Identification and Characterization of sQTLs and eQTLs Associated with Growth Traits in Yellow-Feathered Broilers

In-depth investigation of genetic variants influencing muscle yield in chickens is crucial for maximizing the efficiency of improving production performance in local chicken breeding programs. To identify variants and genes affecting muscle yield in Chinese indigenous chickens, we performed a genome-wide association study (GWAS) on growth traits using genomic variants from Xinghua chickens. Subsequently, we mapped expression quantitative trait loci (eQTLs) and splicing quantitative trait loci (sQTLs) by integrating genotypic variation and transcriptomic data from muscle tissue. We identified a co-expression module comprising 348 genes associated with protein synthesis and ribosome biogenesis. Additionally, we detected 7948 eQTL-related genes and 1526 sQTL-related genes. Among the identified e/sQTLs, approximately 60% were located within gene bodies and were enriched in regions flanking transcription start sites or splice sites. Integrated analysis revealed that the overlap between eQTLs and sQTLs, as well as between eGenes and sGenes, was less than 5%, suggesting their distinct roles in gene expression and transcript splicing. Interestingly, the overlapping eGenes and sGenes were significantly enriched in pathways related to protein synthesis and translation, highlighting the potential importance of genes and variants involved in these processes for muscle growth in yellow-feathered broilers. In conclusion, this study provides novel insights and a valuable resource for understanding the genetic regulation of gene expression and alternative splicing in muscle tissue of yellow-feathered broilers.