Analysis of insertion/deletion variation of litter size in Guizhou black goat

This study aimed to explore the genetic differences between high-litter size (HL) and low-litter size (LL) groups of Guizhou black goats, focusing on InDel variations and their potential association with reproductive traits. Whole-genome resequencing was performed on goats from the HL and LL groups to identify InDel variants. Selection signal analysis was conducted using Fst and π to detect loci potentially linked to reproductive performance. The variants were annotated, and functional enrichment analysis was performed. Principal component analysis and phylogenetic tree construction revealed clear genetic differentiation between HL and LL groups based on InDel variation. A total of 24 candidate genes potentially related to litter size were identified. Functional enrichment analysis also enriched for functions related to reproduction. The identified candidate genes and enriched pathways offer new insights into the genetic architecture underlying reproductive performance and present potential targets for marker-assisted selection in goat breeding.