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

Molly E. McCue, Danika L. Bannasch, Jessica L. Petersen, Jessica Gurr, Ernie Bailey, Matthew M. Binns, Ottmar Distl, Gérard Guérin, Telhisa Hasegawa, Emmeline W. Hill, Tosso Leeb, Gabriella Lindgren, M. Cecilia T. Penedo, Knut H. Røed, Oliver A. Ryder, June E. Swinburne, Teruaki Tozaki, Stephanie J. Valberg, Mark Vaudin, Kerstin Lindblad-TohClaire M. Wade, James R. Mickelson

Research output: Contribution to journalArticle

120 Citations (Scopus)

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.

Original languageEnglish (US)
Article numbere1002451
JournalPLoS genetics
Volume8
Issue number1
DOIs
StatePublished - Jan 1 2012

Fingerprint

Perissodactyla
Phylogeny
horse
Horses
chromosome mapping
Single Nucleotide Polymorphism
phylogeny
breeds
horses
genetic variation
genotyping
horse breeds
linkage disequilibrium
genome
Equidae
Linkage Disequilibrium
disequilibrium
Genome
Equus przewalskii
Tapiridae

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

Cite this

A high density SNP array for the domestic horse and extant Perissodactyla : Utility for association mapping, genetic diversity, and phylogeny studies. / McCue, Molly E.; 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.

In: PLoS genetics, Vol. 8, No. 1, e1002451, 01.01.2012.

Research output: Contribution to journalArticle

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, MCT, 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 genetics, vol. 8, no. 1, e1002451. https://doi.org/10.1371/journal.pgen.1002451
McCue, Molly E. ; 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. / A high density SNP array for the domestic horse and extant Perissodactyla : Utility for association mapping, genetic diversity, and phylogeny studies. In: PLoS genetics. 2012 ; Vol. 8, No. 1.
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