Genome-wide association and functional genomic analyses of teat placement traits derived from robotic milking systems in American Holstein cattle

Automated milking systems (AMS) enable the generation of objective measurements of teat placement, a key factor influencing milking efficiency and udder health. In this context, we performed GWAS to investigate the genetic background of 2 teat placement traits, i.e., rear teat distance (RTD) and front teat distance (FTD), derived from Cartesian coordinates recorded by AMS in American Holstein cows. Phenotypic data were collected from 36 AMS robots, resulting in 4,232,026 records from 4,118 cows genotyped for 57,598 SNPs. The GWAS was performed using the POSTGSF90 software, with SNP effects estimated by back-solving genomic EBV, followed by calculation of approximate P-values. For RTD, we identified 7 chromosome-wise significant SNPs located on chromosomes BTA8, BTA9, and BTA26. These genomic regions overlap with strong candidate genes, including HTR1B, PRLHR, EMX2, and GRK5, which have been previously associated with milk production, growth, and muscular development. A total of 203 previously reported QTL were found in the BTA9 and BTA26 regions identified for RTD, indicating the complex genetic background of this trait. For FTD, 8 significant SNPs were identified on BTA2, BTA8, BTA18, and BTA28, encompassing key genes such as UBE2R2, UBAP2, and NLRP12. We identified 46 QTL overlapping with these regions, which were previously associated with traits such as susceptibility to bovine respiratory disease, length of productive life, and stayability. These results suggest a genetic link between teat spacing and cow health and longevity. Overall, our findings indicate a polygenic basis for both FTD and RTD, with numerous small-effect variants associated with teat placement. The identified genomic regions and candidate genes associated with these traits contribute to enhancing our understanding of the biological mechanisms underlying teat placement traits in American Holstein cattle.