Genome-Wide Association Study on Reproduction-Related Body-Shape Traits of Chinese Holstein Cows

Simple Summary Reproduction plays a pivotal role in dairy cow farming. Good reproductive performance in cows can decrease the elimination rate of cows, increase the success rate of breeding, and thereby enhance milk production. Identification of the genetic variants in reproduction-related traits helps to increase the genetic improvement of cows’ reproductive performance. In this study, we estimated the genetic parameters of three indicators of reproductive ability, namely, Loin Strength (LS), Rump Angle (RA), and Pin Width (PW), and conducted a genome-wide association study of them. The heritability of these three traits was medium, and in total, 11 significant single-nucleotide polymorphisms (SNPs) were detected. Through a bioinformatics analysis of the genes adjacent to these variants, 16 candidate genes were identified as being associated with these three traits. We expect that the results could help with the genetic improvement of Chinese Holstein cows’ reproductive performance. Abstract Reproduction is an important production activity for dairy cows, and their reproductive performance can directly affect the level of farmers’ income. To better understand the genomic regions and biological pathways of reproduction-related traits of dairy cows, in the present study, three body shape traits—Loin Strength (LS), Rump Angle (RA), and Pin Width (PW)—were selected as indicators of the reproductive ability of cows, and we conducted genome-wide association analyses on them. The heritability of these three traits was medium, ranging from 0.20 to 0.38. A total of 11 significant single-nucleotide polymorphisms (SNPs) were detected associated with these three traits. Bioinformatics analysis was performed on genes close to the significant SNPs (within 200 Kb) of LS, RA, and PW, and we found that these genes were totally enriched in 20 gene ontology terms and six KEGG signaling pathways. Finally, the five genes CDH12, TARP, PCDH9, DTHD1, and ARAP2 were selected as candidate genes that might affect LS. The six genes LOC781835, FSTL4, ATG4C, SH3BP4, DMP1, and DSPP were selected as candidate genes that might affect RA. The five genes USP6NL, CNTN3, LOC101907665, UPF2, and ECHDC3 were selected as candidate genes that might affect the PW of Chinese Holstein cows. Our results could provide useful biological information for the improvement of body shape traits and contribute to the genomic selection of Chinese Holstein cows.