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

Litter size is an economically important reproductive trait in dairy goats, but its genetic improvement remains challenging because of its complex genetic architecture and the influence of multiple environmental factors. This study aimed to identify genomic loci associated with litter size-related traits and to evaluate the potential of an intergenic variant near the candidate gene CTNND2 as a molecular marker in Saanen dairy goats. A total of 341 does with reproductive records were analyzed using a genome-wide association study (GWAS), followed by candidate SNP genotyping and association analysis. A shared association signal for litter size and live-born kid number was identified on chromosome 20, leading to the selection of the intergenic SNP CM048886.1:g.61357858G>A located near CTNND2 for further evaluation. Three genotypes (GG, AG, and AA) were detected, and the locus exhibited moderate genetic diversity (PIC = 0.27) while conforming to Hardy–Weinberg equilibrium. Association analysis revealed nominal associations between the SNP and both litter size (p = 0.0445) and live-born kid number (p = 0.0448), whereas no significant association was observed with average kid birth weight (p = 0.125). Goats carrying the A allele showed numerically higher litter size and live-born kid number than those carrying the G allele. These findings identify CM048886.1:g.61357858G>A, an intergenic variant near CTNND2, as a promising candidate marker for litter size-related traits in Saanen dairy goats and provide a foundation for future validation studies and the development of molecular breeding strategies to improve reproductive performance.