Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data.
Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data.
复制标题
利用基因组重测序数据表征猪群规模上的简单序列重复变异。
DOI：
10.1038/s41598-017-02600-8
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发表时间：
2017-05-24
影响因子：
4.6
通讯作者：
Zhao S
中科院分区：
文献类型：
--
作者：
Liu C;Liu Y;Zhang X;Xu X;Zhao S
简单序列重复（SSR）在许多物种中被用作多态性分子标记。它们在一系列复杂性状中贡献了非常重要的功能变异；然而，人们对猪群中大多数 SSR 的变化知之甚少。在这里，我们利用基因组重测序数据，从 100 多个个体中鉴定出了约 63 万个多态性 SSR 位点。通过对该数据集的深入分析，我们发现SSR基序组成、基序长度、等位基因总长度和等位基因分布都有助于SSR变异。此外，我们发现含有CG的SSR表现出显着较低的多态性和较高的跨物种保守性。通过严格的筛选程序，我们提供了16,527个高质量多态性SSR的目录，这些目录为系统发育关系分析提供了可靠的结果，并为从8个中国地方猪品种、6个商业瘦肉型猪品种和中国野猪中平均选择的30个个体提供了有价值的汇总统计。此外，从高质量多态性SSR目录中，我们鉴定了四个具有潜在功能丧失等位基因的位点。总体而言，这些分析为现有的猪遗传变异数据库提供了有价值的多态性 SSR 目录，我们相信该目录可用于未来的全基因组遗传分析。
Simple sequence repeats (SSRs) are used as polymorphic molecular markers in many species. They contribute very important functional variations in a range of complex traits; however, little is known about the variation of most SSRs in pig populations. Here, using genome resequencing data, we identified ~0.63 million polymorphic SSR loci from more than 100 individuals. Through intensive analysis of this dataset, we found that the SSR motif composition, motif length, total length of alleles and distribution of alleles all contribute to SSR variability. Furthermore, we found that CG-containing SSRs displayed significantly lower polymorphism and higher cross-species conservation. With a rigorous filter procedure, we provided a catalogue of 16,527 high-quality polymorphic SSRs, which displayed reliable results for the analysis of phylogenetic relationships and provided valuable summary statistics for 30 individuals equally selected from eight local Chinese pig breeds, six commercial lean pig breeds and Chinese wild boars. In addition, from the high-quality polymorphic SSR catalogue, we identified four loci with potential loss-of-function alleles. Overall, these analyses provide a valuable catalogue of polymorphic SSRs to the existing pig genetic variation database, and we believe this catalogue could be used for future genome-wide genetic analysis.