Genomic selection and association analyses for improving semen traits in Thai native roosters

Semen quality is a major determinant of reproductive efficiency in poultry production systems. In Thai native chickens, the relatively low male-to-female mating ratio increases the reproductive importance of individual sires, making semen quality traits critical for maintaining flock fertility. Thai native chickens represent an important genetic resource characterized by high adaptability to tropical environments and unique genetic diversity, yet remain relatively under-studied compared with commercial lines. Therefore, accurate estimation of genetic parameters and a clear understanding of the genetic architecture underlying semen traits are required to support effective breeding programs. However, despite their importance, semen quality traits in Thai native chickens remain poorly characterized at the genomic level, and the effectiveness of genomic evaluation approaches for improving these traits has not been fully explored. This study estimated genetic parameters, characterized the genetic architecture of semen traits, and evaluated the impact of genomic information on prediction accuracy in Thai native chickens. We evaluated the predictive performance of sperm quality traits using three genetic evaluation models: pedigree-based best linear unbiased prediction (PBLUP), single-step genomic BLUP (ssGBLUP), and weighted ssGBLUP (WssGBLUP). Estimates of heritability for mass movement, semen volume, and sperm concentration were low (0.149, 0.165, and 0.060, respectively), indicating limited additive genetic variation for these traits. Incorporation of genomic information improved prediction accuracy, with ssGBLUP and WssGBLUP increasing accuracy by 5.88% and 7.49%, respectively, compared with PBLUP. A strong positive genetic correlation (0.977) was observed between mass movement and sperm concentration, suggesting that selection for improved mass movement is likely to result in a favorable correlated genetic response in sperm concentration. In addition, WssGWAS identified genomic regions on chromosomes 6, 11, 19, 21, and 22 that harbored 14 candidate genes associated with sperm structure and metabolic processes. These findings suggest that the identified genomic regions may influence semen quality through biological pathways related to sperm membrane integrity, energy metabolism, and cellular regulation, which are essential for maintaining sperm motility and function. Our results demonstrate the utility of genomic information, particularly the WssGBLUP approach, for improving semen quality traits in Thai native chickens. These findings provide biologically relevant insights to support the development of sustainable genetic improvement programs.