Selection signatures of litter size in Dazu black goats based on a whole genome sequencing mixed pools strategy

Litter size is considered to be the most important index for estimating domestic animal productivity. Due to its complexity, the molecular mechanism of litter size has not been elucidated, and it has restricted the use of marker-assisted selection to create high-yield populations in goats. A genome-wide selective sweep analysis was performed with 31 Dazu black goats to identify significant genomic regions and candidate genes related to litter size by a mixed pools strategy. A total of 96 candidate genes were identified, including NR6A1, STK3, IGF2BP2, AR, HMGA2, NPTX1, ANKRD17, DPYD, CLRB, PPP3CA, PLCB1, STK3 and HMGA2, using mixed pool analysis with ZHp and FST. We classified these candidate genes based on the functional classification and annotation of signaling pathways. According to the GO and KEGG analysis results, a total of 43 GO terms and 108 pathways were annotated from these genes. In particular, some novel candidate genes were enriched in reproduction-related pathways, such as the estrogen signaling pathway and oocyte meiosis. These findings provide insight into the influences of coding genes on the fecundity traits of goats.