Genome-wide association analysis reveals potential candidate genes and genomic regions associated with rear teat morphology in dairy cattle

A.M. Sallam*,1, P.M. VanRaden1, D.J. Null1, L. Ma2, and J.B. Cole1

1USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
2Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742

*Corresponding author

2020 J. Dairy Sci. (?)
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There is growing interest in type traits associated with rear teats because of the importance of teat and udder conformation in voluntary (robotic) milking systems. Several purebred dairy cattle associations now include reat teat placement (RTP), rear teats-rear view (RTR), and rear teats-side view (RTS) in their type appraisal programs because they influence the milking system. There are now enough data to publish routine genetic evaluations for RTP, which as a moderate heritability and is correlated with other important milking traits. Little is known about chromosomal regions or genes associated with RTP, but association analysis using dense whole-genome markers is a powerful approach to detect variants which underlie complex phenotypes. In this study, we used deregressed predicted transmitting abilities for 32,832 Jersey and 36,260 Holstein to investigate the genetic architecture of RTP. The full pedigree and genotypic information for 79,295 single nucleotide polymorphisms (SNP) were used to identify individual markers and larger genomic regions associated with RTP in dairy cattle. Genome-wide association analyses identified multiple SNP and chromosomal regions to be associated with the studied traits. For RTP in Holstein, five of the 10 highest significantly SNP (P = 2.56 x 10-19) were located at 37-38 Mb on Bos taurus autosome (BTA) 26 which includes PRLHR (Prolactin Releasing Hormone Receptor) that is well-known to be involved in lactation. The same genome window accounted for more than 0.53% of the variance explained by all genome windows. Likewise, an interval at 113 Mb on BTA3 included 3 of the 10 most-significantly associated SNP for RTR in Jersey (P = 2.05 x 10-73, 1.24 x 10-53, and 1.32 x 10-48) and accounted for more than 0.26% of the variance explained by all genome windows. Notably, several genes biologically related to muscle development and creatine formation were located in the identified regions for RTS in Jersey, including the PRRX1 and KRTAP gene families, as well as the TBX3 and TBX5 (T-box transcription factors) genes, which influence limb pattern formation and tooth and genital development in mammals. Candidate genes not clearly related to the traits studied may indicate pleiotropic effects or correlated response to selection. Such genes in this study include FRMD4B, FERMT3, TRPM8, MROH2A, and ARHGAP12. These markers may provide useful information when selecting for ideal rear teat morphology in dairy cattle.