Genomic Prediction and Genome-Wide Association Analysis of Egg Fertility and Hatchability Traits in Thai Native Grandparent Stock

Fertility and hatchability are key reproductive traits affecting the efficiency and sustainability of poultry production; however, their genetic improvement remains challenging because of low heritability and complex biological control. In this study, we estimated the genetic parameters and compared the pedigree- and genomic-based prediction models for fertility rate (FER), hatchability of fertile eggs (HOF), and hatchability of eggs set (HOS) in Thai native chickens. In total, 7075 egg records from 1558 animals were analyzed, including pedigree data for 2646 individuals and genotypes for 400 animals. Prediction performance was evaluated using pedigree-based best linear unbiased prediction (PBLUP), single-step genomic BLUP (ssGBLUP), and weighted ssGBLUP (WssGBLUP). Additive heritability estimates for all traits ranged from low to moderate (0.051–0.068), indicating that environmental factors play an important role in the expression of these traits. Across all traits, WssGBLUP achieved the highest accuracy (0.647–0.648) and showed improved dispersion close to unity, indicating better model stability. Compared with PBLUP, WssGBLUP increased the prediction accuracy by 30–39%, respectively, whereas ssGBLUP outperformed PBLUP by approximately 14–22%. Genome-wide association analysis identified 65 candidate genes across multiple chromosomes, with a strong enrichment of significant signals on the Z chromosome, thus highlighting the role of sex-linked genetic variation. Individual loci explained small proportions of variance, confirming the polygenic nature of these traits. These findings demonstrate that weighted genomic approaches can substantially improve the accuracy and reliability of genetic evaluations for reproductive traits. Overall, this study provides practical support for implementing genomic selection in Thai native chickens, potentially contributing to enhanced reproductive performance, genetic progress, and sustainable poultry production.