Genome Variation Map of Domestic Qinghai-Tibet Plateau Yaks by SLAF-Seq Reveals Genetic Footprint during Artificial Selection

SIMPLE SUMMARY: The yak is endemic to the Qinghai-Tibetan Plateau (QTP) and serves as an important livestock animal for Tibetan pastoral society. Phenotypic traits vary among domestic yaks. However, genomic characteristics, population structure, and the genetic relationship of domestic yaks with wild yaks have not been effectively characterized until now. In this study, six domestic populations were sequenced, and selective sweep regions involved in yak domestication were detected. Furthermore, divergence time for domestic and wild yaks was estimated. This study revealed new insight into selection for domestic and wild yaks. ABSTRACT: The yak (Bos grunniens) was domesticated in the high-altitude QTP. Research about their genetic diversity and population structure is limited. In this study, we resequenced the genome of 494 domestic yaks using Specific-Locus Amplified Fragment Sequencing (SLAF-seq). The survey was conducted on six populations sampled from isolated locations in China in order to analyze their structure and genetic diversity. These six domestic populations were clearly grouped into two independent clusters, with Jinchuan, Changtai, and Jiulong showing a tight genetic relationship with the wild yak. Nerve development pathways were enriched with GO enrichment analysis of 334 domesticated genes. Major genomic regions associated with the differentiation of domestic yaks were detected. These findings provide preliminary information on the yak genome variability, useful to understand the genomic characteristics of different populations in QTP.