Data from: Genome-wide variation within and between wild and domestic yak

The yak is one of the few animals that can thrive in the harsh environment of the Qinghai-Tibetan Plateau and adjacent alpine regions. Yak provide essential resources allowing Tibetans to live at high altitudes. However, genetic variation within and between wild and domestic yak remain unknown. Here, we present a genome-wide study of the genetic variation within and between wild and domestic yak. Using next-generation sequencing technology, we re-sequenced three wild and three domestic yak with a mean of 5-fold coverage using our published domestic yak genome as a reference. We identified a total of 8.38 million SNPs (7.14 million novel), 383,241 InDels and 126,352 structural variants between the six yak. We observed higher linkage disequilibrium in domestic yak than in wild yak and a modest but distinct genetic divergence between these two groups. We further identified more than a thousand of Potential Selected Regions (PSRs) for the three domestic yak by scanning the whole genome. These genomic resources can be further used to study genetic diversity and select superior breeds of yak and other bovid species.牦牛是少数能够在青藏高原及其毗邻高寒山区的严苛环境中繁衍生息的动物之一。牦牛为藏族群众在高海拔地区的生存提供了不可或缺的核心资源。然而，野生与家养牦牛群体内部及其间的遗传变异情况仍未得到明确解析。本研究开展了一项全基因组范围的分析，旨在探究野生与家养牦牛群体内部及其间的遗传变异。本研究借助下一代测序技术，以本课题组已发表的家养牦牛基因组作为参考序列，对3头野生牦牛与3头家养牦牛进行了重测序，平均测序深度达5倍。本次分析共在这6头牦牛中鉴定出总计838万个单核苷酸多态性（SNPs，其中714万个为新鉴定位点）、383241个插入缺失位点（InDels）以及126352个结构变异。本研究发现，家养牦牛的连锁不平衡水平高于野生牦牛，且两类群体间存在程度适中但清晰可辨的遗传分化。本研究进一步通过全基因组扫描，在这3头家养牦牛中鉴定出超过1000个潜在受选区域（Potential Selected Regions，简称PSRs）。本研究获得的这些基因组资源，可进一步用于探究牦牛及其他牛科物种的遗传多样性，并助力其优良品种的选育工作。