A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.
A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.
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猪短串联重复序列及其与进化和环境适应的关联的全球地图
DOI：
10.1186/s12711-021-00631-4
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发表时间：
2021-04-23
期刊：
影响因子：
--
通讯作者：
Huang L
中科院分区：
文献类型：
--
作者：
Wu Z;Gong H;Zhang M;Tong X;Ai H;Xiao S;Perez-Enciso M;Yang B;Huang L
背景短串联重复序列(STR)是一种比单核苷酸多态(SNPs)具有更大突变率的遗传标记，广泛应用于遗传学研究和法医学。结果本研究从全球22个家养猪品种/群体、欧亚野猪和众多的水猪外群中筛选出394个基因组，鉴定出878,967个多态STR(PSTR)，这是迄今为止猪中最大的PSTR库。我们发现了多条证据表明，编码区的pSTR受纯化选择的影响。三核苷酸pSTR在编码序列(CDS)、5‘非编码区和H3K4me3区的富集性表明，三核苷酸STR是相应基因外显子和启动子的重要组成部分。我们证明，与SNP相比，pSTR在确定个体的品种身份方面提供了类似甚至更高的准确性。我们发现在亚洲和欧洲的家猪和野猪之间存在显著的种群分化。我们还观察到一些pSTR与环境变量显著相关，如中国地方品种起源地的年平均温度或海拔，其中我们发现了与AHR、LAS1LandPDK1等基因重叠的功能丧失和/或扩展的STR。最后，我们的结果显示，在100kb的窗口内，几个pSTR在家猪-野猪的分化或与所分析的环境变量的关联中显示出比侧翼SNPs更强的信号。结论本研究基于基因组测序数据提供了不同猪群体中pSTR的全基因组高密度图谱，使人们能够更全面地描述它们在进化和环境适应中的作用。
BackgroundShort tandem repeats (STRs) are genetic markers with a greater mutation rate than single nucleotide polymorphisms (SNPs) and are widely used in genetic studies and forensics. However, most studies in pigs have focused only on SNPs or on a limited number of STRs.ResultsThis study screened 394 deep-sequenced genomes from 22 domesticated pig breeds/populations worldwide, wild boars from both Europe and Asia, and numerous outgroup Suidaes, and identified a set of 878,967 polymorphic STRs (pSTRs), which represents the largest repository of pSTRs in pigs to date. We found multiple lines of evidence that pSTRs in coding regions were affected by purifying selection. The enrichment of trinucleotide pSTRs in coding sequences (CDS), 5′UTR and H3K4me3 regions suggests that trinucleotide STRs serve as important components in the exons and promoters of the corresponding genes. We demonstrated that, compared to SNPs, pSTRs provide comparable or even greater accuracy in determining the breed identity of individuals. We identified pSTRs that showed significant population differentiation between domestic pigs and wild boars in Asia and Europe. We also observed that some pSTRs were significantly associated with environmental variables, such as average annual temperature or altitude of the originating sites of Chinese indigenous breeds, among which we identified loss-of-function and/or expanded STRs overlapping with genes such asAHR,LAS1LandPDK1. Finally, our results revealed that several pSTRs show stronger signals in domestic pig—wild boar differentiation or association with the analysed environmental variables than the flanking SNPs within a 100-kb window.ConclusionsThis study provides a genome-wide high-density map of pSTRs in diverse pig populations based on genome sequencing data, enabling a more comprehensive characterization of their roles in evolutionary and environmental adaptation.
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影响因子：
--
作者：
Araujo PR;Yoon K;Ko D;Smith AD;Qiao M;Suresh U;Burns SC;Penalva LO
通讯作者：
Penalva LO
影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O
影响因子：
14.9
作者：
Bult CJ;Blake JA;Smith CL;Kadin JA;Richardson JE;Mouse Genome Database Group
通讯作者：
Mouse Genome Database Group
影响因子：
7.7
作者：
Dawson, Deborah A.;Horsburgh, Gavin J.;Burke, Terry
通讯作者：
Burke, Terry
影响因子：
14.9
作者：
Benson, G
通讯作者：
Benson, G