Genome-wide association study of growth, carcass, and meat quality traits in Liangshan Yanying chickens

This study investigated the genetic basis of growth, carcass, and meat quality traits in Yanying chickens, an indigenous breed adapted to high-altitude environments. A total of 19 growth traits and 29 carcass and meat quality traits were measured, and genome-wide association study (GWAS) was performed to identify loci associated with these economically important traits. In total, 455 significant single nucleotide polymorphisms (SNPs) were identified, and 176 candidate genes were obtained. Among these, 1 had been directly associated with the corresponding trait in previous chicken studies, while approximately 5 others had been implicated in related traits. Further regional association and linkage disequilibrium (LD) analyses highlighted RYR2 and ARNTL as positional candidate genes associated with spleen weight and breast muscle pH, respectively. In addition, expression-based analysis provided additional evidence consistent with ARNTL being a positional candidate gene for breast muscle pH. Functional enrichment analysis identified significant Gene Ontology (GO) terms related to cell adhesion and calcium ion binding, whereas Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested nominal enrichment of ECM-receptor interaction and MAPK signaling pathways. Overall, these findings provide new insight into the genetic architecture of growth, carcass, and meat quality traits in this indigenous breed and offer useful information for future functional validation and genetic improvement of local poultry populations.