Genome-wide association study of egg number and egg weight in indigenous Tilili chickens in Ethiopia using whole genome sequencing

Abstract

Egg production traits, especially egg number and egg weight, are economically important in chicken breeding programs. However, the genetic basis of these traits in Ethiopian indigenous chicken populations remains unexploited. The study aimed to identify suggestive genomic loci and candidate genes associated with part-period egg number (PPEN; onset of lay to 45 weeks of age) and average egg weight (AEW) in Tilili indigenous chicken population under a selective breeding program. A total of 437 hens were phenotyped and genotyped using low-coverage (0.5x) whole-genome sequencing and imputation against a 30× reference panel. After quality control, 4,846,509 high-quality SNPs were retained for genome-wide association analysis using a linear mixed model. None of the SNPs reached the predefined genome-wide significance threshold ( P  < 1 × 10⁻⁸); however, 40 suggestive SNPs for PPEN and 67 suggestive SNPs for AEW ( P  < 1 × 10⁻⁵) were identified across 14 chromosomes, consistent with a polygenic genetic architecture for both traits. Candidate genes for PPEN include APOB , AGPATs , CACNA1B , GSTA2 , GSTA3 , GSTA4 , HDAC4 , and MBD3 , whereas HMGA2 , DIAPH3 , SSTR2 , F7 , F10 , and PROZ were associated with AEW. Functional enrichment analysis highlighted pathways related to glutathione metabolism, detoxification, transcriptional regulation, and developmental processes. Overall, the results identify hypothesis-generating genomic regions and candidate genes for egg production traits in Tilili indigenous chickens and provide a basis for further validation in large sample size Tilili chicken population and independent populations.