New Candidate Genes for a Chicken Pectoralis Muscle Weight QTL Identified by a Hypothesis-Free Integrative Genetic Approach

<b>Background/Objectives</b>: Identifying candidate genes underlying quantitative trait loci (QTL) in poultry has traditionally required labor-intensive positional cloning. Previous studies using an F₂ population derived from native Japanese Nagoya (NAG) and White Plymouth Rock (WPR) breeds revealed a major QTL on chromosome 2 affecting 3-week body weight and 4-week pectoralis muscle weight. This study aimed to identify candidate genes for this QTL using a hypothesis-free integrative genetic approach. <b>Methods</b>: We employed a multi-step analytical framework combining QTL remapping, transcriptome analysis, gene enrichment analysis, haplotype frequency comparison, and correlation analysis. QTL remapping was performed using individual traits and their first principal component (PC1) in 239 F₂ chickens. RNA-sequencing (RNA-seq) of liver tissue was conducted for F₂ individuals with extreme PC1 scores, followed by reverse transcription quantitative polymerase chain reaction (RT-qPCR) validation. <b>Results</b>: QTL remapping refined the 95% confidence interval to a chromosome 2 region containing 329 genes. RNA-seq analysis identified 23 differentially expressed genes (DEGs) within this interval. Although gene enrichment analysis initially highlighted GATA binding protein 6 (<i>GATA6</i>) as a potential candidate, RT-qPCR in NAG, WPR, and F₁ chickens showed no significant expression differences, excluding <i>GATA6</i>. Haplotype frequency and correlation analyses prioritized cadherin-17 (<i>CDH17</i>) as the strongest candidate gene and ring finger protein 151 (<i>RNF151</i>) as a secondary candidate. <b>Conclusions</b>: Our hypothesis-free integrative approach effectively refined candidate genes for a chromosome 2 QTL influencing early growth and pectoralis muscle weight. <i>CDH17</i> and <i>RNF151</i> represent promising targets for functional validation and may support marker-assisted selection to improve muscle-related traits in chickens.