FREE SHIPPING over $40
OVER 10000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
PLoS genetics2012; 8(1); e1002451; doi: 10.1371/journal.pgen.1002451

A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies.

Abstract: An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50-100 kb and reached background levels within 1-2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of ∼750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species.
Get Full Text
Publication Date: 2012-01-12 PubMed ID: 22253606PubMed Central: PMC3257288DOI: 10.1371/journal.pgen.1002451Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Journal Article
  • Research Support
  • N.I.H.
  • Extramural
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research discusses the development and evaluation of a high density SNP genotyping array for the domestic horse and its relatives in the Perissodactyla order. The array, comprising of more than 54,000 polymorphic SNPs, was tested on samples from 14 domestic horse breeds and 18 related species, demonstrating its utility in studies related to association mapping, genetic diversity, and phylogeny.

Development and Evaluation of SNP Genotyping Array

  • A high density SNP genotyping array was created for the domestic horse and related species in the Perissodactyla order. An average inter-SNP spacing of approximately 43 kilobases was achieved with over 54,000 polymorphic SNPs.
  • The array was evaluated using samples from 14 different domestic horse breeds. The mean minor allele frequency across these breeds was measured to be 0.23 and the number of polymorphic SNPs ranged from 43,287 to 52,085 depending on the breed.

Analysis of Linkage Disequilibrium and Inbreeding

  • The research also studied Genome-wide linkage disequilibrium (LD) among different breeds. It was observed to decline rapidly over the first 50-100 kb and reached background levels within 1-2 Mb.
  • The extent of LD and the level of inbreeding were found to be highest in the Thoroughbred breed and the lowest in the Mongolian and Quarter Horse breeds.

Phylogeny and Association Mapping

  • The close relationship between the domestic horse and the Przewalski’s horse, a rare and endangered subspecies of wild horse, was demonstrated through multidimensional scaling (MDS) analyses and pair-wise genetic distance.
  • The genotyping SNP array was also used for other Perissodactyla species like zebras, asses, tapirs, and rhinoceros with varying degrees of success. The Call rates and the number of polymorphic loci varied across these species.
  • Parsimony analysis indicated the modern horse as a sister taxa to Equus przewalski, further highlighting the phylogenetic relationship between the species.
  • The utility of the SNP array in genome-wide association was confirmed by mapping the recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of around 750 kb across all breeds.

Conclusion

  • The research concludes that the high density SNP genotyping array developed is of high quality and useful for diverse genome analyses of horses and related species. It is particularly effective for studies concerning genetic diversity, association mapping, and phylogeny.

Cite This Article

APA
McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM, Distl O, Guérin G, Hasegawa T, Hill EW, Leeb T, Lindgren G, Penedo MC, Røed KH, Ryder OA, Swinburne JE, Tozaki T, Valberg SJ, Vaudin M, Lindblad-Toh K, Wade CM, Mickelson JR. (2012). A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies. PLoS Genet, 8(1), e1002451. https://doi.org/10.1371/journal.pgen.1002451

Publication

PLoS genetics
ISSN: 1553-7404
NlmUniqueID: 101239074
Country: United States
Language: English
Volume: 8
Issue: 1
Pages: e1002451

Researcher Affiliations

McCue, Molly E
  • College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA. mccų@umn.edu
Bannasch, Danika L
    Petersen, Jessica L
      Gurr, Jessica
        Bailey, Ernie
          Binns, Matthew M
            Distl, Ottmar
              Guérin, Gérard
                Hasegawa, Telhisa
                  Hill, Emmeline W
                    Leeb, Tosso
                      Lindgren, Gabriella
                        Penedo, M Cecilia T
                          Røed, Knut H
                            Ryder, Oliver A
                              Swinburne, June E
                                Tozaki, Teruaki
                                  Valberg, Stephanie J
                                    Vaudin, Mark
                                      Lindblad-Toh, Kerstin
                                        Wade, Claire M
                                          Mickelson, James R

                                            MeSH Terms

                                            • Animals
                                            • Biological Evolution
                                            • Breeding
                                            • Chromosome Mapping
                                            • Gene Frequency
                                            • Genetic Linkage
                                            • Genetic Variation
                                            • Genotyping Techniques
                                            • Haplotypes
                                            • Horses / genetics
                                            • Linkage Disequilibrium
                                            • Perissodactyla / genetics
                                            • Phylogeny
                                            • Polymorphism, Single Nucleotide / genetics

                                            Grant Funding

                                            • K08 AR055713 / NIAMS NIH HHS
                                            • 1K08AR055713-01A2 / NIAMS NIH HHS

                                            Conflict of Interest Statement

                                            The authors have declared that no competing interests exist.

                                            References

                                            This article includes 43 references
                                            1. Olsen SO. Early Horse Domestication on the Eurasian Steppe. In: Zeder M, Bradley D, Emshwiller E, Smith B, editors. Documenting Domestication: New Genetic and Archaeological Paradigms. Berkley: University of Claifornia Press; 2006. pp. 245–269.
                                            2. Hendricks B. International Encyclopedia of Horse Breeds. Norman: University of Oklahoma Press; 1995.
                                            3. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 2009;326:865–867.
                                              pmc: PMC3785132pubmed: 19892987
                                            4. Price SA, Bininda-Emonds ORP. A comprehensive phylogeny of extant horses, rhinos and tapirs (Perissodactyla) through data combination. Zool Reihe 2009;85:277–292.
                                              doi: 10.1002/zoos.200900005google scholar: lookup
                                            5. Marklund L, Moller MJ, Sandberg K, Andersson L. A missense mutation in the gene for melanocyte-stimulating hormone receptor (MC1R) is associated with the chestnut coat color in horses. Mamm Genome 1996;7:895–899.
                                              pubmed: 8995760
                                            6. Rieder S, Taourit S, Mariat D, Langlois B, Guerin G. Mutations in the agouti (ASIP), the extension (MC1R), and the brown (TYRP1) loci and their association to coat color phenotypes in horses (Equus caballus). Mamm Genome 2001;12:450–455.
                                              pubmed: 11353392
                                            7. Rosengren PG, Golovko A, Sundstrom E, Curik I, Lennartsson J. A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse. Nat Genet 2008;40:1004–1009.
                                              pubmed: 18641652
                                            8. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF. Development and Characterization of a High Density SNP Genotyping Assay for Cattle. PLoS ONE 2009;4:e5350.
                                              doi: 10.1371/journal.pone.0005350pmc: PMC2669730pubmed: 19390634google scholar: lookup
                                            9. Ramos AM, Crooijmans RPMA, Affara NA, Amaral AJ, Archibald AL. Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology. PLoS ONE 2009;4:e6524.
                                              doi: 10.1371/journal.pone.0006524pmc: PMC2716536pubmed: 19654876google scholar: lookup
                                            10. Karlsson EK, Baranowska I, Wade CM, Salmon Hillbertz NH, Zody MC. Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet 2007;39:1321–1328.
                                              pubmed: 17906626
                                            11. Oliphant A, Barker DL, Stuelpnagel JR, Chee MS. BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques Suppl 2002:56–1.
                                              pubmed: 12083399
                                            12. Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 2005;438:803–819.
                                              pubmed: 16341006
                                            13. The Bovine HapMap Consortium. Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds. Science 2009;324:528–532.
                                              pmc: PMC2735092pubmed: 19390050
                                            14. Tozaki T, Takezaki N, Hasegawa T, Ishida N, Kurosawa M. Microsatellite Variation in Japanese and Asian Horses and Their Phylogenetic Relationship Using a European Horse Outgroup. J Hered 2003;94:374–380.
                                              pubmed: 14557389
                                            15. Bjornstad G, Gunby E, Roed KH. Genetic structure of Norwegian horse breeds Die genetische Struktur von norwegischen Pferderassen. Journal of Animal Breeding and Genetics 2000;117:307–317.
                                              doi: 10.1046/j.1439-0388.2000.00264.xgoogle scholar: lookup
                                            16. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC. Linkage disequilibrium in the human genome. Nature 2001;411:199–204.
                                              pubmed: 11346797
                                            17. Pritchard JK, Przeworski M. Linkage disequilibrium in humans: models and data. Am J Hum Genet 2001;69:1–14.
                                              pmc: PMC1226024pubmed: 11410837
                                            18. Cunningham EP, Dooley JJ, Splan RK, Bradley DG. Microsatellite diversity, pedigree relatedness and the contributions of founder lineages to thoroughbred horses. Animal Genetics 2001;32:360–364.
                                              pubmed: 11736806doi: 10.1046/j.1365-2052.2001.00785.xgoogle scholar: lookup
                                            19. Kijas JW, Townley D, Dalrymple BP, Heaton MP, Maddox JF. A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds. PLoS ONE 2009;4:e4668.
                                              doi: 10.1371/journal.pone.0004668pmc: PMC2652362pubmed: 19270757google scholar: lookup
                                            20. Bjornstad G, Nilsen N+, Roed KH. Genetic relationship between Mongolian and Norwegian horses?. Animal Genetics 2003;34:55–58.
                                              pubmed: 12580788doi: 10.1046/j.1365-2052.2003.00922.xgoogle scholar: lookup
                                            21. Oakenfull EA, Clegg JB. Phylogenetic Relationships Within the Genus Equus and the Evolution of α and β Globin Genes. Journal of Molecular Evolution 1998;47:772–783.
                                              pubmed: 9847419
                                            22. George M Jr, Ryder OA. Mitochondrial DNA evolution in the genus Equus. Mol Biol Evol 1986;3:535–546.
                                              pubmed: 2832696
                                            23. Norman JE, Ashley MV. Phylogenetics of Perissodactyla and tests of the molecular clock. J Mol Evol 2000;50:11–21.
                                              pubmed: 10654255
                                            24. Mohr Erna. The Asiatic Wild Horse. J A Allen & Go ltd 1973.
                                            25. Bowling AT, Zimmermann W, Ryder O, Penedo C, Peto S. Genetic variation in Przewalski's horses, with special focus on the last wild caught mare, 231 Orlitza III. Cytogenetic and Genome Research 2003;102:226–234.
                                              pubmed: 14970708
                                            26. Geyer CJ, Thompson EA, Ryder OA. Gene survival in the Asian wild horse (Equus przewalskii): II. Gene survival in the whole population, in subgroups, and through history. Zoo Biol 1989;8:313–329.
                                              doi: 10.1002/zoo.1430080402google scholar: lookup
                                            27. Brooks SA, Gabreski N, Miller D, Brisbin A, Brown HE. Whole-Genome SNP Association in the Horse: Identification of a Deletion in Myosin Va Responsible for Lavender Foal Syndrome. PLoS Genet 2010;6:e1000909.
                                              doi: 10.1371/journal.pgen.1000909pmc: PMC2855325pubmed: 20419149google scholar: lookup
                                            28. Hill EW, McGivney BA, Gu J, Whiston R, Machugh DE. A genome-wide SNP-association study confirms a sequence variant (g.66493737C>T) in the equine myostatin (MSTN) gene as the most powerful predictor of optimum racing distance for Thoroughbred racehorses. BMC Genomics 2010;11:552.
                                              pmc: PMC3091701pubmed: 20932346
                                            29. Lykkjen S, Dolvik NI, McCue ME, Rendahl AK, Mickelson JR. Genome-wide association analysis of osteochondrosis of the tibiotarsal joint in Norwegian Standardbred trotters. Animal Genetics 2010;41:111–120.
                                              pubmed: 21070284doi: 10.1111/j.1365-2052.2010.02117.xgoogle scholar: lookup
                                            30. Binns MM, Boehler DA, Lambert DH. Identification of the myostatin locus (MSTN) as having a major effect on optimum racing distance in the Thoroughbred horse in the USA. Animal Genetics 2010;41:154–158.
                                              pubmed: 21070290doi: 10.1111/j.1365-2052.2010.02126.xgoogle scholar: lookup
                                            31. Cook D, Gallagher PC, Bailey E. Genetics of swayback in American Saddlebred horses. Animal Genetics 2010;41:64–71.
                                              pubmed: 21070278doi: 10.1111/j.1365-2052.2010.02108.xgoogle scholar: lookup
                                            32. Ludwig A, Pruvost M, Reissmann M, Benecke N, Brockmann GA. Coat Color Variation at the Beginning of Horse Domestication. Science 2009;324:485.
                                              pmc: PMC5102060pubmed: 19390039
                                            33. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559–575.
                                              pmc: PMC1950838pubmed: 17701901
                                            34. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005;21:263–265.
                                              pubmed: 15297300
                                            35. Goloboff PA, Farris JS, Nixon KC. TNT, a free program for phylogenetic analysis. Cladistics 2008;24:774–786.
                                              doi: 10.1111/j.1096-0031.2008.00217.xgoogle scholar: lookup
                                            36. Brunberg E, Andersson L, Cothran G, Sandberg K, Mikko S. A missense mutation in PMEL17 is associated with the Silver coat color in the horse. BMC Genet 2006;7:46.
                                              pmc: PMC1617113pubmed: 17029645
                                            37. Santschi EM, Purdy AK, Valberg SJ, Vrotsos PD, Kaese H. Endothelin receptor B polymorphism associated with lethal white foal syndrome in horses. Mamm Genome 1998;9:306–309.
                                              pubmed: 9530628
                                            38. Metallinos DL, Bowling AT, Rine J. A missense mutation in the endothelin-B receptor gene is associated with Lethal White Foal Syndrome: an equine version of Hirschsprung Disease. Mammalian Genome 1998;9:426–431.
                                              pubmed: 9585428
                                            39. Brooks SA, Terry RB, Bailey E. A PCR-RFLP for KIT associated with tobiano spotting pattern in horses. Animal Genetics 2002;33:301–303.
                                              pubmed: 12139510doi: 10.1046/j.1365-2052.2002.00854.xgoogle scholar: lookup
                                            40. Brooks S, Bailey E. Exon skipping in the KIT gene causes a Sabino spotting pattern in horses. Mammalian Genome 2005;16:893–902.
                                              pubmed: 16284805
                                            41. Cook D, Brooks S, Bellone R, Bailey E. Missense Mutation in Exon 2 of SLC36A1 Responsible for Champagne Dilution in Horses. PLoS Genet 2008;4:e1000195.
                                              doi: 10.1371/journal.pgen.1000195pmc: PMC2535566pubmed: 18802473google scholar: lookup
                                            42. Denis M, Sead T, Goerard Gr. A mutation in the MATP gene causes the cream coat colour in the horse. Genet Sel Evol 2003;35:119–133.
                                              pmc: PMC2732686pubmed: 12605854doi: 10.1051/gse:2002039google scholar: lookup
                                            43. Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 2006;78:629–644.
                                              pmc: PMC1424677pubmed: 16532393

                                            Citations

                                            This article has been cited 112 times.
                                            Subscribe to our newsletter
                                            Join 100,113 horse owners like you who receive our email updates on horse health and nutrition.