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PMID: 22253606 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

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 ·2012-01-00 ·Pages e1002451

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

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.

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
Authors & Affiliations
22 authors, click to expand affiliations / ORCID
McCue Molly E
College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA. [email protected]
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
Conflict of Interest

The authors have declared that no competing interests exist.

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Article Info
Journal
PLoS genetics
Abbr.
PLoS Genet
ISSN
1553-7404
DOI
10.1371/journal.pgen.1002451
Email
[email protected]
Published
2012-01-00
Epub
2012-00-12
Pages
e1002451
Language
English
Region
United States
NLM ID
101239074
PMCID
PMC3257288
Subset
IM
Grants
NIAMS NIH HHS · K08 AR055713 · United States
NIAMS NIH HHS · 1K08AR055713-01A2 · United States
External Links
PubMed source DOI: 10.1371/journal.pgen.1002451 PMC Full Text View journal details
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