Integrated genomic, transcriptomic, and metabolomic profile analysis reveals molecular mechanism underlying meat quality traits in Chinese Kangle chickens

The local Chinese Kangle chicken breed has plump muscles, tender-tasting meat, and strong disease resistance. We aimed to identify muscle metabolites and associated regulatory genes that determine Kangle chicken muscle quality and flavor by elucidating the as yet unknown underlying molecular regulatory mechanism through omics-based analyses. Phenotype analysis and genome-wide association study (GWAS) showed that intramuscular fat (IMF) exhibited a high coefficient of variation and identified two SNPs that reached genome-wide significance levels (<i>P</i> < 1.23 × 10^-6), with QTLs affecting IMF located on chromosomes 1, 2, 4, and 7. Transcriptome analysis screened 201 differential expression genes between chickens with high and low IMF content. Among these, the expression level of the FYVE-type zinc finger containing (<i>PIKFYVE</i>) gene located in the significant QTL region was significantly downregulated in the High-IMF group, which was validated by qRT-PCR. Metabolomics identified 17 intergroup differential metabolites, and the High-IMF group was significantly enriched in vitamin B6 metabolism and glycine, serine, and threonine metabolism. Differentially expressed gene and metabolite analyses in breast muscles and pathway enrichment and co-occurring network analyses showed that <i>PIKFYVE</i> impacted IMF. Its expression significantly and negatively correlated with most lipid metabolites. This study is the first to establish <i>PIKFYVE</i> as the primary regulatory gene of IMF in Kangle chickens. It provides crucial and valuable practical insights into genetically breeding high-quality meat chicken breeds.