Li Guangzhen, Luo Jing, Wang Fuwen, Xu Donghui, Ahmed Zulfiqar, Chen Shengmei, Li Ruizhe, Ma Zhijie
Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China.
Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Xining, China.
Front Genet. 2023 Jan 10;13:1034094. doi: 10.3389/fgene.2022.1034094. eCollection 2022.
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. 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 (, , and ), heat stress (, , and ), pigmentation (, , and ), vision (, , and ), milk quality ( and ), neurodevelopment (, , and ), and meat quality (), using the integrated PI, composite likelihood ratio (CLR), and 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.
中国青海省位于青藏高原东北部，拥有丰富的牦牛遗传资源。先前对考古记录、线粒体DNA和Y染色体标记的研究表明，青海是牦牛驯化的主要中心。在本研究中，我们利用高深度全基因组重测序数据，对来自9个牦牛品种/群体（野生、大通、环湖、雪多、玉树、祁连、格尔木、同德和互助白）的113头青海牦牛的基因组多样性、分化和选择信号进行了研究，其中包括42头新测序的青海牦牛和71个公开可用的个体。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子连续区域），我们观察到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和两个祖先起源，九个牦牛品种/群体被聚类为野生牦牛、格尔木牦牛和其他七个家养牦牛品种/群体三个不同的组。FST值显示野生牦牛、格尔木牦牛与其他青海牦牛品种/群体之间存在中等程度的遗传分化。使用综合PI、复合似然比（CLR）和FST方法，在与抗病性（SLC39A8、IFI27和IRF1）、热应激（HSP90AA1、HSPB1和HSPA8）、色素沉着（TYR、ASIP和MC1R）、视觉（RHO、OPN1LW和OPN1MW）、牛奶品质（CSN1S1和CSN2）、神经发育（BDNF、NCAM1和NTNG1）和肉质（CAST）相关的候选基因中检测到正选择信号。这些发现为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。
