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.

牦牛是少数能在青藏高原及周边高寒山区的严苛环境中存活繁衍的动物之一。牦牛为藏族人群在高海拔地区的生存提供了必需的生活资源。然而，目前野生牦牛与家养牦牛群体内部及二者之间的遗传变异情况仍不明晰。本研究针对野生与家养牦牛的群体内部及群体间遗传变异开展全基因组层面的分析：采用下一代测序技术，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头家养牦牛进行重测序，平均测序深度达5倍。本研究在6头牦牛中共鉴定得到838万个单核苷酸多态性位点（Single Nucleotide Polymorphism, SNP，其中714万个为新发现位点）、383241个插入缺失变异（Insertion-Deletion, InDel）以及126352个结构变异（Structural Variant, SV）。研究发现，家养牦牛的连锁不平衡程度高于野生牦牛，且两类群体间存在程度适中但显著的遗传分化。本研究进一步通过全基因组扫描，为3头家养牦牛鉴定得到千余个潜在选择区域（Potential Selected Regions, PSRs）。上述基因组资源可进一步用于牦牛及其他牛科物种的遗传多样性研究与优良品种选育工作。