Selection signatures of Qinchuan cattle based on whole-genome sequences

Qinchuan cattle has gradually improved in body shape and growth rate in the long-term breeding process from the draft cattle to beef cattle. As the head of the five local yellow cattle in China, the Qinchuan cattle has been designated as a specialized beef cattle breed. We investigated the selection signatures using whole genome sequencing data in Qinchuan cattle. Based on <i>F</i>st, we detected hundreds of candidate genes under selection across Qinchuan, Red Angus, and Japanese Black cattle. Through protein-protein interaction analysis and functional annotation of candidate genes, the results revealed that <i>KMT2E</i>, <i>LTBP1</i> and <i>NIPBL</i> were related to brain size, body characteristics, and limb development, respectively, suggesting that these potential genes may affect the growth and development traits in Qinchuan cattle. <i>ARIH2</i>, <i>DACT1</i> and <i>DNM2</i>, <i>et al.</i> are related to meat quality. Meanwhile, <i>TBXA2R</i> can be used as a gene associated with reproductive function, and <i>USH2A</i> affect coat color. This provided a glimpse into the formation of breeds and molecular genetic breeding. Our findings will promote genome-assisted breeding to improve animal production and health.