DOCSLIB.ORG

Livestock Genomics Comes of Age Michel Georges and Leif Anclersson 2

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Livestock Genomics Comes of Age Michel Georges and Leif Anclersson 2 Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Livestock Genomics Comes of Age Michel Georges and Leif Anclersson 2 1Department of Genetics, Faculty of Veterinary Medicine, University of Liege, 4000-Liege, Belgium; 2Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala Biomedical Centre, 24 Uppsala, Sweden It is estimated that man 1 first domesticated ani- as by an undefined number of polygenes or quan- mals as early as 10,000 BP. Since then, farmers titative trait loci (QTL). Their heritabilities typi- have been unwittingly manipulating livestock cally range from less than 5% to over 50%. Ani- genes by selective breeding. This early genetic en- mal geneticists therefore have had a long-stand- gineering generated a wealth of variation for a ing interest in the genetics of complex inherit- myriad of traits in the different livestock species. ance, the relevance of which is being recognized The dramatic size difference between the Shire increasingly in medical genetics as well. and Shetland pony or the plethora of dog breeds The implementation of breeding schemes are just two illustrations of the diversification ob- that proved so efficient would have been impos- tained by artificial selection. The resulting carica- sible without the organization of extensive phe- ture of naturally occurring variation has played a notypic record keeping. Particularly illustrative major role in Darwin's formalization of his in this respect is the collection of individual re- theory of the evolution of species by natural se- cords (milk yield and composition, type traits, lection. The first chapter of his acclaimed The Ori- health traits, etc.) that is performed on a monthly gin of Species (1859) is devoted to "Variation Un- basis for millions of cows as part of dairy herd der Domestication." improvement programs in the United States, In the beginning of this century, the coales- Western Europe, and several other parts of the cence of biometrics and Mendelian genetics pio- world. Likewise, breeding companies carefully neered by R.A. Fisher, J.B.S. Haldane, and S. monitor their pig and poultry breeding stock for Wright led to the foundation of quantitative ge- a whole range of phenotypic measurements. netics, which in turn allowed development of the Given the tradition of eagerly adopting mod- theory of animal breeding that is still imple- ern technology that might increase genetic re- mented to this date. This biometrical era of ani- sponse as well as the availability of unique mate- mal genetics has led to spectacular increases in rial, it is quite surprising that animal geneticists productivity in all major livestock species during have been reluctant to invest in genomics when the second half of this century. As an example, in compared with plant breeders or human medical the United States milk yield has increased from geneticists. This is likely due in part to the real- approximately 4500 kg per cow per year to more ization that the majority of economically impor- than 6800 kg in less than 20 years (Pearson et al. tant traits in livestock are typical multifactorial 1990). traits and are therefore the most difficult ones to It is noteworthy that the vast majority of pro- tackle using genomic strategies. Moreover, given duction traits undergoing selection are typical the spectacular genetic progress achieved by quantitative traits, that is, they exhibit a continu- means of conventional breeding programs, some ous rather than a discrete distribution and they skepticism has prevailed regarding the cost- are influenced by environmental factors as well effectiveness of biotechnology in livestock pro- duction. It is only during the last 5 years that we have witnessed a growing interest of animal ge- neticists in genomics. This has undoubtedly been 3Corresponding author. catalyzed by the successes of the Human Genome E-MAIL michel@stat'fmv'ulg'ac'be; FAX 32-41-66-41-22. Initiative. This review will summarize the state of 6:907-921 9 by Cold Spring Harbor Laboratory Press ISSN 1054-9803/96 $5.00 GENOME RESEARCH ~ 907 Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press GEORGES AND ANDERSSON the art in livestock genomics, while emphasizing tion provided by linked markers is considered some specificities of animal studies, and will jointly. Moreover, animal geneticists may have identify some of the major challenges for the the option to arrange matings between breeds future. and even subspecies in a manner reminiscent of the Mus musculus domesticus x Mus spretus or cas- Current Status of Genome Analysis taneus crosses, enhancing the information con- tent at the marker as much as trait loci (see be- Primary Microsateilite-basedMaps Are Being low). Nevertheless, continued marker develop- Generated for Host Livestock Species ment seems advisable in most domestic species to The description of microsatellites as an abundant ensure adequate information content across the source of highly polymorphic, well-dispersed, respective genomes. and conveniently typed markers has boosted the Sequence conservation has proven to be suf- generation of primary maps in livestock species ficiently high between cattle and sheep to allow (for review, see Beattie 1994). Individual as well for -50% of primer sequences developed in one as internationally coordinated efforts have lead species to work in the other (Moore et al. 1991; A. to the generation of a number of linkage maps in Crawford and N. Cockett, pers. comm.). This per- the different species: cattle (Barendse et al. 1994; centage is considerably higher than what has Bishop et al. 1994; Ma et al. 1996), pig (Ellegren been observed for the mouse and rat, which are et al. 1994; Rohrer et al. 1994; Archibald et al. thought to be as closely related evolutionarily. As 1995; Marklund et al. 1996; Rohrer et al. 1996), expected, this cross-species use of microsatellite sheep (Crawford et al. 1995), and poultry (Bum- markers has proven inefficient for more distantly stead and Palyga 1992; Levin et al. 1994; Cheng related domestic species despite the occasional et al. 1996; Crooijmans et al. 1996) in particular. demonstration of remarkable conservation of mi- When several parallel efforts have been under- crosatellite position (Moore et al. 1991; Ellegren taken in a given species, the number of common et al. 1993; Sun and Kirkpatrick 1996). markers fortunately has usually been sufficiently Most of the linkage groups have been an- high to allow for efficient cross-referencing (Eg- chored and oriented to specific chromosomes in gen and Fries 1995; Marklund et al. 1996). At this cattle and pig using fluorescence in situ hybrid- point, the available maps number -1100 markers ization (FISH) mapping. In poultry, establishing for cattle and pig (C. Beattie, pers. comm.; Rohrer connections between the linkage and cytogenetic et al. 1996), 700 for sheep (A.M. Crawford, pers. maps is complicated by nonidentifiable mini- comm.), and 450 for poultry (M.A.M. Groenen chromosomes, which might represent as much as and N. Bumstead, pets. comm.). These maps pro- 30% of the genome. vide very adequate genome coverage, especially These mapping data are being compiled in a for cattle and pig, where the average between number of data bases conveniently accessed via marker interval is now -2.5-5 cM. the internet (e.g., http://www.ri.bbsrc.ac.uk/ Artificial breeding schemes often result in a genome_mapping.html; http://dirk.invermay. reduction in effective population size. Assuming cri.nz; http://locus.jouy.inra.fr/cgi-bin/bovmap/ selective neutrality of microsatellite alleles, one Bovmap/intro.pl; http://sol.marc.usda.gov/marc/ could therefore expect reduced allele numbers html/genel.html; http://probe.nalusda.gov: and heterozygosity when compared with the hu- 8000/index.html). man. In addition, because fewer markers have Thus, with the available genetic maps, we been developed in animal species, less selection have reached the point where the marker re- has taken place based on information content in sources are no longer the limiting factor when putting together marker panels for genome scans. attempting to map trait loci by exploiting within- As an example, the battery of markers used to family linkage disequilibrium. It can be argued, scan the bovine genome in a search for QTL af- however, that in a number of instances the map- fecting milk production had an average hetero- ping method of choice would be based on linkage zygosity of 56% in the studied Holstein-Friesian disequilibrium existing across the population population (Georges et al. 1995), compared with (such as in identity-by-descent mapping meth- heterozygosities typically >70% in human micro- ods). Efficient implementation of such strategies satellite-based studies. Part of the segregation in- will require further development of a substantial formation can be recovered by performing mul- number of additional markers in the different tipoint linkage analyses in which the informa- livestock species. 908 ~ GENOME RESEARCH Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press LIVESTOCK GENOMICS Comparative Mapping Confirms the Remarkable cessfully applied to the bovine and porcine Conservation of Synteny Amongst karyotypes, allowing for the majority of chromo- Mammalian Species somes to be sorted as pure fractions (Schmitz et al. 1992, 1995; Langford et al. 1993; Yerle et al. Although microsatellites undoubtedly form the 1993). These advances should facilitate the devel- scaffold of all livestock linkage maps, a sufficient opment of chromosome-specific libraries and number of evolutionarily conserved Type I mark- markers in the near future. Likewise, a number of ers (O'Brien 1991; O'Brien et al. 1993) are inter- successful applications of chromosome or chro- spersed in these maps to confirm the extensive mosome-band microdissection for the develop- conservation of synteny among distantly related ment of region-specific markers are being re- mammals that was predicted from early mapping ported (Schmutz et al.
Load more

Recommended publications
  • The Genome Sequence of Taurine Cattle: a Window to Ruminant Biology and Evolution the Bovine Genome Sequencing and Analysis Consortium, Christine G
    REPORTS second model, the two main conditions were para- different issues. In particular, Bhatt and Camerer found 34. W. Seeley et al., J. Neurosci. 27, 2349 (2007). metrically modulated by the two categories, higher insula and ACC activity when comparing choices to 35. J. Downar, A. Crawley, D. Mikulis, K. Davis, Nat. Neurosci. first-order beliefs in dominance-solvable games. 3, 277 (2000). respectively (SOM, S5.1). The activation of the 3. We are considering here coordination without visual or 36. J. Downar, A. Crawley, D. Mikulis, K. Davis, J. Neurophysiol. precuneus was higher for hard dominance-solvable other contact. Nonhuman primates seem able to 87, 615 (2002). games than for easy ones (Fig. 4A and table S10). coordinate their actions (simultaneously pulling on bars 37. K. Davis et al., J. Neurosci. 25, 8402 (2005). The activation of the insula was higher for the to obtain food) when they are in visual contact (45). 38. K. Taylor, D. Seminowicz, K. Davis, Hum. Brain Mapp., 4. J. Mehta, C. Starmer, R. Sugden, Am. Econ. Rev. 84, 658 in press; published online 15 December 2008; highly focal coordination games than for less fo- (1994). 10.1002/hbm.20705. cal ones (Fig. 4B and table S11). Previous studies 5. T. Schelling, J. Conflict Resolution 2, 203 (1958), p. 211. 39. See (47). The NCI can be interpreted as the probability also found that precuneus activity increased when 6. D. Kahneman, Am. Psychol. 58, 697 (2003). that two randomly chosen individuals make the same the number of planned moves increased (40, 41). 7. K.
    [Show full text]
  • Bovinehd Genotyping Beadchip More Than 777,000 Snps That Deliver the Densest Coverage Available for the Bovine Genome
    Data Sheet: Agrigenomics BovineHD Genotyping BeadChip More than 777,000 SNPs that deliver the densest coverage available for the bovine genome. of the markers are mapped to the UMD3 bovine genome assembly,3 Highlights which include coverage of autosomal, mitochondrial, and sex-linked • Comprehensive and Uniform Coverage (X/Y) SNPs. Uniform genomic coverage, with an average gap size Evenly distributed polymorphic SNPs with a median < 3 kb of 3.43 kb and a median gap size of 2.68 kb, provides excellent gap spacing SNP density to power robust genome-association studies and CNV detection in cattle (Figure 2).4 The BovineHD BeadChip is the most • Unrivaled Call Rates and Accuracy comprehensive tool in the Illumina portfolio of bovine products. > 99% average call rates and > 99.9% reproducibility • Simple Workflow More than 93% of SNPs featured on the BovineHD BeadChip target PCR- and ligation-free protocol novel SNP loci that were discovered by sequencing > 20 individual breeds of economically important beef and dairy cattle (Table 3). Using • High-Throughput Format Illumina next-generation paired-end sequencing technology, > 90% Up to 8 samples can be interrogated in parallel of the included SNPs were identified from over 180× coverage of the mappable Btt genome. Prioritization for SNP selection included the following parameters: 1) breed-specific expected MAF, 2) Infinium HD Introduction design score, 3) unmapped contig coverage, 4) breed weighting, 5) breed‐specific spacing, and 6) and position based on region of The BovineHD BeadChip (Figure 1) is the most comprehensive genome (ie, exon, repetitive, segmental duplication/CNV). genome-wide genotyping array, providing superior power to interrogate genetic variation across any breed of beef and dairy cattle.
    [Show full text]
  • Bovine Genomic Sequencing Initiative Cattle-Izing the Human Genome
    Bovine Genomic Sequencing Initiative Cattle-izing the Human Genome Richard Gibbs and George Weinstock, Baylor College of Medicine, Human Genome Sequencing Center; Steven Kappes, USDA-ARS, US Meat Animal Research Center; Lawrence Schook, University of Illinois; Loren Skow and James Womack, Texas A&M University Rationale and Objective. Completion of the human genome sequence provides the starting point for understanding the genetic complexity of man and how genetic variation contributes to diverse phenotypes and disease. It is clear that model organisms have played an invaluable role in capturing this information. It is also noted that additional species must be sequenced to resolve the genetic complexity of human evolution and to effectively extrapolate genetic information from comparative (veterinary) medicine to human medicine. The selection of animals representing evolutionary clades distinct from primates or rodents provides considerable power for analysis of the human genomic sequence. The domesticated, eutherian mammals that have co-evolved with man (cows, pigs, dogs and cats), represent taxa with diverse selected phenotypes and have in place strong scientific and veterinary medical communities to support and utilize genome sequence information. Thus, this “white paper” provides support for sequencing the bovine genome (6X coverage) to identify new genes and novel regulatory elements in humans, mice and rats. The bovine genome will serve as a reference non-primate, non- rodent, eutherian genome. The bovine genome is uniquely positioned for genomic sequencing because of the advanced stage of the reagents. An international bovine BAC map with a 15X coverage will be fingerprinted and all fingerprinted clones end-sequenced by February 2003. A minimum tilling path of BAC clones will be sequenced with a whole genome shotgun sequencing effort using random insert libraries.
    [Show full text]
  • Unlocking the Bovine Genome
    See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/24358846 Unlocking the Bovine Genome Article in BMC Genomics · May 2009 DOI: 10.1186/1471-2164-10-193 · Source: PubMed CITATIONS READS 48 142 6 authors, including: Ross L Tellam Danielle Lemay The Commonwealth Scientific and Industrial Research Organisation University of California, Davis 247 PUBLICATIONS 7,657 CITATIONS 148 PUBLICATIONS 3,445 CITATIONS SEE PROFILE SEE PROFILE Kim Carlyle Worley Baylor College of Medicine 411 PUBLICATIONS 86,467 CITATIONS SEE PROFILE Some of the authors of this publication are also working on these related projects: Vaccines against ticks and myiasis flies View project Milk and innate immunity View project All content following this page was uploaded by Danielle Lemay on 13 May 2014. The user has requested enhancement of the downloaded file. BMC Genomics BioMed Central Commentary Open Access Unlocking the bovine genome Ross L Tellam*1, Danielle G Lemay2, Curtis P Van Tassell3, Harris A Lewin4, Kim C Worley5 and Christine G Elsik6 Address: 1CSIRO Livestock Industries, 306 Carmody Rd, St Lucia 4067, QLD, Australia, 2Department of Food Science and Technology, University of California, One Shields Ave, Davis, CA 95616, USA, 3Bovine Functional Genomics laboratory, USDA/ARS, BARC-East, Beltsville, MD, 20705, USA, 4Institute for Genomic Biology and Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, 5Human Genome Sequencing Center, Department of Molecular
    [Show full text]
  • Livestock 2.0 – Genome Editing for Fitter, Healthier, and More Productive Farmed Animals Christine Tait-Burkard, Andrea Doeschl-Wilson, Mike J
    Tait-Burkard et al. Genome Biology (2018) 19:204 https://doi.org/10.1186/s13059-018-1583-1 REVIEW Open Access Livestock 2.0 – genome editing for fitter, healthier, and more productive farmed animals Christine Tait-Burkard, Andrea Doeschl-Wilson, Mike J. McGrew, Alan L. Archibald, Helen M. Sang, Ross D. Houston, C. Bruce Whitelaw and Mick Watson* increased affluence in low- and middle-income countries Abstract (LMICs). Terrestrial and aquatic animal production in The human population is growing, and as a result we these countries is heavily reliant on small-holder need to produce more food whilst reducing the farmers, who collectively play a crucial role in global ani- impact of farming on the environment. Selective mal protein production. For example, of the 570 million breeding and genomic selection have had a farms worldwide, over 1 in 4 (150 million) have at least transformational impact on livestock productivity, and one milk-producing animal [4], and farms with fewer now transgenic and genome-editing technologies than 100 animals account for over 99.7% of global dairy offer exciting opportunities for the production of fitter, production [5]. In LMICs, livestock accounts for over healthier and more-productive livestock. Here, we 60% of agricultural gross domestic product (GDP) [6], review recent progress in the application of genome and farmed animals provide livelihoods for over 1 billion editing to farmed animal species and discuss the people globally [7]. While increasing reliance on potential impact on our ability to produce food. plant-based diets is often raised as a potential solution to food insecurity and as part of the effort required to address climate change [8], omission of animal protein Introduction from human diets risks nutritional deficiencies and mal- There are an estimated 7.6 billion humans on the planet, nutrition [9].
    [Show full text]
  • Diversity and Evolution of 11 Innate Immune Genes in Bos Taurus Taurus and Bos Taurus Indicus Cattle
    Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle Christopher M. Seaburya,1, Paul M. Seaburyb, Jared E. Deckerc, Robert D. Schnabelc, Jeremy F. Taylorc, and James E. Womacka,1 aDepartment of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843-4467; bElanTech, Inc., Greenbelt, MD 20770; and cDivision of Animal Sciences, University of Missouri, Columbia MO 65211-5300 Contributed by James E. Womack, November 11, 2009 (sent for review September 29, 2009) The Toll-like receptor (TLR) and peptidoglycan recognition protein family members are primarily expressed by antigen-presenting 1(PGLYRP1) genes play key roles in the innate immune systems of cells, such as macrophages or dendritic cells, and previous in- mammals. While the TLRs recognize a variety of invading patho- vestigations have elucidated the ligand specificities for most gens and induce innate immune responses, PGLYRP1 is directly mammalian TLRs, with six gene family members (TLR1, TLR2, microbicidal. We used custom allele-specific assays to genotype TLR4, TLR5, TLR6, TLR9) known to recognize microbial and validate 220 diallelic variants, including 54 nonsynonymous (bacteria, fungi, protozoa) and synthetic ligands, and five gene SNPs in 11 bovine innate immune genes (TLR1-TLR10, PGLYRP1) family members (TLR3, TLR4, TLR7–TLR9) known to recog- for 37 cattle breeds. Bayesian haplotype reconstructions and me- nize viral components (1, 11, 15). TLR10 is the only functional dian joining networks revealed haplotype sharing between Bos member of the human TLR gene family for which specific li- taurus taurus and Bos taurus indicus breeds at every locus, and gands are yet to be identified (16).
    [Show full text]
  • The Genome 10K Project: a Way Forward
    The Genome 10K Project: A Way Forward Klaus-Peter Koepfli,1 Benedict Paten,2 the Genome 10K Community of Scientists,Ã and Stephen J. O’Brien1,3 1Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russian Federation; email: [email protected] 2Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064 3Oceanographic Center, Nova Southeastern University, Fort Lauderdale, Florida 33004 Annu. Rev. Anim. Biosci. 2015. 3:57–111 Keywords The Annual Review of Animal Biosciences is online mammal, amphibian, reptile, bird, fish, genome at animal.annualreviews.org This article’sdoi: Abstract 10.1146/annurev-animal-090414-014900 The Genome 10K Project was established in 2009 by a consortium of Copyright © 2015 by Annual Reviews. biologists and genome scientists determined to facilitate the sequencing All rights reserved and analysis of the complete genomes of10,000vertebratespecies.Since Access provided by Rockefeller University on 01/10/18. For personal use only. ÃContributing authors and affiliations are listed then the number of selected and initiated species has risen from ∼26 Annu. Rev. Anim. Biosci. 2015.3:57-111. Downloaded from www.annualreviews.org at the end of the article. An unabridged list of G10KCOS is available at the Genome 10K website: to 277 sequenced or ongoing with funding, an approximately tenfold http://genome10k.org. increase in five years. Here we summarize the advances and commit- ments that have occurred by mid-2014 and outline the achievements and present challenges of reaching the 10,000-species goal. We summarize the status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and provide our present and futurevision of the landscape of Genome 10K.
    [Show full text]
  • A Primary Assembly of a Bovine Haplotype Block Map Based On
    Genetics: Published Articles Ahead of Print, published on April 15, 2007 as 10.1534/genetics.106.069369 A primary assembly of a bovine haplotype block map based on a 15k SNP panel genotyped in Holstein-Friesian cattle Mehar S. Khatkar*,§,1, Kyall R. Zenger*,§, Matthew Hobbs*,§, Rachel J. Hawken†,§, Julie A. L. Cavanagh*,§, Wes Barris†,§, Alexander E. McClintock*,§, Sara McClintock‡,§, Peter C. Thomson*,§, Bruce Tier§, Frank W. Nicholas*,§ and Herman W. Raadsma*,§ * Centre for Advanced Technologies in Animal Genetics and Reproduction (ReproGen), University of Sydney, Camden NSW 2570, Australia † CSIRO Livestock Industries, St Lucia QLD 4067, Australia. ‡ Animal Genetics and Breeding Unit*, University of New England, NSW 2351, Australia. § CRC for Innovative Dairy Products, William Street, Melbourne, Vic, 3000, Australia. 1 Running title: Haplotype blocks in bovine genome Keywords: Linkage disequilibrium, haplotype blocks, tag SNPs, bovine, genome- wide, maps 1Corresponding author: Centre for Advanced Technologies in Animal Genetics and Reproduction (ReproGen), University of Sydney, PMB 3, Camden NSW 2570, Australia. E-mail: [email protected] FAX: +61-2-9351 1693 Tele: +61-2-9351 1687 2 ABSTRACT Analysis of data on 1,000 Holstein-Friesian bulls genotyped for 15,036 SNPs has enabled genome-wide identification of haplotype blocks and tag SNPs. A final subset of 9,195 SNPs in Hardy-Weinberg equilibrium and mapped on autosomes on the bovine sequence assembly (release Btau 3.1) were used in the present study. The average inter-marker spacing was 251.8 kb. The average MAF was 0.29 (0.05-0.5). Following recent precedents in human HapMap studies, a haplotype block was defined where 95 % of combinations of SNPs within a region are in very high linkage disequilibrium.
    [Show full text]
  • A Primary Assembly of a Bovine Haplotype Block Map Based on a 15,036-Single-Nucleotide Polymorphism Panel Genotyped in Holstein–Friesian Cattle
    Copyright Ó 2007 by the Genetics Society of America DOI: 10.1534/genetics.106.069369 A Primary Assembly of a Bovine Haplotype Block Map Based on a 15,036-Single-Nucleotide Polymorphism Panel Genotyped in Holstein–Friesian Cattle Mehar S. Khatkar,*,†,1 Kyall R. Zenger,*,† Matthew Hobbs,*,† Rachel J. Hawken,†,‡ Julie A. L. Cavanagh,*,† Wes Barris,†,‡ Alexander E. McClintock,*,† Sara McClintock,†,§ Peter C. Thomson,*,† Bruce Tier,† Frank W. Nicholas*,† and Herman W. Raadsma*,† *Centre for Advanced Technologies in Animal Genetics and Reproduction (ReproGen), University of Sydney, Camden NSW 2570, Australia, ‡CSIRO Livestock Industries, St. Lucia QLD 4067, Australia, §Animal Genetics and Breeding Unit, University of New England, Armidale NSW 2351, Australia and †CRC for Innovative Dairy Products, Melbourne, Vic 3000, Australia Manuscript received December 6, 2006 Accepted for publication April 3, 2007 ABSTRACT Analysis of data on 1000 Holstein–Friesian bulls genotyped for 15,036 single-nucleotide polymorphisms (SNPs) has enabled genomewide identification of haplotype blocks and tag SNPs. A final subset of 9195 SNPs in Hardy–Weinberg equilibrium and mapped on autosomes on the bovine sequence assembly (release Btau 3.1) was used in this study. The average intermarker spacing was 251.8 kb. The average minor allele frequency (MAF) was 0.29 (0.05–0.5). Following recent precedents in human HapMap studies, a haplotype block was defined where 95% of combinations of SNPs within a region are in very high linkage dis- equilibrium. A total of 727 haplotype blocks consisting of $3 SNPs were identified. The average block length was 69.7 6 7.7 kb, which is 5–10 times larger than in humans.
    [Show full text]
  • Introduction to Genomic Selection
    Introduction to Genomic Selection Notes for a short course taught in 2017 in Maringa, Brazil Daniela Lourenco et al., 11/16/2017 1. A Little bit of history (based on Lourenco et al., 2017 @ BIF Conference) [http://www.bifconference.com/bif2017/proceedings/01-lourenco.pdf] Long before genomics found its way into livestock breeding, most of the excitement pertaining to research into livestock improvement via selection involved developments in the BLUP mixed model equations, methods to construct the inverse of the pedigree relationship matrix recursively (Henderson, 1976; Quaas, 1988), parameter estimation and development of new, measureable traits of economic importance. In particular for several decades (1970’s through the early 2000’s), lots of resources were invested in finding the most useful evaluation model for various traits. Since the 1970’s, the use of pedigree and phenotypic information has been the major contributing factor to the large amount of genetic progress in the livestock industry. During the late 1970’s and early 1980’s, geneticists developed techniques that allowed the investigation of DNA, and they discovered several polymorphic markers in the genome. Soller and Beckmann (1983) described the possible uses of new discovered polymorphisms, and surprisingly, their vision of using markers was not much different than how DNA is used today in the genetic improvement of livestock. They hypothesized that markers would be beneficial in constructing more precise genetic relationships, followed by parentage determination, and the identification of quantitative trait loci (QTL). The high cost of genotyping animals for such markers probably prevented the early widespread use of this technology.
    [Show full text]
  • Novel Functional Sequences Uncovered Through a Bovine Multi-Assembly Graph (Version 1.0) [Dataset]
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.08.425845; this version posted January 8, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Novel functional sequences uncovered through a bovine multi-assembly graph Danang Crysnanto*, Alexander S. Leonard, Zih-Hua Fang, Hubert Pausch Animal Genomics, ETH Zürich, Zürich, Switzerland Email addresses: DC: [email protected] AL: [email protected] ZHF: [email protected] HP: [email protected] *Corresponding author: Danang Crysnanto, [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.08.425845; this version posted January 8, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Linear reference genomes are typically assembled from single individuals. They are unable to reflect the genetic diversity of populations and lack millions of bases. To overcome such limitations and make non-reference sequences amenable to genetic investigations, we build a multi-assembly graph from six reference-quality assemblies from taurine cattle and their close relatives. We uncover 70,329,827 bases that are missing in the bovine linear reference genome. The missing sequences encode novel transcripts that are differentially expressed between individual animals.
    [Show full text]
  • Whole-Genome Resequencing of Two Elite Sires for the Detection of Haplotypes Under Selection in Dairy Cattle
    Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle Denis M. Larkina, Hans D. Daetwylerb, Alvaro G. Hernandezc, Chris L. Wrightc, Lorie A. Hetrickc, Lisa Boucekc, Sharon L. Bachmanc, Mark R. Bandc, Tatsiana V. Akraikoc, Miri Cohen-Zinderd, Jyothi Thimmapuramc, Iona M. Macleode, Timothy T. Harkinsf, Jennifer E. McCagueg, Michael E. Goddardb,e, Ben J. Hayesb,h, and Harris A. Lewina,d,1,2 aDepartment of Animal Sciences, cThe W. M. Keck Center for Comparative and Functional Genomics, and dInstitute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801; bBiosciences Research Division, Department of Primary Industries, Bundoora 3083, Victoria, Australia; eDepartment of Food and Agricultural Systems, University of Melbourne, Parkville 3011, Victoria, Australia; fRoche, Indianapolis, IN 46250; g454 Life Sciences, Branford, CT 06405; and hBiosciences Research Centre, La Trobe University, Bundoora 3086, Victoria, Australia Edited* by James E. Womack, Texas A&M University, College Station, TX, and approved March 23, 2012 (received for review September 16, 2011) Using a combination of whole-genome resequencing and high- lactation in the 1940s to 19,000 pounds per lactation in 2005 (http:// density genotyping arrays, genome-wide haplotypes were recon- aipl.arsusda.gov/publish/presentations/ADSA05/ADSA05_culling. structed for two of the most important bulls in the history of the ppt). Thus, retrospective semen collections such as the US Dairy dairy cattle industry, Pawnee Farm Arlinda Chief (“Chief”) and his Bull DNA Repository (7) are invaluable for gaining a molecular son Walkway Chief Mark (“Mark”), each accounting for ∼7% of all understanding of the genomic changes that occur as a result of current genomes.
    [Show full text]