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基于基因组重测序数据的大规模猪群体简单重复序列变异特征分析。

Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data.

机构信息

Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Lab of Swine Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.

The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China.

出版信息

Sci Rep. 2017 May 24;7(1):2376. doi: 10.1038/s41598-017-02600-8.

DOI:10.1038/s41598-017-02600-8
PMID:28539617
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5443785/
Abstract

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.

摘要

简单序列重复（SSRs）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产生非常重要的功能变异；然而，对于大多数猪群体中的 SSR 变异知之甚少。在这里，我们使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、等位基因的总长度和等位基因的分布都有助于 SSR 的变异性。此外，我们发现含有 CG 的 SSR 表现出显著较低的多态性和较高的跨物种保守性。通过严格的过滤程序，我们提供了 16527 个高质量的多态性 SSR 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 个中国本地猪品种、6 个商业瘦肉猪品种和中国野猪中随机选择的 30 个个体提供了有价值的汇总统计数据。此外，从高质量的多态性 SSR 目录中，我们鉴定出了 4 个可能具有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。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/511a/5443785/57f9cb5b2039/41598_2017_2600_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/511a/5443785/1bbb4ef3186a/41598_2017_2600_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/511a/5443785/1f98162fc59a/41598_2017_2600_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/511a/5443785/22aad526f94b/41598_2017_2600_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/511a/5443785/407bcf07398c/41598_2017_2600_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/511a/5443785/242a71b51679/41598_2017_2600_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/511a/5443785/57f9cb5b2039/41598_2017_2600_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/511a/5443785/1bbb4ef3186a/41598_2017_2600_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/511a/5443785/1f98162fc59a/41598_2017_2600_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/511a/5443785/22aad526f94b/41598_2017_2600_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/511a/5443785/407bcf07398c/41598_2017_2600_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/511a/5443785/242a71b51679/41598_2017_2600_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/511a/5443785/57f9cb5b2039/41598_2017_2600_Fig6_HTML.jpg

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