Genome-wide association and functional genomic analyses for udder conformation traits derived from data recorded by robotic milking systems in American Holstein cattle

The implementation of automatic milking systems (AMS) in modern dairy farming has significantly facilitated genetic evaluation of udder conformation traits in dairy cattle. As AMS-based udder conformation traits are highly heritable in Holstein cattle, this study aimed to identify genomic regions, QTL, and genes significantly associated with 3 udder conformation traits derived from Cartesian coordinates recorded by AMS in American Holstein cows. The traits evaluated included udder depth (UD), udder balance (UB), and distance front-rear (DFR). Phenotypic data consisted of 4,232,026 visit records to 36 Lely Astronaut A5 AMS robots for 4,280 American Holstein cows. A total of 4,118 cows also had genomic information for 57,598 SNPs. The SNP effects, together with their approximate P-values and proportion of the total additive genetic variance explained by them, were back solved from the GEBV using the POSTGSF90 software (version 2024-12-26, BLUPF90 Family of Programs, University of Georgia, Athens, GA). Multiple testing correction was applied using a modified Bonferroni method based on the number of independent chromosomal segments, and functional enrichment analyses were performed for the candidate positional genes and QTL. We identified 5 (BTA4, BTA22, and BTA29), 15 (BTA2, BTA8, BTA9, BTA15, BTA18, BTA23, and BTA26), and 19 (BTA1, BTA4, BTA6, BTA9, BTA10, BTA14, BTA17, BTA18, BTA23, and BTA25) genome-wide SNPs significantly associated with UB, DFR, and UD, respectively. There were no significant SNPs capturing more than 0.5% of the total additive genetic variance, highlighting the highly polygenic nature of these traits. The candidate genes overlapping with these genomic regions were previously reported to have biological functions that included but were not limited to transcription regulation, DNA repair mechanisms, inflammatory responses, epithelial differentiation processes, nutrient transport, extracellular matrix stabilization, cell division, and immune regulation. The strongest candidate genes associated with udder conformation traits are AFM, AFP, CREBBP, NLRP12, SP3, EBF2, B4GALT1, HDAC9, CDK13, and KDM2A. Furthermore, many QTL known to be associated with various milk production, reproduction, and health traits overlapped with the significant SNPs identified in this study. In summary, we identified significant genetic markers, candidate genes, and genomic regions associated with these traits, offering insights into the genetic architecture underlying udder conformation in Holstein cattle and its implications for dairy production.