A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies

Authors

Molly E. McCue, University of Minnesota - Twin CitiesFollow
Danika L. Bannasch, University of California - Davis
Jessica Lynn Petersen, University of Nebraska-LincolnFollow
Jessica Gurr, University of Sydney
Ernie Bailey, University of Kentucky
Matthew M. Binns, Equine Analysis Systems
Ottmar Distl, University of Veterinary Medicine Hannover
Gérard Guérin, Génétique Animale et Biologie Intégrative, Biologie Intégrative et Génétique Equine
Telhisa Hasegawa, Japan Racing Association
Emmeline W. Hill, University College Dublin
Tosso Leeb, University of Bern
Gabriella Lindgren, Swedish University of Agricultural Sciences
M. Cecilia T. Penedo, University of California - Davis
Knut H. Røed, Norwegian School of Veterinary Science
Oliver A. Ryder, San Diego Zoo's Institute for Conservation Research
June E. Swinburne, Animal Health Trust
Teruaki Tozaki, Laboratory of Racing Chemistry
Stephanie J. Valberg, University of Minnesota - Twin Cities
Mark Vaudin, Animal Health Trust
Kerstin Lindblad-Toh, Uppsala Universitet
Claire M. Wade, University of Sydney
James R. Mickelson, University of Minnesota - Twin Cities

Document Type

Article

Date of this Version

1-2012

Citation

PLoS Genetics (January 2012) 8(1): e1002451. DOI: 10.1371/journal.pgen.1002451.

Comments

Copyright 2012, the authors. Used by permission.

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.