Structural Variations Associated with Adaptation and Coat Color in Qinghai‐Tibetan Plateau Cattle

Abstract Structural variations (SVs) play crucial roles in the evolutionary adaptation of domesticated animals to natural and human‐controlled environments, but SVs have not been explored in Tibetan cattle, which recently migrated and rapidly adapted to the high altitudes of the Qinghai‐Tibetan Plateau (QTP). In this study, a de novo chromosome‐level genome assembly for Tibetan cattle is constructed. It is found that using a lineage‐specific reference genome significantly increased variant detection accuracy and completeness. Analysis of long‐read sequencing data from 36 high‐altitude QTP and 48 low‐altitude cattle identified 222 528 SVs and 259 SV hotspot regions. Positively selected SVs in high‐altitude cattle are related to energy metabolism erythropoiesis and angiogenesis, and peroxisomal metabolism. A 102‐bp intronic deletion in GNPAT likely upregulated its expression. It is distinguished 7293 SVs that may be introgressed from yak, including variants upstream of the hypoxia‐inducing gene EGLN1 . Finally, a ≈2‐Mb heterozygous inversion and two translocations on chromosome 6 are likely associated with the cattle gray coat via regulatory effects on the KIT gene. The results confirm the importance of SVs in evolutionary adaptation and the contribution yak‐introgressed SVs to the rapid acclimatization of QTP cattle.