Development and characterization of a high density SNP genotyping assay for cattle.
Development and characterization of a high density SNP genotyping assay for cattle.
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DOI：
10.1371/journal.pone.0005350
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发表时间：
2009
期刊：
影响因子：
3.7
通讯作者：
Van Tassell CP
中科院分区：
文献类型：
--
作者：
Matukumalli LK;Lawley CT;Schnabel RD;Taylor JF;Allan MF;Heaton MP;O'Connell J;Moore SS;Smith TP;Sonstegard TS;Van Tassell CP
全基因组关联（GWA）研究的成功检测影响人类复杂性状的序列变异，激发了人们的兴趣，在使用大规模的高密度单核苷酸多态性（SNP）基因分型的数量性状位点（QTL）的识别和标记辅助选择模式和农业物种。描述了一种用于开发定制基因分型测定的成本效益和有效的方法，所述定制基因分型测定询问54，001个SNP位点以支持牛中的GWA应用。一种用于实现压缩的标记间间隔分布的新算法被证明是非常成功的，中值间隔为37 kb，最大预测间隙<350 kb。在来自21个牛品种和6个外群物种的576只动物的一组动物上测试该测定，并显示从39，765到46，492个SNP在个体品种内是多态的（平均次要等位基因频率（MAF）范围从0.24到0.27）。该试验还在牛中鉴定了79种推定的拷贝数变异。通过将已知的毛色变异和角的存在/不存在定位到其正确的基因组位置来证明GWA的实用性。SNP选择和新的间隔算法的组合允许在具有完全或甚至中等质量草图序列的物种中开发高密度基因分型平台的有效方法。该方法的各个方面可以在缺乏可用基因组序列的物种中利用。本文所述的BovineSNP 50测定可从Illumina商购获得，并且提供了用于在牛中定位疾病基因和QTL的稳健平台。
The success of genome-wide association (GWA) studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (SNP) genotyping for the identification of quantitative trait loci (QTL) and for marker-assisted selection in model and agricultural species. A cost-effective and efficient approach for the development of a custom genotyping assay interrogating 54,001 SNP loci to support GWA applications in cattle is described. A novel algorithm for achieving a compressed inter-marker interval distribution proved remarkably successful, with median interval of 37 kb and maximum predicted gap of <350 kb. The assay was tested on a panel of 576 animals from 21 cattle breeds and six outgroup species and revealed that from 39,765 to 46,492 SNP are polymorphic within individual breeds (average minor allele frequency (MAF) ranging from 0.24 to 0.27). The assay also identified 79 putative copy number variants in cattle. Utility for GWA was demonstrated by localizing known variation for coat color and the presence/absence of horns to their correct genomic locations. The combination of SNP selection and the novel spacing algorithm allows an efficient approach for the development of high-density genotyping platforms in species having full or even moderate quality draft sequence. Aspects of the approach can be exploited in species which lack an available genome sequence. The BovineSNP50 assay described here is commercially available from Illumina and provides a robust platform for mapping disease genes and QTL in cattle.
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作者：
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