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（yak）是少数可在青藏高原及毗邻高山严酷生境中繁衍生息的动物之一。牦牛为藏族人群在高海拔地区的生存提供了至关重要的基础资源。然而，野生与家养牦牛种群内部及种群间的遗传变异情况仍有待探明。本研究针对野生与家养牦牛种群内部及种群间的遗传变异开展了一项全基因组研究（genome-wide study）。借助下一代测序技术（next-generation sequencing technology），本研究以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，平均测序覆盖度达5倍。本研究在这6头牦牛中共鉴定得到838万个单核苷酸多态性位点（SNPs，其中714万个为新发现位点）、383241个插入缺失（InDels）以及126352个结构变异。研究发现，家养牦牛的连锁不平衡（linkage disequilibrium）程度高于野生牦牛，且两类种群间存在适度但显著的遗传分化。通过全基因组扫描，本研究进一步为这3头家养牦牛鉴定出了超过一千个潜在选择区域（Potential Selected Regions, PSRs）。这些基因组资源可被进一步用于研究牦牛及其他牛科物种的遗传多样性，并辅助培育优良牦牛品种。