Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in Qinghai, China.
Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in Qinghai, China.
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DOI：
10.3389/fgene.2022.1034094
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发表时间：
2022
影响因子：
3.7
通讯作者：
中科院分区：
文献类型：
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中国青海省位于青藏高原东北部地区，拥有丰富的牦牛遗传资源。此前对考古记录、线粒体DNA和Y染色体标记的调查表明，青海是牦牛驯化的主要中心。在本研究中，我们使用高深度全基因组重测序数据检查了来自9个牦牛品种/群体（野生、大同、环湖、雪朵、玉树、祁连、格尔木、同德和互助白）的113头青海牦牛（包括42头新测序的青海牦牛和71头公开个体）的基因组多样性、分化和选择特征。我们观察到，基于四个基因组参数（核苷酸多样性、近交系数、连锁不平衡衰减和纯合性运行），大多数青海牦牛品种/群体具有丰富的基因组多样性。群体遗传结构分析表明，青海牦牛有两个谱系、两个祖先起源，9个牦牛品种/群体聚集成三个不同的类群：野牦牛、格尔木牦牛和其他7个家养牦牛品种/群体。 F ST 值显示野牦牛、格尔木牦牛和其他青海牦牛品种/群体之间存在中等遗传分化。在与抗病性（CDK2AP2、PLEC和CYB5B）、热应激（NFAT5、HSF1和SLC25A48）、色素沉着（MCAM、RNF26和BOP1）、视力（C1QTNF5、MFRP和TAX1BP3）、牛奶质量（OPLAH和GRINA）、神经发育（SUSD4、INSYN1和PPP1CA) 和肉类质量 (ZRANB1)，使用集成 PI、复合似然比 (CLR) 和 F ST 方法。这些发现为了解牦牛目标性状的遗传机制提供了新的见解，并为了解青海牦牛品种/群体的基因组特征提供了重要信息。
The Qinghai Province of China is located in the northeast region of the Qinghai–Tibetan Plateau (QTP) and carries abundant yak genetic resources. Previous investigations of archaeological records, mitochondrial DNA, and Y chromosomal markers have suggested that Qinghai was the major center of yak domestication. In the present study, we examined the genomic diversity, differentiation, and selection signatures of 113 Qinghai yak, including 42 newly sequenced Qinghai yak and 71 publicly available individuals, from nine yak breeds/populations (wild, Datong, Huanhu, Xueduo, Yushu, Qilian, Geermu, Tongde, and Huzhu white) using high-depth whole-genome resequencing data. We observed that most of Qinghai yak breeds/populations have abundant genomic diversity based on four genomic parameters (nucleotide diversity, inbreeding coefficients, linkage disequilibrium decay, and runs of homozygosity). Population genetic structure analysis showed that Qinghai yak have two lineages with two ancestral origins and that nine yak breeds/populations are clustered into three distinct groups of wild yak, Geermu yak, and seven other domestic yak breeds/populations. F ST values showed moderate genetic differentiation between wild yak, Geermu yak, and the other Qinghai yak breeds/populations. Positive selection signals were detected in candidate genes associated with disease resistance (CDK2AP2, PLEC, and CYB5B), heat stress (NFAT5, HSF1, and SLC25A48), pigmentation (MCAM, RNF26, and BOP1), vision (C1QTNF5, MFRP, and TAX1BP3), milk quality (OPLAH and GRINA), neurodevelopment (SUSD4, INSYN1, and PPP1CA), and meat quality (ZRANB1), using the integrated PI, composite likelihood ratio (CLR), and F ST methods. These findings offer new insights into the genetic mechanisms underlying target traits in yak and provide important information for understanding the genomic characteristics of yak breeds/populations in Qinghai.