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

被引：157

作者：

McCue, Molly E. ^{[1
]}

Bannasch, Danika L. ^{[2
]}

Petersen, Jessica L. ^{[1
]}

Gurr, Jessica ^{[3
]}

Bailey, Ernie ^{[4
]}

Binns, Matthew M. ^{[5
]}

Distl, Ottmar ^{[6
]}

Guerin, Gerard ^{[7
]}

Hasegawa, Telhisa ^{[8
]}

Hill, Emmeline W. ^{[9
]}

Leeb, Tosso ^{[10
]}

Lindgren, Gabriella ^{[11
]}

Penedo, M. Cecilia T. ^{[12
]}

Roed, Knut H. ^{[13
]}

Ryder, Oliver A. ^{[14
]}

Swinburne, June E. ^{[15
]}

Tozaki, Teruaki ^{[16
]}

Valberg, Stephanie J. ^{[1
]}

Vaudin, Mark ^{[15
]}

Lindblad-Toh, Kerstin ^{[17
,18
]}

Wade, Claire M. ^{[3
]}

Mickelson, James R. ^{[1
]}

机构：

[1] Univ Minnesota, Coll Vet Med, St Paul, MN 55108 USA

[2] Univ Calif Davis, Sch Vet Med, Dept Populat Hlth & Reprod, Davis, CA 95616 USA

[3] Univ Sydney, Fac Vet Sci, Sydney, NSW 2006, Australia

[4] Univ Kentucky, Dept Vet Sci, Maxwell H Gluck Equine Res Ctr, Lexington, KY 40546 USA

[5] Equine Anal Syst, Midway, KY USA

[6] Univ Vet Med Hannover, Inst Anim Breeding & Genet, Hannover, Germany

[7] INRA, UMR 1313, Jouy En Josas, France

[8] Japan Racing Assoc, Equine Res Inst, Utsunomiya, Tochigi, Japan

[9] Univ Coll Dublin, Sch Agr & Food Sci, Anim Genom Lab, Dublin 2, Ireland

[10] Univ Bern, Vetsuisse Fac, Inst Genet, Bern, Switzerland

[11] Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden

[12] Univ Calif Davis, Vet Genet Lab, Davis, CA 95616 USA

[13] Norwegian Sch Vet Sci, Dept Basic Sci & Aquat Med, Oslo, Norway

[14] San Diego Zoos Inst Conservat Res, Escondido, CA USA

[15] Anim Hlth Trust, Newmarket CB8 7DW, Suffolk, England

[16] Dept Mol Genet, Lab Racing Chem, Utsunomiya, Tochigi, Japan

[17] Uppsala Univ, Dept Med Biochem & Microbiol, Sci Life Lab, Uppsala, Sweden

[18] Broad Inst, Cambridge, MA USA

来源：

PLOS GENETICS | 2012年 / 8卷 / 01期

基金：

爱尔兰科学基金会;

关键词：

OPTIMUM RACING DISTANCE; WHITE FOAL SYNDROME; COAT COLOR; MISSENSE MUTATION; LINKAGE DISEQUILIBRIUM; GENOTYPING ASSAY; SPOTTING PATTERN; GENOME SEQUENCE; POPULATION; EQUUS;

D O I：

10.1371/journal.pgen.1002451

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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 similar to 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 similar to 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.

引用

页数：14

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