title: 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.
authors.affiliation: College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA. mccu0173@umn.edu
authors.forename: Molly E
authors.initials: ME
authors.lastname: McCue
authors.forename: Danika L
authors.initials: DL
authors.lastname: Bannasch
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Petersen
authors.forename: Jessica
authors.initials: J
authors.lastname: Gurr
authors.forename: Ernie
authors.initials: E
authors.lastname: Bailey
authors.forename: Matthew M
authors.initials: MM
authors.lastname: Binns
authors.forename: Ottmar
authors.initials: O
authors.lastname: Distl
authors.forename: Gérard
authors.initials: G
authors.lastname: Guérin
authors.forename: Telhisa
authors.initials: T
authors.lastname: Hasegawa
authors.forename: Emmeline W
authors.initials: EW
authors.lastname: Hill
authors.forename: Tosso
authors.initials: T
authors.lastname: Leeb
authors.forename: Gabriella
authors.initials: G
authors.lastname: Lindgren
authors.forename: M Cecilia T
authors.initials: MC
authors.lastname: Penedo
authors.forename: Knut H
authors.initials: KH
authors.lastname: Røed
authors.forename: Oliver A
authors.initials: OA
authors.lastname: Ryder
authors.forename: June E
authors.initials: JE
authors.lastname: Swinburne
authors.forename: Teruaki
authors.initials: T
authors.lastname: Tozaki
authors.forename: Stephanie J
authors.initials: SJ
authors.lastname: Valberg
authors.forename: Mark
authors.initials: M
authors.lastname: Vaudin
authors.forename: Kerstin
authors.initials: K
authors.lastname: Lindblad-Toh
authors.forename: Claire M
authors.initials: CM
authors.lastname: Wade
authors.forename: James R
authors.initials: JR
authors.lastname: Mickelson
mesh_terms: D000818:Animals; D005075:Biological Evolution; D001947:Breeding; D002874:Chromosome Mapping; D005787:Gene Frequency; D008040:Genetic Linkage; D014644:Genetic Variation; D060005:Genotyping Techniques; D006239:Haplotypes; D006736:Horses / Q000235:genetics*; D015810:Linkage Disequilibrium; D010527:Perissodactyla / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*