Integrating genomic selection and genome-wide association study to enhance growth performance in swamp buffalo

The Thai swamp buffalo (Bubalus bubalis) represents an important genetic resource in Southeast Asia but exhibits slow growth and limited productivity, constraining meat production efficiency. This study aimed to characterise the genetic architecture of growth traits and evaluate the effectiveness of genomic selection in improving growth performance. Data comprised 2 077 phenotypic records (birth weight, weaning weight at 240 days, and BW at 400 days) and 474 genotyped animals analysed using the weighted single-step genomic best linear unbiased prediction (WssGBLUP) and weighted single-step genome-wide association study (WssGWAS) models. Variance components were estimated via multiple-trait animal models. Heritability estimates from WssGBLUP were moderate to high (0.52, 0.59, and 0.41 for the three traits, respectively), confirming strong genetic control. Incorporating genomic information improved prediction accuracy of genomic estimated breeding values (GEBVs) by 3-8% compared with pedigree-based EBVs. Significant genomic regions associated with growth traits were identified on chromosomes 1, 3, 6, and 23, encompassing 17 major SNPs linked to candidate genes including MUSK, SVEP1, ATP1A2, CASQ1, DMBT1, and CUZD1. These genes are involved in muscle development, calcium homeostasis, cellular growth, and immunity, suggesting pleiotropic roles across growth stages. Strong genetic correlations between weaning and post-weaning BWs (0.80) indicate that selection for weaning weight could yield correlated responses in mature weight. Overall, this study demonstrates the potential of WssGBLUP for enhancing genetic evaluation and provides genomic insights that can guide the implementation of sustainable breeding programmes for growth improvement in Thai swamp buffalo.