Pleiotropic Genes Affecting Milk Production, Fertility, and Health in Thai-Holstein Crossbred Dairy Cattle: A GWAS Approach

Understanding the genetic basis of economically important traits is essential for enhancing the productivity, fertility, and health of dairy cattle. This study aimed to identify the pleiotropic genes associated with the 305-day milk yield (MY305), days open (DO), and milk fat-to-protein ratio (FPR) in Thai-Holstein crossbred dairy cattle using a genome-wide association study (GWAS) approach. The dataset included 18,843 records of MY305 and milk FPR, as well as 48,274 records of DO, collected from first-lactation Thai-Holstein crossbred dairy cattle. A total of 868 genotyped animals and 43,284 informative SNPs out of 50,905 were used for the analysis. The single-nucleotide polymorphism (SNP) effects were evaluated using a weighted single-step GWAS (wssGWAS), which estimated these effects based on genomic breeding values (GEBVs) through a multi-trait animal model with single-step genomic BLUP (ssGBLUP). Genomic regions explaining at least 5% of the total genetic variance were selected for candidate gene analysis. Single-step genomic REML (ssGREML) with a multi-trait animal model was used to estimate components of (co)variance. The heritability estimates from additive genetic variance were 0.262 for MY305, 0.029 for DO, and 0.102 for milk FPR, indicating a moderate genetic influence on milk yield and a lower genetic impact on fertility and milk FPR. The genetic correlations were 0.559 (MY305 and DO), −0.306 (MY305 and milk FPR), and −0.501 (DO and milk FPR), indicating potential compromises in genetic selection. wssGBLUP showed a higher accuracy than ssGBLUP, although the improvement was modest. A total of 24, 46, and 33 candidate genes were identified for MY305, DO, and milk FPR, respectively. Pleiotropic effects, identified by SNPs showing significant influence with more than trait, were observed in 14 genes shared among all three traits, 17 genes common between MY305 and DO, 14 genes common between MY305 and milk FPR, and 26 genes common between DO and milk FPR. Overall, wssGBLUP is a promising approach for improving the genomic prediction of economic traits in multi-trait analyses, outperforming ssGBLUP. This presents a viable alternative for genetic evaluation in dairy cattle breeding programs in Thailand. However, further studies are needed to validate these candidate genes and refine marker selection for production, fertility, and health traits in dairy cattle.