Genome-wide variation landscape reveals temperature adaptation in Chinese indigenous cattle

BACKGROUND: The significant temperature variations across northern and southern China have driven the adaptive evolution of Chinese native cattle breeds, allowing them to thrive in diverse and extreme bioclimate environments. Understanding how these breeds have adapted to varying temperatures is essential for identifying genetic factors that contribute to their survival in such conditions. RESULTS: In this study, using whole-genome sequence data of 336 individuals (with an average sequencing depth of 30.12 ×) from 21 cattle breeds, including 8 breeds from cold regions, 3 from warm regions, and 10 from hot regions, clear genetic differentiation among the three groups of breeds was revealed. Using whole-genome SNP, InDel, and SV data, a series of selective genomic regions, genes, and variants/SVs associated with cold or hot temperature adaptability were identified. Key genes, including KLB, HSPA4, ECSCR, DNAJC18 and SLC9A1 are speculated to be responsible for cold/hot adaptability based on the extreme difference in allele frequency of the selective variants/SVs harbored by these genes, their known biological functions, protein-protein interaction network, findings from previous studies on their relation to environmental adaptation, and their tissue specificities. CONCLUSIONS: By integrating SNP, InDel, and SV data, this study provides a comprehensive genetic framework for understanding selective environmental adaptation. These findings enhance our understanding of the mechanisms underlying temperature adaptation in cattle and offer a molecular foundation for the development of new breeds.