Genomic insights into Yanbian cattle: Breed-specific selective sweeps identified by whole-genome sequencing

Abstract

The Chinese Yanbian Yellow cattle are an indigenous East Asian breed, closely related to the Korean Hanwoo cattle, and presumably share the same origin. However, unlike Hanwoo, which has undergone approximately 40 years of intensive artificial selection, Yanbian cattle have remained relatively unselected, preserving diverse genetic characteristics. In this study, we used whole-genome sequencing data from 45 individuals to investigate the unique traits in Yanbian cattle. To identify selective sweep regions and compare the results depending on different methods, we applied three approaches: cross-population extended haplotype homozygosity (XP-EHH), cross-population composite likelihood ratio (XP-CLR), and population branch statistics (PBS) based on the fixation index. Our results highlight the PEX14 gene and SIRT6 gene which play a role in cold adaptation, showing high XP-CLR value with clear evidence of fixation. Notably, the genomic region containing PEX14, which is involved in the browning of white adipose tissue in response to cold exposure, exhibited reduced nucleotide diversity and low Tajima’s D value in Yanbian cattle. This suggests that natural selection has acted on this gene to facilitate cold adaptation. Furthermore, genomic regions with early fixation events were primarily associated with environmental adaptation, whereas more recent fixation events were related to economically important traits. These findings enhance our understanding of the genomic characteristics of Yanbian cattle and support their potential for environmental adaptation, providing valuable insights for future improvement efforts.