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

Molly E. Mccue (1) , Danika L. Bannasch (2) , Jessica L. Petersen (1) , Jessica Gurr (3) , Ernie Bailey (4) , Matthew M. Binns (5) , Ottmar Distl (6) , Gerard Guérin (7) , Telhisa Hasegawa (8) , Emmeline W. Hill (9) , Tosso Leeb (10) , Gabriella Lindgren (11) , Cecilia T. Penedo (12) , Knut H. Røed (13) , Oliver A. Ryder (14) , June E. Swinburne (15) , Teruaki Tozaki (16) , Stephanie J. Valberg (1) , Mark Vaudin (15) , Kerstin Lindblad-Toh (17, 18) , Claire M. Wade (3) , James R. Mickelson (1)

1 College of Veterinary Medicine
2 Department of Population Health and Reproduction, School of Veterinary Medicine
3 Faculty of Veterinary Science
4 Maxwell H. Gluck Equine Research Center, Department of Veterinary Science
5 Equine Analysis Systems
6 Institute of Animal Breeding and Genetics
7 GABI - Génétique Animale et Biologie Intégrative
8 Equine Research Institute
9 Animal Genomics Laboratory, School of Agriculture and Food Science
10 Institute of Genetics, Vetsuisse Faculty
11 Department of Animal Bredding and Genetics
12 Veterinary Genetics Laboratory
13 Department of Basic Sciences and Aquatic Medicine
14 San Diego Zoo's Institute for Conservation Research
15 AHT - Animal Health Trust
16 Department of Molecular Genetics
17 Science for Life Laboratory, Department of Medical Biochemistry and Microbiology
18 Broad Institute [Cambridge]

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.

Domaines: Sciences du Vivant [q-bio]

Molly E. Mccue, Danika L. Bannasch, Jessica L. Petersen, Jessica Gurr, Ernie Bailey, et al.. A high density SNP array for the domestic horse and extant perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies. PLoS Genetics, 2012, 8 (1), Non paginé. ⟨10.1371/journal.pgen.1002451⟩. ⟨hal-01191252⟩