Genome-wide analyses to identify genomic regions associated with udder morphology traits in dairy sheep

In dairy sheep, mammary morphology-related phenotypes are crucial functional traits due to their connection to machine milking aptitude, udder health, particularly mastitis, and animal welfare. This study aimed to dissect the genetic architecture underlying 5 mammary morphology traits (Udder depth, Udder attachment, Teat placement, Teat size, and Udder shape) in Churra dairy sheep by using data generated with the Illumina OvineSNP50 BeadChip. The analyzed population, part of the Churra Dairy Selection Nucleus (ANCHE), comprised 1,680 ewes distributed across 16 half-sib families. Genome scans using linkage analysis and a GWAS detected 5 genome-wide significant QTL regions. Comparison with previously reported sheep QTL revealed no direct overlap; however, several of the identified regions coincided with QTL reported in cattle for mammary morphology and mastitis resistance traits, suggesting the possibility of conserved genetic mechanisms underlying these traits across ruminant species and further supporting the relevance and validity of the genomic regions detected in this study. Interestingly, the genome-wide significant QTL region detected on OAR13 for Teat placement showed overlapping with chromosome-wide effects on Udder shape, suggesting for this region a potential pleiotropy effect or the presence of closely linked variants affecting multiple udder traits. To further explore the genome-wide significant regions identified in this study, all genes within each region were annotated. Among the 84 annotated genes, 3 of them, NCOA3, ASS1, and TMEFF2, directly overlapped with a previously defined reference gene list for udder traits and were therefore considered direct functional candidate genes. These genes were associated with epithelial branching, extracellular matrix regulation, cytoskeletal dynamics, and signaling pathways. For the remaining annotated genes in the target regions, a prioritization analysis was performed to identify additional potential candidate genes that may be relevant to the traits under study. The results reported here offer a valuable insight into the genetic basis of udder morphology traits in dairy sheep and are a first step into the identification of genetic markers that could improve the efficiency of future genomic selection programs in dairy sheep.