Integrating Genomic Selection and Genome-Wide Association Study to Enhance Reproductive Traits in Thai Swamp Buffalo

Reproductive inefficiencies, such as delayed age at first calving (AFC) and a prolonged calving interval (CI), hinder the productivity of Thai swamp buffaloes. This study aimed to improve the genetic evaluation of these traits by integrating genomic selection (GS) and genome-wide association studies (GWASs). Reproductive records (n = 1034) and genotypes (n = 474) from swamp buffaloes across Thailand were analyzed. Variance components were estimated using pedigree data, and genomic predictions were performed via weighted single-step genomic best linear unbiased prediction. AFC heritability was moderate (0.36 and 0.45), whereas CI heritability was low (0.051 and 0.043). The positive genetic correlation (rg = 0.495 and 0.517) between AFC and CI suggested potential for the simultaneous genetic improvement of both traits through selection. The WssGBLUP method showed greater effectiveness, with the prediction accuracy increasing by up to 41% for CI and 28% for AFC when compared to the ABLUP method. The GWAS revealed 20 associated single-nucleotide polymorphisms (SNPs) on chromosomes 3, 4, 14, 15, and 25. Candidate genes COLEC10, TNFRSF11B, PDZRN4, and MACROD2 were linked to immune function, hormonal regulation, and reproductive tissue development. Pleiotropic SNPs affecting both traits were identified, indicating shared genetic control mechanisms. These findings support the application of tailored GS programs to improve reproduction in swamp buffaloes under tropical smallholder systems.