Genomic analysis reveals convergent signatures of selection for milk traits in sheep and goats

Abstract Background Convergent evolution offers a unique lens through which to explore the molecular underpinnings of significant phenotypic transformations. Similar selective pressures likely drove the evolution of analogous milk traits in sheep and goats. Consequently, the current study aimed to identify common selection signals for milk traits across dairy and non-dairy breeds of sheep and goats worldwide. Results We utilized a total of 308 whole-genome sequences from diverse sheep and goat breeds, including both dairy and non-dairy types, across the world. We characterized the population structure and genetic diversity of dairy and non-dairy sheep and goat breeds. We identified species-specific genes associated with milk traits, such as POU2F1 , ABCD2 , TRNAC - GCA in sheep and PRPF6 , VPS13C , TPD52L2 , NFX1 and B4GALT1 in goats. Further gene annotation and bioinformatics analyses indicated that different biological pathways are important for milk traits in each species: fatty acid oxidation and AMP metabolic process in sheep, the U2-type spliceosomal complex and propanoate metabolism in goats. Additionally, we also found common signatures of selection such as CLASP1 , PDS5B , ZNF83 , CCDC73 in sheep and goats. Haplotype and transcriptional analyses further confirmed the role of these genes in milk production and provided evidence for their analogous evolution in sheep and goats. The gene CLASP1 was identified as a target of convergent selection, representing a promising candidate for genetic improvement programs in dairy species. Conclusions These results provide insights into the genetic basis of convergent dairy traits, offering valuable targets for improving milk production and advancing dairy sheep and goat breeding programs.