Signatures of selection in indigenous Chinese cattle genomes reveal adaptive genes and genetic variations to cold climate
Ning Huang, Lihong Zhao, Jinpeng Wang, Qiang Jiang, Zhihua Ju, Xiuge Wang, Chunhong Yang, Yaping Gao, Xiaochao Wei, Yaran Zhang, Yao Xiao, Wenhao Liu, Shaoxiong Lu, Jinming Huang
Abstract
Cold climate shapes the genome of animals and drives them to carry sufficient genetic variations to adapt to changes in temperature. However, limited information is available about the genome-wide pattern of adaptations to cold environments in cattle. In the present study, we used 777K SNP genotyping (15 Chinese cattle breeds, 198 individuals) and whole genome resequencing data (54 cattle breeds of the world, 432 individuals) to disentangle divergent selection signatures, especially between the cold-adapted (annual average temperature of habitat, 6.24 °C to 10.3 °C) and heat-adapted (20.2 °C to 24.73 °C) Chinese native cattle breeds. Genomic analyses revealed a set of candidate genes (e.g., UQCR11, DNAJC18, EGR1, and STING1) were functionally associated with thermogenesis and energy metabolism. We also characterized the adaptive loci of cattle exposed to cold temperatures. Our study finds new candidate genes and provides new insights into adaptations to cold climates in cattle.