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A high density SNP array for the domestic horse and extant Perissodactyla: Utility for association mapping,genetic diversity,and phylogeny studies
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نویسنده
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mccue m.e. ,bannasch d.l. ,petersen j.l. ,gurr j. ,bailey e. ,binns m.m. ,distl o. ,guérin g. ,hasegawa t. ,hill e.w. ,leeb t. ,lindgren g. ,penedo m.c.t. ,røed k.h. ,ryder o.a. ,swinburne j.e. ,tozaki t. ,valberg s.j. ,vaudin m. ,lindblad-toh k. ,wade c.m. ,mickelson j.r.
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منبع
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plos genetics - 2012 - دوره : 8 - شماره : 1
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چکیده
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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. © 2012 mccue et al.
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آدرس
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college of veterinary medicine,university of minnesota,st. paul,mn, United States, department of population health and reproduction,school of veterinary medicine,university of california davis,davis,ca, United States, college of veterinary medicine,university of minnesota,st. paul,mn, United States, faculty of veterinary science,university of sydney,sydney, Australia, maxwell h. gluck equine research center,department of veterinary science,university of kentucky,lexington,ky, United States, equine analysis systems,midway,ky, United States, institute of animal breeding and genetics,university of veterinary medicine hannover,hannover, Germany, inra,umr 1313,génétique animale et biologie intégrative,biologie intégrative et génétique equine,jouy-en-josas, France, equine research institute,japan racing association,utsunomiya, Japan, animal genomics laboratory,school of agriculture and food science,university college dublin,dublin, Ireland, institute of genetics,vetsuisse faculty,university of bern,berne, Switzerland, department of animal breeding and genetics,swedish university of agricultural sciences,uppsala, Sweden, veterinary genetics laboratory,university of california davis,davis,ca, United States, department of basic sciences and aquatic medicine,norwegian school of veterinary science,oslo, Norway, san diego zoo's institute for conservation research,escondido,ca, United States, animal health trust,suffolk, United Kingdom, department of molecular genetics,laboratory of racing chemistry,utsunomiya, Japan, college of veterinary medicine,university of minnesota,st. paul,mn, United States, animal health trust,suffolk, United Kingdom, science for life laboratory,department of medical biochemistry and microbiology,uppsala university,uppsala,sweden,broad institute,cambridge,ma, United States, faculty of veterinary science,university of sydney,sydney, Australia, college of veterinary medicine,university of minnesota,st. paul,mn, United States
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Authors
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