Signatures of Selection and Interspecies Introgression in the Genome of Chinese Domestic Pigs.
Signatures of Selection and Interspecies Introgression in the Genome of Chinese Domestic Pigs.
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中国家猪基因组的选择和种间渗入特征
DOI：
10.1093/gbe/evx186
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发表时间：
2017-10-01
影响因子：
3.3
通讯作者：
Huang L
中科院分区：
文献类型：
--
作者：
Zhu Y;Li W;Yang B;Zhang Z;Ai H;Ren J;Huang L
摘要 中国家猪几千年来经历了强烈的人工选择。然而，中国家猪选择引起表型变化的分子机制仍然很大程度上未知。在这里，我们使用了来自中国 9 个不同品种的 54 头猪和来自中国 7 个地区的 16 头野猪的全基因组重测序数据，以确定在驯化过程中显示正选择证据的基因。通过遗传分化和变异的选择性扫描分析，共检测到14个候选驯化区域，并发现这些候选驯化区域中的一组基因与代谢过程、发育、繁殖、嗅觉、行为和神经系统相关。最有希望的候选基因——TBX19——可能是代谢改变和发育特征的基础，也可能与中国家猪的胆怯有关。有趣的是，我们发现几乎所有中国家猪共有的TBX19位点的单倍型可能是从另一个猪种渗入的。我们还发现与女性生殖相关的 AHR 基因处于强正选择之下。这些结果增进了我们对中国家猪进化史的理解，并为识别有助于猪表型多样性的功能性重要基因/突变提供了见解。
Abstract Chinese domestic pigs have experienced strong artificial selection for thousands of years. However, the molecular mechanisms underlying the selection-causing phenotypic changes in Chinese domestic pigs are still largely unknown. Here we used whole-genome resequencing data of 54 pigs from 9 Chinese diverse breeds and 16 wild boars from 7 localities across China to identify genes that show evidence of positive selection in the process of domestication. A total of 14 candidate domestication regions were detected by selective sweep analyses of genetic differentiation and variability, and a set of genes in these candidate domestication regions were found to be related to metabolic process, development, reproduction, olfactory, behavior, and nervous system. The most promising candidate gene under selection - TBX19 - probably underlies the metabolic alteration and developmental traits, and may also associate with timidity of Chinese domestic pigs. Intriguingly, we found that the haplotype at TBX19 locus shared by nearly all Chinese domestic pigs was possibly introgressed from another Sus species. We also revealed the AHR gene associated with female reproduction is under strong positive selection. These results advance our understanding of the evolutionary history of Chinese domestic pigs and shed insights into identifying functionally important genes/mutations contributing to the phenotypic diversity in pigs.
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