Weighted Single-Step Genomic Evaluation of Body Structural Traits for Early Selection of Growth Performance in Thai Swamp Buffalo

Early identification of genetically superior animals is important for improving growth performance and accelerating genetic gain in swamp buffalo breeding programs. This study investigated the genetic relationships between growth and body structural traits and evaluated their potential use as early selection indicators in Thai swamp buffalo. Phenotypic records from 1034 animals and genotypic data from 462 buffaloes genotyped with 30,979 SNP markers were analyzed using weighted single-step genomic best linear unbiased prediction (WssGBLUP) and weighted single-step Genome-Wide Association Study (WssGWAS) approaches. Moderate to high heritability estimates were observed for growth traits (0.41–0.59), whereas body structural traits showed low to moderate heritability (0.08–0.27). Positive genetic correlations were identified between growth traits and several structural traits, particularly heart girth, hip height, and body depth. Principal component analysis identified two major components explaining 80.1% of the total phenotypic variation, with the first principal component (PC1) representing overall body size and skeletal development. PC1 also showed relatively high heritability (0.57), indicating its potential utility as a composite selection trait. Genome-wide association analysis identified significant SNPs and candidate genes associated with weaning weight and PC1, including ST6GALNAC5, EPHA6, SYN3, DDIT4, DNAJB12, BLCAP, and NNAT, which are involved in growth regulation, metabolism, cellular development, and stress-response pathways. These findings demonstrate that body structural traits are genetically associated with growth performance and may serve as effective early selection indicators in genomic breeding programs for Thai swamp buffalo.