Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

Wade, Claire M.; Giulotto, Elena; Sigurðsson, Snaevar; Zoli, Monica; Gnerre, Sante; Imsland, Freyja; Lear, Teri L.; Adelson, David L.; Bailey, Ernest; Bellone, Rebecca R.; Blöcker, Helmut; Distl, O.; Edgar, Robert C.; Garber, Manuel; Leeb, Tosso; Mauceli, Evan; MacLeod, James N.; Penedo, M. C. T.; Raison, Joy M.; Sharpe, Ted; Vogel, Jan-Hinnerk; Andersson, Leif; Antczak, Douglas F.; Biagi, Tara; Binns, M. M.; Chowdhary, Bhanu P.; Coleman, Stephen J.; Valle, Giuliano Della; Fryc, Sarah; Guérin, Gérard; Hasegawa, Telhisa; Hill, E. W.; Jurka, Jerzy; Kiialainen, Anna; Lindgren, Gabriella; Liu, J.; Magnani, Elisa; Mickelson, James R.; Murray, James D.; Nergadze, Solomon G.; Onofrio, Robert C.; Pedroni, S.; Piras, Francesca M.; Raudsepp, Terje; Rocchi, Mariano; Røed, Knut; Ryder, Oliver A.; Searle, S.; Skow, Loren C.; Swinburne, June; Syvänen, Ann‐Christine; Tozaki, Teruaki; Valberg, Stephanie J.; Vaudin, Mark D.; White, Jared; Zody, Michael C.; Lander, Eric S.; Lindblad‐Toh, Kerstin

doi:10.1126/science.1178158

Cited by 708 publications

(732 citation statements)

References 18 publications

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“…This may be a result of the difficulty of calling repeats with high similarity from shortread sequencing data 23 . However, the general distribution patterns of transposable element classes across chromosomes are similar to that of other assembled mammalian genomes 24,25 (Supplementary Fig. 8).…”

Section: Repetitive Sequences and Transposable Elementssupporting

confidence: 61%

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

et al. 2012

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Section: Repetitive Sequences and Transposable Elementssupporting

confidence: 61%

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

et al. 2012

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“…For example, in the Hanoverian Warmblood, N e was estimated to be 372 (Hamann and Distl, 2008). Wade et al (2009) found unusually high LD in Thoroughbreds compared with other horse breeds. Nevertheless, GS should be feasible, because strength of LD across several horse breeds (Wade et al, 2009) is comparable to LD in Holstein cattle (Qanbari et al, 2010), where GS was implemented successfully.…”

Section: Resultsmentioning

confidence: 99%

“…The availability of 50-K SNP chip technology, as well as the recent release of the horse genome sequence (Wade et al, 2009), provides the framework to estimate highly reliable GEBVs analogous to dairy cattle (e.g. VanRaden et al, 2009).…”

Section: Resultsmentioning

confidence: 99%

Integration of genomic information into sport horse breeding programs for optimization of accuracy of selection

Haberland

Borstel

Simianer

et al. 2012

Animal

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Reliable selection criteria are required for young riding horses to increase genetic gain by increasing accuracy of selection and decreasing generation intervals. In this study, selection strategies incorporating genomic breeding values (GEBVs) were evaluated. Relevant stages of selection in sport horse breeding programs were analyzed by applying selection index theory. Results in terms of accuracies of indices (r TI ) and relative selection response indicated that information on single nucleotide polymorphism (SNP) genotypes considerably increases the accuracy of breeding values estimated for young horses without own or progeny performance. In a first scenario, the correlation between the breeding value estimated from the SNP genotype and the true breeding value (5 accuracy of GEBV) was fixed to a relatively low value of r mg 5 0.5. For a low heritability trait (h 2 5 0.15), and an index for a young horse based only on information from both parents, additional genomic information doubles r TI from 0.27 to 0.54. Including the conventional information source 'own performance' into the before mentioned index, additional SNP information increases r TI by 40%. Thus, particularly with regard to traits of low heritability, genomic information can provide a tool for well-founded selection decisions early in life. In a further approach, different sources of breeding values (e.g. GEBV and estimated breeding values (EBVs) from different countries) were combined into an overall index when altering accuracies of EBVs and correlations between traits. In summary, we showed that genomic selection strategies have the potential to contribute to a substantial reduction in generation intervals in horse breeding programs.Keywords: accuracy of selection, breeding strategies, generation interval, genomic selection, sport horse ImplicationsThe availability of genomic information demands proper assessment of its impact on practical horse breeding programs. Accuracies of conventional breeding values do not increase significantly until a stallion is aged 8 to 12 years and his progeny enters competition. We showed that additional genomic information considerably increases the accuracy of breeding values estimated for foals, young horses without own performance, and horses without progeny performance. Therefore, genomic selection (GS) enables selection at an earlier stage, shortening generation intervals and opening room for increased genetic progress. Our results indicate that horse breeding organizations could likely benefit from the application of GS.

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“…Genome‐wide association studies (GWASs) rapidly gained popularity after the sequencing of the genomes of several animal species, including human beings 31, 32, 33, 34. The completion of the sequencing and assembly of these reference genomes (an assembly of the DNA sequence and its chromosomal locations representing the genetic baseline of a species) provided a tool that could be used as a map indicating where elements of the genome reside.…”

Section: Genome‐wide Association Studiesmentioning

confidence: 99%

“…The resultant scatter plots are known as Manhattan plots because they resemble the skyline of a major city with some points that tower over the majority of others. Determining the genome sequence of the domestic horse led to the development of 2 equine SNP arrays that could be used for GWAS by researchers 32, 39…”

Section: Genome‐wide Association Studiesmentioning

confidence: 99%

Genetic Susceptibility to Rhodococcus equi

McQueen

Dindot

2015

Veterinary Internal Medicne

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Rhodococcus equi pneumonia is a major cause of morbidity and mortality in neonatal foals. Much effort has been made to identify preventative measures and new treatments for R. equi with limited success. With a growing focus in the medical community on understanding the genetic basis of disease susceptibility, investigators have begun to evaluate the interaction of the genetics of the foal with R. equi. This review describes past efforts to understand the genetic basis underlying R. equi susceptibility and tolerance. It also highlights the genetic technology available to study horses and describes the use of this technology in investigating R. equi. This review provides readers with a foundational understanding of candidate gene approaches, single nucleotide polymorphism‐based, and copy number variant‐based genome‐wide association studies, and next generation sequencing (both DNA and RNA).

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Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

Cited by 708 publications

References 18 publications

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

Integration of genomic information into sport horse breeding programs for optimization of accuracy of selection

Genetic Susceptibility to Rhodococcus equi

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