Genome-Wide Association Screening and Candidate SNP Analysis Identify an Intergenic Variant Near CTNND2 Associated with Litter Size Traits in Saanen Dairy Goats

Abstract

Simple Summary Litter size is an important determinant of reproductive efficiency and economic profitability in dairy goat production, but improving this trait through conventional breeding is challenging because it is influenced by multiple genes and environmental factors. In this study, we identified a chromosome 20 genomic region associated with litter size-related traits in Saanen dairy goats and detected an intergenic variant near the candidate gene CTNND2 (CM048886.1:g.61357858G>A) that was associated with favorable litter size and live-born kid number. No association was observed with average kid birth weight. These findings suggest that this variant may represent a promising candidate marker for improving reproductive performance in dairy goats and provide a foundation for future validation studies and the development of marker-assisted breeding strategies.