Genomic Prediction and Genome-Wide Association Analysis of Egg Fertility and Hatchability Traits in Thai Native Grandparent Stock
Simple Summary Fertility and hatchability are important reproductive traits that directly influence chick production and the efficiency of poultry breeding programs. However, genetic improvement of these traits is challenging because they are influenced by many genes and environmental factors. This study evaluated fertility rate, hatchability of fertile eggs, and hatchability of eggs set in Thai native chickens using pedigree and genomic information. Three genetic evaluation methods were compared: pedigree-based BLUP (PBLUP), single-step genomic BLUP (ssGBLUP), and weighted single-step genomic BLUP (WssGBLUP). The results showed that genomic approaches improved prediction accuracy compared with pedigree-based evaluation, with WssGBLUP providing the highest accuracy and reliability. Several candidate genes associated with reproductive performance were identified, particularly on the Z chromosome. These findings support the implementation of genomic selection to improve reproductive efficiency and accelerate sustainable genetic improvement in Thai native chicken populations.