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Home / Equine Research Bank / PLoS Genet / A high density SNP array for the domestic horse and extant P...
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.
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Publication Date: 2012-01-12 PubMed ID: 22253606PubMed Central: PMC3257288DOI: 10.1371/journal.pgen.1002451Google Scholar: Lookup
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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.

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                                            Citations

                                            This article has been cited 112 times.
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