Genome-wide Association Analysis of Body Conformation Traits in Chinese Holstein Cattle

Background The body conformation traits of dairy cattle are closely related to their production performance and health. The present study aimed to identify gene variants associated with body conformation traits in Chinese Holstein cattle and provide marker loci for genomic selection in dairy cattle breeding. The study findings could offer robust theoretical support to optimize the health of dairy cattle and enhance their production performance. Results This study involved 586 Chinese Holstein cows, using the predicted transmitting abilities (PTAs) of 17 body conformation traits evaluated by the Council on Dairy Cattle Breeding in the USA as phenotypic values. These traits were categorized into body size traits, rump traits, feet/legs traits, udder traits, and dairy characteristic traits. Based on the genomic profiling results from the Genomic Profiler Bovine 100K SNP chip, genotype data were quality-controlled using PLINK software, retaining 586 individuals and 80,713 SNPs for further analysis. Genome-wide association studies (GWAS) were conducted using the GEMMA software, employing both univariate linear mixed models (LMM) and multivariate linear mixed models (mvLMM). The Bonferroni method was used to determine the significance threshold, identifying gene variants significantly associated with body conformation traits in Chinese Holstein cows. The single-trait GWAS identified 24 SNPs significantly associated with body conformation traits (P < 0.01), with annotation leading to the identification of 21 candidate genes. The multivariate GWAS identified 54 SNPs, which were annotated to 57 candidate genes, including 39 new SNPs not identified in the single-trait GWAS. Additionally, 14 SNPs in the 86.84–87.41 Mb region of chromosome 6 were significantly associated with multiple traits such as body size, udder, and dairy characteristics. Four genes—SLC4A4, GC, NPFFR2, and ADAMTS3—were annotated in this region. Conclusions A total of 63 SNPs were identified as significantly associated with the 17 body conformation traits in Chinese Holstein cows through both single-trait and multivariate GWAS analyses. Sixty-six candidate genes were annotated, with 12 genes identified by both methods, including SLC4A4 , GC , NPFFR2 , and ADAMTS3 , which are involved in biological processes such as active glucose transport, adipogenesis, and neural development. Thus, the study findings provided potential genetic marker information related to body conformation traits for the breeding of Chinese Holstein cattle.