. Farin. 1995. Transfer of umres.2011.05.003. Council for Agricultural Science and Technology bovine embryos produced in vivo or in vitro: Bixby, D. E., C. J. Christman, C. J. Ehrmann, and (CAST). 1984. Animal germplasm preserva- Survival and fetal development. Biol Reprod D. P. Sponenberg. 1994. Taking Stock: The tion and utilization in agriculture. Task Force 52 (3): 676–82. North American Livestock Census. The Live- Report 101. CAST, Ames, Iowa. Flowers, W. L. 2015. Evolution and adoption of ar- stock Conservancy, Pittsboro, North Carolina. Cseh, S., V. Faigl, and G.S. Amiridis. 2012. Semen tificial insemination (A.I.) in the U.S.J Anim Blackburn, H. D. 2006. The National Animal Germ- processing and artificial insemination in health Sci (abstract). plasm Program: challenges and opportuni- management of small ruminants. Anim Repro Food and Agriculture Organization of the United ties for poultry genetic resources. Poult Sci Sci 130 (3/4): 187–192. doi:10.1016/j.anire- Nations (FAO). 2007. Global plan of action 85:210–215. prosci.2012.01.014. for animal genetic resources and the Inter- Blackburn, H. D. 2012. Genetic selection and Danchin-Burge, C., S. J. Hiemstra, and H. Black- laken Declaration. Commission on the Genetic conservation of genetic diversity. Reprod Dom burn. 2011. Ex situ conservation of Holstein- Resources for Food and Agriculture. FAO, Anim 47 (Suppl. 4): 249–254. Friesian cattle: Comparing the Dutch, French, Rome, Italy Blackburn. H. Biobanking genetic material for ag- and US germplasm collections. J Dairy Sci Food and Agriculture Organization of the United ricultural animal species. Annu Rev of Animal 94:4100–4108. Nations (FAO). 2012 Cryopreservation of Biosciences 6:6982. https://doi.org/10.1146/ Dairy Cattle Reproduction Council. Implications of animal genetic resources. FAO Animal Pro- annurev-animal-030117-014603. inbreeding in the dairy industry. http://www. duction and Health Guidelines No. 12. FAO, Blackburn, H. D., F. G. Silversides, and P. H. Purdy. dcrcouncil.org/wp-content/uploads/2017/04/ Rome, Italy. 2009. Inseminating fresh or cryopreserved Implications-of-inbreeding-in-the-dairy-indus- Food and Agriculture Organization of the United semen from maximum efficiency: Implica- try.pdf (Accessed August 2019) Nations (FAO). 2015. The Second Report on tions for gene banks and industry. Poult Sci Dinnyes, A., J. Liu, and T. L. Nedambale. 2007. the State of the World’s Genetic Resources 88:2184–2191. Novel gamete storage. Reprod Fertil Dev for Food and Agriculture. Commission on the Blackburn, H. D., Y. Toishibekov, M. Toishibekov, 19:719–731. Genetic Resources for Food and Agricul- C. S. Welsh, S. F. Spiller, M. Brown, and S. Dohner, Janet V., 2001. The Encyclopedia of His- ture. FAO, Rome, Italy. http://www.fao. R. Paiva. 2011. Genetic diversity of Ovis aries toric and Endangered Livestock and Poultry org/3/a-i4787e.pdf populations near domestication centers and in Breeds. Yale University Press, New Haven, Food and Agriculture Organization of the United the New World. Genetica 139:1169–1178. Connecticut. Nations. 2019. FAOSTAT Production data: Blackburn, H.D., Plante, Y., Rohrer, G., Welch, Donnez J., M. M. Dolmans, D. Demylle, P. Jadoul, live animals, livestock primary, and livestock E.W., and Paiva, S.R. 2014. Impact of genetic C. Pirard, J. Squifflet, B. Martinez-Madrid, processed. http://www.fao.org/faostat/en/#data drift on access and benefit sharing under the and A. van Langendonckt. 2004. Livebirth af- (Accessed 7 June 2019) Nagoya Protocol: The case of the Meishan ter orthotopic transplantation of cryopreserved Gandini, G., F. Pizzi, A. Stella, and P.J. Boettcher. pig. J Anim Sci 92 (4): 1405–1411. ovarian tissue. Lancet 362 (9443): 1405–10. 2007.The costs of breed reconstruction from Blackburn, H. D., B. Krehbiel, S. A. Ericsson, C. Dorsch M., D. Wedekind, K. Kamino, and H. J. He- cryopreserved material in mammalian live- Wilson, A. R. Caetano, S. R. Paiva. 2017. drich.2004. Orthotopic transplantation of rat stock species. Genet Sel Evol 39 (4): 465–479. A fine structure genetic analysis evaluating ovaries as a tool for strain rescue. Lab Anim Gard, J. 2015. Control of embryo-borne pathogens. ecoregional adaptability of a Bos taurus breed 38 (3): 307–12. Pp. 749–757. In R. M. Hopper (ed.). Bovine (Hereford). PLoS One 12 (5): e0176474. Du, X., B. Servin, J. E. Womack, J. Cao, M. Yu, Y. Reproduction, John Wiley & Sons, Ames, doi:10.1371/journal.pone.0176474 Dong, W. Wang, and S. Zhao. 2014. An update Iowa. Blesbois, E. 2007. Current status in avian semen of the goat genome assembly using dense Gollin, D., E. Van Dusen, and H. Blackburn. 2009. cryopreservation. World Poult Sci J 63:213– radiation hybrid maps allows detailed analysis Animal genetic resource trade flows: Eco- 222. of evolutionary rearrangements in Bovidae. nomic assessment. Livest Sci 120:248–255. Blesbois, E., F. Seigneurin, I. Grasseau, C. Limou- BMC Genomics 15:625 doi:10.1186/1471- Gosden R. G., D. T. Baird, J. C. Wade, and R.

20 COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY Webb. 1994. Restoration of fertility to genetic analysis of relatedness between com- of gonadal tissue transfer in various chicken oophorectomized sheep by ovarian autografts mercial and heritage turkeys (Meleagris gal- breeds in the poultry gene conservation. Anim stored at -196 degrees C. Hum Reprod 9 (4): lopavo). Poult Sci 86 (1): 46–9. Reprod Sci 141 (1-2): 86–9. doi: 10.1016/j. 597–603. Kishida, K. M. Sakase, K. Minami, M M. Arai, R. anireprosci.2013.06.016. Groenen, M. A., A L. Archibald, H. Uenishi, C. K. Syoji, N. Kohama, T. Akiyama, A. Oka, H. Liu, J., K. M. Cheng, and F. G. Silversides. 2013a. Tuggle, Y. Takeuchi, M. F. Rothschild, C. Ro- Harayama, and M. Fukushima 2015. Effects of Fundamental principles of cryobiology and gel-Gaillard, C. Park, D. Milan, H. J. Megens, acrosomal conditions of frozen-thawed sper- application to conservation of avian species. S. Li, D. M. Larkin, H. Kim, L. A. Frantz, M. matozoa on the results of artificial insemination Avian Biol Res 6:187–197. Caccamo, H. Ahn, B. L. Aken, A. Anselmo, in Japanese Black cattle. J Reprod Dev 61 (6): Liu, J., K. M. Cheng, and F. G. Silversides. 2013b. C. Anthon, L. Auvil, B. Badaoui, C. W. Beat- 519–524. doi:10.1262/jrd.2015-073. Production of live offspring from testicular tis- tie, C. Bendixen, D. Berman, F. Blecha, J. Kobayashi, S., M. Takei, M. Kano, M. Tomita, and sue cryopreserved by vitrification procedures Blomberg, L. Bolund, M. Bosse, S. Botti, Z. S. P. Leibo. 1998. Piglets produced by transfer in Japanese quail (Coturnix japonica). Biol Bujie, et al.: 2012. Analyses of pig genomes of vitrified porcine embryos after stepwise dilu- Reprod 88:1–6. provide insight into porcine demography and tion of cryoprotectants. Cryobiology 36:20–31. Liu, J., K. M. Cheng, and F. G. Silversides. 2013c. evolution. Nature 491 (7424): 393–398. Kraeling, R. R. and S. K. Webel. 2015. Current strat- A model for cryobanking female germplasm in Hansen, P. J. 2014. Current and future assisted re- egies for reproductive management of gilts and Japanese quail (Coturnix japonica). Poult Sci productive technologies for mammalian farm sows in North America. J Anim Sci Biotechno 92:2772–2775. animals. In C. G. Lamb and N. DiLorenzo, 6:3 http://www.jasbsci.com/content/6/1/3. Liu, J., K. M. Cheng, and F. G. Silversides. 2015. (eds) Current and Future Reproductive Lake, P. E. and J. M. Stewart. 1978. Preservation Recovery of fertility from adult ovarian tissue Technologies and World Food Production. Ad- of fowl semen in liquid nitrogen-an improved transplanted into week-old Japanese quail vances in Experimental Medicine and Biology method. Brit Poult Sci 19:187–194. chicks. Reprod Fert Develop 27:281–284. 752:1–22 doi:10.1007/978-1-4614-8887-3_1 Larkin, D.M., Kim H, Frantz LA, Caccamo M, Ahn Liu, J., Y. Song, K. M. Cheng, and F. G. Silversides. Hayashi, S., K. Kobayashi, J. Mizuno, K. Saitoh, H, Aken BL, Anselmo A, Anthon C, Auvil L, 2010. Production of donor-derived offspring and S. Hirano. 1989. Birth of piglets from Badaoui B, Beattie CW, Bendixen C, Berman from cryopreserved ovarian tissue in Japanese frozen embryos. Vet Rec 125:43–44. D, Blecha F, Blomberg J, Bolund L, Bosse quail (Coturnix japonica). Biol Reprod Hillier, L. W. and the International Chicken Genome M, Botti S, Bujie Z, et al.: 2012. Analyses 83:15–19. Sequencing Consortium. 2004. Sequence and of pig genomes provide insight into porcine Liu, J., M. C. Robertson, K. M. Cheng, and F. G. comparative analysis of the chicken genome demography and evolution. Nature 491 (7424): Silversides. 2013. Chicks with chimeric plum- provide unique perspectives on vertebrate 393–398. age coloration produced by ovarian transplan- evolution. Nature 432:695–716. Larson, G. T. Cucchi, M. Fujita, E. Matisoo-Smith, tation in chickens. Poult Sci 92:1073–1076. Holt, W. V., and L. M. Penfold. 2014. Fundamental J. Robins, A. Anderson, B. Rolett, M. Spriggs, Long, J. A. 2006. Avian semen cryopreservation: and practical aspects of semen cryopreserva- Gaynor Dolman, T. Kim, N. Thi Dieu Thuy, What are the biological challenges? Poult Sci tion. Pp. 76–99. In P. J. Chenoweth and S. P. E. Randi, M. Doherty, R. A. Due, R. Bollt, T. 85:232–236. Lorton (eds.) Animal Andrology: Theories and Djubiantono, B. Griffin, M. Intoh, E. Keane, Long, J. A., P. H. Purdy, K. Zuidberg, S.-J. Hiem- Applications, CAB International, Wallingford, P. Kirch, K. Li, M. Morwood, L. M. Pedriña, stra, S. G. Velleman, and H. Woelders. 2014. Oxfordshire, United Kingdom P. J. Piper, R. J. Rabett, P. Shooter, G. Van den Cryopreservation of turkey semen: Effect of Hwang, I. S. and S. Hochi. 2014. Recent Bergh, E. West, S. Wickler, J. Yuan, A. Cooper, breeding line and freezing method on post- progress in cryopreservation of bovine and K.Dobney. 2007. Phylogeny and ancient thaw sperm quality, fertilization, and hatching. oocytes. BioMed Res Int 2014:570647 DNA of Sus provides insights into neolithic ex- Cryobiology 68:371–378. doi:10.1155/2014/570647. pansion in Island Southeast Asia and Oceania. Mackay, R. 2014. The Atlas of Endangered Species. Ibeka, C., H. D. Blackburn, S. R. Paiva, and A. S. Proc Natl Acad Sci USA 104:4834–4839. 3rd Ed. Routledge, New York, New York, 128 Mariante. 2014. Merging Molecular Data for Larson, G., D. R. Piperno, R. G. Allaby, M. D. pp. Evaluating Cross Country Genetic Diversity Purugganan, L. Andersson, M. Arroyo-Kalin, Maiwashe, A. N. and H. D. Blackburn. 2004. of Pigs. In 10th World Congress on Genetics L. Barton, C. Climer Vigueira, T. Denham, Genetic diversity in and conservation strategy Applied to Livestock Production, Vancouver, K. Dobney, A. N. Doust, P. Gepts, M. T. P. considerations for Navajo Churro sheep. J British Columbia, Canada, 17–22 Aug. 2014. Gilbert, K. J. Gremillion, L. Lucas, L. Lukens, Anim Sci 82:2900–2905. https://asas.org/docs/default-source/wcgalp- F. B. Marshall, K. M. Olsen, J. C. Pires, P. J. Marshall, F. B., K. Dobney, T. Denham, and J. posters/442_paper_9203_manuscript_1397_0. Richerson, R. Rubio de Casas, O. I. Sanjur, M. M. Capriles. 2014. Evaluating the roles of pdf?sfvrsn=2 G. Thomas, and D. Q. Fuller. 2014. Current directed breeding and gene flow in animal do- Irwin, G., L. Wessel, and H. Blackburn. 2012. perspectives and the future of domestication mestication. Proc Natl Acad Sci USA 111 (17): The Animal Genetic Resource Information studies. Nat’l Acad Sci 111:6139-6146. 6153–6158, doi:10.1073/pnas.1312984110. Network (AnimalGRIN) Database: A database van de Lavoir, M. C., C. Mather-Love, P. Leighton, Massip A., P. van der Zwalmen, B. Scheffen, and F. design and implementation case. J Informa- J. H. Diamond, B. S. Heyer, R. Roberts, L. Ectors. 1986. Pregnancies following transfer tion Systems Education 23 (1): 19–27. Zhu, P. Winters-Digiacintoa, A. Kerchner, T. of cattle embryos preserved by vitrification. Jackiw, R. N, G. Mandil, and H. A. Hager. 2015. Gessaro, S. Swanberg, M. E. Delany, and R. J. Cryo-Letters 7:270–3. A framework to guide the conservation of Etches. 2006. High-grade transgenic somatic Massip, A., S. P. Leibo, and E. Blesbois. 2004. species hybrids based on ethical and ecologi- chimeras from chicken embryonic stem cells. Cryobiolgoy of gametes and the breeding of cal considerations. Conserv Biol (in press) Mech Devel 123:31–41. domestic animals. Pp. 371–392. In B. J. Fuller, doi:10.1111/cobi.12526. Lawson H., L. J., K. Byrne, F. Santucci, S. N. Lane, and E. E. Benson (eds). Life in the Jiang, Y., X. M. Xie, W. Chen; et al. 2014. The Townsend, M. Taylor, M. W. Bruford, and G. Frozen State, CRC Press, New York. sheep genome illuminates biology of the M. Hewitt. 2007. Genetic structure of European Mazur, P. 1970. Cryobiology: the freezing of biolog- rumen and lipid metabolism. Science 344 sheep breeds. Heredity 99:620–631. ical systems. Science 168:939–949. (6188): 1168–1173. DOI: 10.1126/sci- Leavitt, Charles T. 1933. Attempts to improve cattle McCann, B. E., M. J. Malek, R. A. Newman, B. S. ence.1252806. breeds in the United States, 1790–1860. Agr Schmit, S. R. Swafford, R. A. Sweitzer, and Johnson, R. K., M. K. Nielsen, and D. S. Casey. History 7:51–67. R. B. Simmons. 2014. Mitochondrial diversity 1999. Responses in ovulation rate, embryonal Leibo, S. P. and N. M. Loskutoff. 1993. Cryobiology supports multiple origins for invasive pigs. J survival, and litter traits in swine to 14 genera- of in vitro derived bovine embryos. Therio- Wildlife Manage 78:202–213. tions of selection to increase litter size. J Anim genology 39:81–94. Mitra, A., J. Luo, H. Zhang, K. Cui, K. Zhao, and Sci 77:541–557. Lemmer, G. F. 1947. The spread of improved cattle J. Song. 2012. Marek’s disease virus infection Kalk, B. 1994. Case studies of livestock extinction. through the eastern United States to 1850. Agr induces widespread differential chromatin In D. E. Bixby, C. J. Christman, C. J. Ehrman, History 21: 79–93. marks in inbred chicken line. BMC Genomics and D. P. Sponenberg (eds.). Taking Stock, The Li, J. J. and L. Z. Lu. 2010. Recent progress on tech- 13:557. North American Livestock Census. The Live- nologies and applications of transgenic poultry. Muir, W. M., G. K. S. Wong, Y. Zhang, J. Wang, M. stock Conservancy, Pittsboro, North Carolina. Afric J Biotech 9:3481–3488. A. M. Groenen, R. P. M. A. Crooijmans, H. J. Kamara, D., K. B. Gyenai, T. Geng, H. Hammade, Liptoi K., G. Horvath, J. Gal, E. Varadi, and J. Barna. Megens, H. Zhang, R. Okimoto, A. Vereijken, and E. J. Smith. Microsatellite marker-based 2013. Preliminary results of the application A. Jungerius, G. A. A. Albers, C. Taylor

COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY 21 Lawley, M. E. Delany, S. MacEachern, and of genetics stocks in the USA and Canada. population of Large White pigs: evidence of H. H. Cheng. 2008. Genome-wide assessment Avian Poult Biol Rev 12:1–102. haplotypes affecting meat quality. Genet Sel of worldwide chicken SNP genetic diversity Pisenti, J. M., M. E. Delany, R. L. Taylor, Jr., U. Evol 46:12 http://www.gsejournal.org/con- indicates significant absence of rare alleles in K. Abbott, H. Abplanalp, J. A. Arthur, M. tent/46/1/12. commercial breeds. Proc Natl Acad Sci USA R. Bakst, C. Baxter-Jones, J. J. Bitgood, F. Sathe, S., and C. F. Shipley. 2014. Applied androl- 105 (45): 17312–17317. Bradley, K. M. Cheng, R. R. Dietert, J. B. ogy in sheep, goats and selected cervids. Pp. Mullen, S. F. and G. M. Fahy. 2012. A chronologic Dodgson, A. Donoghue, A. Emsley, R. Etches, 226–253. In P.J. Chenoweth and S. P. Lorton, review of mature oocyte vitrification research R. R. Frahm, A. A. Grunder, R. J. Gerrits, P. (eds.s) Animal Andrology: Theories and Ap- in cattle, pigs, and sheep. Theriogenology 78 F. Goetinck, S. J. Lamont, G. R. Martin, P. plications, CAB International, Wallingford, (8): 1709–1719. E. McGuire, G. P. Moberg, L. J. Pierro, C. Oxfordshire, United Kingdom. Naito, M. 2003. Cryopreservation of avian germline O. Qualset, M. Qureshi, F. Schultz and B. W. Schiewe, M. C., W. F. Rall, L. D. Stuart, and D. E. cells and subsequent production of viable Wilson. 1999. Avian genetic resources at risk: Wildt. 1990. In situ straw dilution of ovine offspring. J Poult Sci 40:1–12. An assessment and proposal for conservation embryos cryopreserved by conventional freez- Nandi S., J. Whyte, L. Taylor, A. Sherman, V. Nair, of genetics stocks in the USA and Canada. ing or vitrification.Theriogenology 33:321 P. Kaiser, and MJ McGrew. 2016. Cryopreser- Report No. 20. University of California Divi- (abstract). vation of specialized chicken lines using sion of Agriculture and Natural Resources, Searchinger, T., C. Hanson, J. Ranganathan, B. cultured primordial germ cells. Poult Sci 95 Genetic Resources Conservation Program, Lipinski, R. Waite, R. Winterbottom, A. (8):1905–11. doi: 10.3382/ps/pew133. Davis, California Dinshaw, and R. Heimlich. 2014. Creating a National Association of Animal Breeders. 2015. Polge, C. 1951. Functional survival of fowl sper- sustainable food future: A menu of solutions NAAB electronic resource guide. http://www. matozoa after freezing at -79C. Nature 16 (7): to sustainably feed more than 9 billion people naab-css.org/sales/table35.html (2 June 2015). 949–950. by 2050. World Resources Report 2013–14: National Research Council (NRC). 1993. Managing Polge, C., A. U. Smith, and A. S. Parkes. 1949. Interim Findings. World Resources Institute, Global Genetic Resources: Livestock. National Revival of spermatozoa after vitrification Washington D.C., 144 pp. Academy Press, Washington, D.C. and dehydration at low temperatures. Nature Senger, P. L. 2012. Pathways to Pregnancy and Paiva, S., C. McManus, and H. Blackburn. 2014. 164:666–667. Parturition, 3rd Ed., Current Conceptions, Conservation of Animal Genetic Resources do Prado Paim, T., D. A. Faria, El Hamidi Hay, C. Redmond, Oregon. p. 219. (AnGR): The Next Decade. In Proceedings of McManus, M. R. Lanari, L. Chaverri Esquiv- Sexton, T. J. 1980. Optimal rates for cooling the 10th World Congress of Genetics Applied el, M. I.l Cascante, E. J. Alfaro, A. Mendez, chicken semen from +5 to -196C. Poult Sci to Livestock Production, 18-24 August 2014, O. Faco, K. de Moraes Silva, C. Mezzadra, A. 59:2765–2770. Vancouver, British Columbia, Canada Mariante, S. Rezende Paiva & H. D. Black- Shaffner, C. S., E. W. Henderson, and C. G. Card. Pelletier N., M. Ibarburu, and H. Xin. 2014. Com��- burn. 2019. New world goat populations are a 1941. Viability of spermatozoa of the chicken parison of the environmental footprint of the genetically diverse reservoir for future use. Sci under various environmental conditions. Poult egg industry in the United States in 1960 and Rep 9. doi:10.1038/s41598-019-38812-3. Sci 20:259–265. 2010. Poult Sci 93 (2): 241–255. doi:10.3382/ Ratliff, E. Taming the Wild. National Geographic Silber, S. J. 2012. Ovary cryopreservation and trans- ps.2013-03390. March 2011:35–59. plantation for fertility preservation. Mol Hum Parks, J. Processing and handling bull semen for Rauch, A. 2013. Cryopreservation of bovine semen Reprod 18:59–67. artificial insemination – don’t add insult to in egg yolk based extenders. M.S. Thesis, Silversides, F. G. and J. Liu. 2012. Novel techniques injury. www.ansci.cornell.edu/pdfs/bullsemen. University of Saskatchewan, Saskatchewan. for preserving genetic diversity in poultry pdf (2 June 2015). Rexroad, C., J. Vallet, L. K. Matukumalli, J. Reecy, germplasm. CAB Rev 7:1–8. Paiva, S. R, C. M. McManus, and H. Blackburn. D. Bickhart, H. Blackburn, M. Boggess, H. Silversides, F. G., P. H. Purdy, and H. D. Black- 2016. Conservation of animal genetic Cheng, A. Clutter, N. Cockett, C. Ernst, J. burn. 2012. Comparative costs of programs to resources—A new tact. Livestock Science. E. Fulton, J. Liu, J. Lunney, H. Neibergs, conserve chicken genetic variation based on 193: 32–38. C. Purcell, T. P. L. Smith, T. Sonstegard, J. maintaining living populations or storing cryo- Papadopoulos S, D. Rizos, P. Duffy, M. Wade, K. Taylor, B. Telugu, A. V. Eenennaam, C. P. V. preserved material. Brit Poult Sci 53:599–607. Quinn, M. P. Boland, and P. Lonergan. 2002. Tassell, and K. Wells. 2019. Genome to Phe- Silversides, F. G., M. C. Robertson, and J. Liu. Embryo survival and recipient pregnancy rates nome: Improving Animal Health, Production, 2013a. Growth of subcutaneous testicular after transfer of fresh or vitrified, in vivo or in and Well-Being - A New USDA Blueprint for transplants. Poult Sci 92:1916–1920. vitro produced ovine blastocysts. Anim Reprod Animal Genome Research 2018-2027. Front Silversides, F. G. M. C. Robertson, and J. Liu. Sci 74 (1-2): 35–44. Genet 10:327. 2013b. Cryoconservation of avian gonads in Perry, G. 2014. 2013 statistics of embryo collec- Roeber F, A. R. Jex, R. B. Gasser. 2013. Impact of Canada. Poult Sci 92:2613–2617. tion and transfer in domestic farm animals. gastrointestinal parasitic nematodes of sheep, Silversides, F. G., Y. Song, R. Renema, B. R. Embryo Transfer Newsletter 32 (4): 14–26. and the role of advanced molecular tools for Rathgeber, and H. L. Classen. 2008. Cryo- Peter, C., M. Bruford, T. Perez, S. Dalamitra, G. exploring epidemiology and drug resistance preservation of avian germplasm kept in Hewitt, G. Erhardt, and the ECONOGENE - an Australian perspective. Parasite Vector. Canadian research institutions. Can J Anim Sci Consortium. 2007. Genetic diversity and sub- 6:153. doi:10.1186/1756-3305-6-153. 88:577–580. division of 57 European and Middle-Eastern Salamon, S. and W. M. C. Maxwell. 1995a. Frozen Simon, C. M. 2006. Southern Pineywoods Cattle. J sheep breeds. Anim Genet 38:37–44. storage of ram semen. I. Processing, freezing, Alabama Folklife Assoc 9:36–41. Peter, C., M. Buford, T. Perez, S. Dalamitra, G. thawing and fertility after cervical insemina- Smith, C. 1984. Estimated costs of genetic conser- Hewitt, G. Erhart, and the ECONGENE tion. Anim Reprod Sci 37 (3/4): 185–249. vation of farm animals. In: Animal Genetic Consortium. 2007. Genetic diversity and sub- Salamon, S., and W. M. C. Maxwell. 1995b. Frozen Resources Conservation and Management, division of 57 European and Middle- Eastern storage of ram semen. II. Causes of low fertil- Data Banks and Training. FAO Animal Pro- sheep breeds. Animal Genetics 38:37–44. ity after cervical insemination and methods duction and Health Paper 44/1. Rome, Italy: Petitte, J. N. 2006. Avian germplasm preservation: of improvement. Anim Reprod Sci 38 (1/2): Food and Agriculture Organization of the embryonic stem cells or primordial germ cells. 1–36. United Nations. Poult Sci 85:237–242. Salamon, S., L. Gillan, G. Evans, and W. M. C. Somfai, T., K. Kikuchi, and T. Nagai. 2012. Factors Pisenti, J. M., M. E. Delany, R. L. Taylor, Jr., U. Maxwell. 2004. Fertility of ram semen after affecting cryopreservation of porcine oocytes. K. Abbott, H. Abplanalp, J. A. Arthur, M. 35 years of frozen storage. Pp. 476. Volume 2. J Reprod Dev 58 (1): 17–24. R. Bakst, C. Baxter-Jones, J. J. Bitgood, F. In Proceedings of the 15th International Con- Song, Y. and F. G. Silversides. 2006. The technique Bradley, K. M. Cheng, R. R. Dietert, J. B. gress on Animal Reproduction, Porto Seguro, of orthotopic ovarian transplantation in the Dodgson, A. Donoghue, A. Emsley, R. Etches, Brazil, August 8-12. chicken. Poult Sci 85:1104–1106. R. R. Frahm, A. A. Grunder, R. J. Gerrits, P. Sanchez, M.-P., T. Tribout, N. Iannuccelli, M.l Song, Y. and F. G. Silversides. 2007a. Offspring F. Goetinck, S. J. Lamont, G. R. Martin, P. Bouffaud, B. Servin, A. Tenghe, P. Dehais, N. produced from orthotopic transplantation of E. McGuire, G. P. Moberg, L. J. Pierro, C. Muller, M. P. Del Schneider, M.-J. Mercat, C. chicken ovaries. Poult Sci 86:107–111. O. Qualset, M. Qureshi, F. Schultz and B. W. Rogel-Gaillard, D. Milan, J.-P. Bidanel, and Song, Y. and F. G. Silversides, 2007b. Heterotopic Wilson. 2001. Avian genetic resources at risk: H. Gilbert. 2014. A genome-wide association transplantation of testes in newly hatched An assessment and proposal for conservation study of production traits in a commercial chickens and subsequent production of

22 COUNCIL FOR AGRICULTURAL SCIENCE AND TECHNOLOGY offspring via intramagnal insemination. Biol Torres, P. A., B. J. Zeng, B. F. Porter, J. Alroy, Suppl.): E177–E184. Reprod 76:598–603. F. Horak, J. Horak, and E. H. Kolodny. Weitzman, M. L. 1993. What to preserve? An appli- Song, Y. and F. G. Silversides. 2008a. Transplanta- 2010. Tay-Sachs disease in Jacob sheep. Mol cation of diversity theory to crane conservation of ovaries in Japanese quail (Coturnix Genet Metab 101 (4): 357–63. doi:10.1016/j. tion. Quarterly Journal of Economics 108 (1): japonica). Anim Reprod Sci 105:430–7. ymgme.2010.08.006. 157–183. Song, Y. and F. G. Silversides. 2008b. Long- Tselutin, K., L. Narubina, T. Mavrodina, and B. Tur. Welsh, C. S., T. S. Stewart, C. Schwab, and H. D. term production of donor-derived offspring 1995. Cryopreservation of poultry semen. Brit Blackburn. 2010. Pedigree analysis of 5 swine from chicken ovarian transplants. Poult Sci Poult Sci 36:805–811. breeds in the United States and the implica- 87:1818–1822. U.S. Bureau of the Census. 1952. Changes in tions for genetic conservation. J Anim Sci Song, Y., K. M. Cheng, M. C. Robertson, and F. G. Agriculture, 1900 to 1950. United States 88:1610–1618. Silversides. 2012. Production of donor-derived Census of Agriculture: 1950. Vol. V, Special Wilkinson, S., Z. Lu, H. Megens, A. Archibald, C. offspring after ovarian transplantation between Reports, Part 6, Agriculture 1950 – A Graphic Haley, I. Jackson, M. Groenen, R. Crooijmans, Muscovy (Cairina moschata) and Pekin (Anas Summary. U.S. Government Printing Office, R. Ogden, and P. Wiener. 2013. Signatures of platyrhynchos) ducks. Poult Sci 91:197–200. Washington, D.C, 1952:69–102. diversifying selection in European pig breeds. Spencer, K. W., P. H. Purdy, H. D. Blackburn, S. United States Department of Agriculture National PLOS Genet 9:4:e1003453. F. Spiller, T. S. Stewart, and R. V. Knox. Genetic Resources Advisory Council (USDA- Willadsen, S. M., C. Polge, and L. E. A. Rowson, 2010. Effect of number of motile, frozen- NGRAC) 2018. Strengthening Strategic and R. M. Moor. 1974. Preservation of sheep thawed boar sperm and number of fixed-time Genetic Resources for Livestock, Poultry and embryos in liquid nitrogen. Cryobiology inseminations on fertility in estrous-synchro- Aquatic Species in the United States. USDA, 11:560 (abstract). nized gilts. Ani Reprod Sci 121:259–266. Washington, D. C. Wilmut, I., and L. E. A. Rowson. 1973. Experiments doi:10.1016/j.anireprosci.2010.07.002. United States Department of Agriculture (USDA). on the low-temperature preservation of cow Splan, R. K. and D. P. Sponenberg. (2004) Charac- 2019a. Animal Genetic Resources https://nrrc. embryos. Vet Rec 92:686–690. terization and conservation of the American ars.usda.gov/A-GRIN/database_collabora- Windsor, D. P. 1997. Variation between ejaculates Milking Devon. Anim Genet Resour 34:11-16. tion_page_dev in the fertility of frozen ram semen used for Sponenberg, D. P. and C. Taylor. 2009. Navajo- United States Department of Agriculture (USDA). cervical insemination of Merino ewes. Anim Churro Sheep and Wool in the USA. Anim 2019b. National Animal Germplasm Program; Reprod Sci 47 (1-2): 21–9. Genet Resour 45:99–106. http://nrrc.ars.usda.gov/A-GRIN/main_web- Wishart, G. J. 1985. Quantitation of the fertilising Sponenberg, D. P., J. Beranger, and A. Martin. page/ars?record_source=US) [sic] ability of fresh compared with frozen 2014. An Introduction to Heritage Breeds Vajta, G., and Z. P. Nagy. 2006. Are programmable and thawed fowl spermatozoa. Brit Poult Sci Saving and Raising Rare-Breed Livestock and freezers still needed in the embryo labora- 26:375–380 Poultry. The Livestock Conservancy. Storey tory? Review on vitrification.Reproductive Woelders, H., C. A. Zuidberg, and S. J. Hiemstra. Publishing, North Adams, MA. 240 pp. BioMedicine Online 12:779–96. 2006. Animal genetic resources conserva- Sponenberg, D. P., and T. A. Olson. 1992. Colonial Viana, J. 2018. 2017 statistics of embryo production in The Netherlands and Europe: poultry Spanish cattle in the USA: History and Present tion and transfer in domestic farm animals. perspective. Poult Sci 85:216–222. Status. Arch Zootec 41:401–414. Embryo Technology Newsletter 36 (4): 8–25. Wood, R. J. and V. Orel. 2001. Genetic prehistory Sztein J., H. Sweet, J. Farley, and L. Mobraaten L. Vishwanath, R. 2003. Artificial insemination: in selective breeding: a prelude to Mendel. 1998. Cryopreservation and orthotopic trans- the state of the art. Theriogenology 59 (2): Oxford University Press U.K. 323 pp. plantation of mouse ovaries: new approach in 571–584 Youngs, C. R. 2011. Cryopreservation of preim- gamete banking. Biol Reprod 58 (4): 1071–1. Vishwanath, R. 2014. Pp. 79–85. SexedULTRA™- plantation embryos of cattle, sheep, and goats. Tait-Burkard C., A. Doeschl-Wilson, M. J. McGrew, raising the fertility bar of sex sorted semen. J Vis Exp 54 http://www.jove.com/details. A. L. Archibald, H. M. Sang, R. D. Houston, In 25th Technical Conference on Artificial php?id=2764 doi: 10.3791/2764. C. B. Whitelaw, and M. Watson. 2018. Live- Insemination and Reproduction, Green Bay, Youngs, C. R., S. P. Leibo, and R. A. Godke. stock 2.0-genome editing for fitter, healthier Wisconsin, September 25–26 September 2004. 2010. Embryo cryopreservation in domestic and more productive farmed animals. Genome Wade, C. M, E. Giulotto, S. Sigurdsson1, M. mammalian livestock species. CAB Reviews: Biology 19:204 https://doi.org/10.1186/ Zoli, S. Gnerre, F. Imsland, T. L. Lear, D. L. Perspectives in Agriculture, Veterinary Sci- s13059-018-1583-1. Adelson, E. Bailey, R. R. Bellone, H. Blöcker, ence, Nutrition and Natural Resources 5 (60), Taylor, Jr., R. L., 2010. Letter to the Editor – Genet- O. Distl, R. C. Edgar, M. Garber, T. Leeb, E. 11 pp., doi:10.1079/PAVSNNR20105060. ics Stocks. Poult Sci 89:3–4. Mauceli, J. N. MacLeod, M. C. T. Penedo, J. Youngs, C. R., T. J. Knight, S. M. Batt, and D. C. Taylor, L., D. Carlson, S. Nandi, A. Sherman, S. M. Raison, T. Sharpe, J. Vogel, L. Andersson, Beitz. 1994. Phospholipid, cholesterol, triacyl- Fahrenkreg and M. J. McGrew. 2017. Ef- D. F. Antczak, T. Biagi, M. M. Binns, B. P. glycerol, and fatty acid composition of porcine ficient TALEN-mediated gene targeting of Chowdhary8, S. J. Coleman, G. Della Valle, blastocysts. Theriogenology 41:343 (abstract). chicken primordial germ calls. Development S. Fryc, G. Guérin, T. Hasegawa, E. W. Hill, Yue, X.-P., Chad Dechow, and Wan-Sheng Liu. 144:928–934. J. Jurka, A. Kiialainen, G. Lindgren, J. Liu, 2015. A limited number of Y chromosome Taylor, R. L., Jr. 2009. The future of poultry science E. Magnani, J. R. Mickelson, J. Murray, S. G. lineages present in North American Holsteins. research: Things I think I think. Poult Sci Nergadze, R. Onofrio, S. Pedroni, M. F. Piras, J Dairy Sci 98:1–8. 88:1334–1338. T. Raudsepp, M. Rocchi, K. H. Røed, O. A. Yuswiati, E., and W. Holtz. 1990. Work in progress: The Livestock Conservancy. 2019. The Livestock Ryder, S. Searle, L. Skow, J. E. Swinburne, successful transfer of vitrified goat embryos. Conservatory. http://www.livestockconser- A. C. Syvänen, T. Tozaki, S. J. Valberg, M. Theriogenology 34:629–32. vancy.org/ (Accessed 3 June 2009.) Vaudin, J. R. White, and M. C. Zody, Broad Zhou, G. B. and N. Li. 2013. Bovine oocytes cryo- The Livestock Conservatory. 2019. The Livestock Institute Genome Sequencing Platform, Broad injury and how to improve their development Conservancy’s Conservation Priority List. Institute Whole Genome Assembly Team1, E. following cryopreservation. Anim Biotechnol https://livestockconservancy.org/index.php/ S. Lander, and K. Lindblad-Toh. 2009. Ge- 24(2):94–106. heritage/internal/conservation-priority-list. nome Sequence, Comparative Analysis, and Zimin, A. V., A. L. Delcher, L. Florea, D. R. Kelley, (Accessed 3 June 2019.) Population Genetics of the Domestic Horse. M. C. Schatz, D. Puiu, F. Hanrahan, G. Pertea, Thélie, A. A. Bailliard, F. Seigneurin, T.Zerjal, M. Science 326:865–867. C. P. Van Tassell, T. S. Sonstegard, G. Mar- Tixier-Boichard, E. Blesbois. 2019. Chicken Wang, Y., Z. Xiao, L. Li, W. Fan, and S. Li. 2008. çais, M. Roberts, P. Subramanian, J. A. Yorke semen cryopreservation and use for the Novel needle immersed vitrification: A practi- and S. L. Salzberg. 2009. A whole-genome restoration of rare genetic resources. Poult Sci cal and convenient method with potential assembly of the domestic cow, Bos Taurus. 98:447–455. advantages in mouse and human ovarian tissue Genome Biol 10:R42, doi:10.1186/gb-2009- Torres, L. and T. R. Tiersch TR. 2018. Addressing cryopreservation. Hum Reprod 23:2256–2265. 10-4-r42. Reproducibility in Cryopreservation, And Wei, H. 2013. The IVF program at Trans Ova Zuckerman, S. 1951. The number of oocytes in Considerations Necessary For Commercializa- Genetics. P. 383. In American Embryo Trans- the mature ovary. Recent Prog Horm Res tion And Community Development In Support fer Association Annual Conference. Reno, 6:63–109. Of Genetic Resources Of Aquatic Species. Nevada. 9–12 October 2013. J of the World Aquaculture Society 49(4): Weigel, K. A. 2001. Controlling inbreeding in 644–663. https://doi.org/10.1111/jwas.12541. modern breeding programs. J Dairy Sci 84 (E.

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Citation: Council for Agricultural Science and Technology (CAST). 2019. Protecting Food Animal Gene Pools for Future Generations—A paper in the series on The Need for Agricultural Innovation to Sustainably Feed the World by 2050. Issue Paper 65. CAST, Ames, Iowa.

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