Genetic Ancestry and Genome-Wide Association Study Combined with Functional Enrichment Analyses Reveal Candidate Genes for Body Conformation Traits in Hexi Cattle.

Hexi cattle are a local cattle population endemic to the Hexi Corridor in Gansu Province, China, and exhibit strong adaptability to the region's arid continental environment. However, comprehensive genomic investigations of this population are still lacking. In the present study, we integrated population genomic analyses with a genome-wide association study (GWAS) to dissect the genetic architecture of Hexi cattle. Whole-genome resequencing data were generated for 264 Hexi cattle, and public genomic datasets from six representative cattle breeds were obtained from the NCBI database for comparative analysis. Multiple analytical approaches-including principal component analysis (PCA), linkage disequilibrium (LD) decay analysis, neighbor-joining (NJ) phylogenetic tree construction, and ADMIXTURE analysis-were adopted to evaluate population structure and evolutionary relationships. A mixed linear model was then used to identify significant SNPs associated with five major body conformation traits in six-month-old cattle: body weight (BW), withers height (WH), hip height (HH), heart girth (HG), and abdominal girth (AG). Our results confirm the admixed nature of Hexi cattle, whose genome is derived primarily from Simmental cattle and secondarily from Mongolian cattle. A total of 69 trait-associated significant SNPs were identified and functionally annotated. Specifically,