Genomic diversity in Chinese Holstein cattle and genome-wide association study for body conformation traits

The genomic diversity of Chinese Holstein cattle remains insufficiently characterized, and the identification of genes associated with body conformation traits is still limited. In this study, we aimed to explore the genome-wide diversity and population structure, and to identify candidate genes associated with 20 body conformation traits in Chinese Holstein cattle from six farms using the GGP Bovine 50 K single nucleotide polymorphism (SNP) chip.

We analyzed runs of homozygosity and population admixture across farms and observed genetic diversity differences among herds. A genome-wide association study identified 21 significant SNPs linked to five body conformation traits. Notably, a missense mutation in TJP1 (BovineHD2100008355) was associated with foot heel depth. Ten SNPs within intronic regions of genes such as GABRG3, NEGR1, and CDH2 were associated with various udder and leg traits. The remaining ten SNPs were located in intergenic regions and influenced transcription factor binding sites. Among them, BovineHD2100013266, BovineHD0500004109, and BTB-00042676 were shown to regulate transcriptional activity through dual-luciferase reporter assays.

Our findings offer valuable insights for managing genetic inbreeding in cattle farms, enhancing the understanding of the genetic architecture underlying body conformation traits in Holstein cattle, and accelerating the genomic selection process in Chinese Holsteins.