A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies.
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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DOI：
10.1371/journal.pgen.1002451
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发表时间：
2012-01
期刊：
影响因子：
4.5
通讯作者：
Mickelson JR
中科院分区：
文献类型：
--
作者：
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
建立了马SNP基因分型阵列，并对14个家马品种和18个进化相关物种的样本进行了评估。超过54,000个多态snp提供了平均间距约43 kb的snp。家马品种间小等位基因平均频率为0.23，多态snp数量为43,287 ~ 52,085个。大多数品种的全基因组连锁不平衡（LD）在前50-100 kb迅速下降，并在1-2 Mb内达到背景水平。纯种马的LD程度和近交水平最高，蒙古马和四分之一马的LD程度最低。多维尺度（MDS）分析表明，在大多数品种中，个体分组紧密，相关品种接近，而在混合品种中分组不紧密。普氏野马与家马的亲缘关系通过双遗传距离和MDS得到了证实。其他野驴目动物（斑马、驴、貘和犀牛）的基因分型成功程度各不相同，不同分类群的召唤率和多态性位点数量各不相同。简约分析认为现代马是普氏野马的姐妹类群。通过绘制已知的隐性栗子毛色位点（MC1R），并在所有品种中定义一个约750 kb的保守单倍型，证实了SNP阵列在全基因组关联中的效用。这些结果证明了该SNP基因分型资源的高质量，其在马的多种基因组分析中的实用性，以及在相关物种中的潜在应用。我们利用之前生成的马基因组序列和一个大型SNP数据库，设计了一个用于家养马和相关物种的~ 54,000个SNP测定。通过全基因组连锁不平衡、近交和品种遗传距离测量，以及多维尺度和简约性分析，证明了该SNP阵列的实用性。关联图谱证实了一个包含家马栗色基因位点的大保守片段。我们还评估了SNP阵列在相关物种中的效用，包括普氏野马、斑马、驴、貘和犀牛。这种SNP基因分型工具将促进马科动物的许多遗传学应用，包括鉴定健康和性能性状的基因，以及对家马起源、品种多样性和相关物种之间进化关系的引人注目的研究。
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. We utilized the previously generated horse genome sequence and a large SNP database to design an ∼54,000 SNP assay for use in the domestic horse and related species. The utility of this SNP array was demonstrated through genome-wide linkage disequilibrium, inbreeding and genetic distance measurements within breeds, as well as multidimensional scaling and parsimony analysis. Association mapping confirmed a large conserved segment containing the chestnut coat color locus in domestic horses. We also assess the utility of the SNP array in related species, including the Przewalski's Horse, zebras, asses, tapirs, and rhinoceros. This SNP genotyping tool will facilitate many genetics applications in equids, including identification of genes for health and performance traits, and compelling studies of the origins of the domestic horse, diversity within breeds, and evolutionary relationships among related species.
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