Identification of key genes and relevant genetic variants regulating muscle color in chicken using a multi-omics approach

Meat color is an important economic trait of chicken that influences the willingness of consumers to buy it. Elucidating the genetic mechanisms regulating chicken color is essential to optimize poultry breeding strategies and improve meat quality. However, the genes and genetic variants involved remain unknown. In this study, the regulatory mechanism of the Jingxing yellow chicken color was revealed by a multi-omics approach, including transcriptomics/RNA sequencing (RNA-seq) analysis, comprehensive metabolomics analysis and carotenoid measurement. Our results showed that a significant region on chromosome 11 (15.36-15.47 Mb) was associated with the breast muscle meat color yellowness (b*), and BCO1 was mapped to this region as a candidate gene. In addition, the detection of the higher expression level of BCO1 mRNA in the group with the high-b* by RNA-seq analysis further supports that BCO1 is a key candidate gene associated with the breast muscle meat color b*. Also, the relevant single-nucleotide polymorphism (SNP) rs315311588 identified among the SNPs present in the 10 introns of BCO1, was found to reduce the expression level of BCO1 and increase the breast muscle meat color b*. Moreover, the multi-omics results reveal that decreased expression level of BCO1 leads to reduced conversion of lycopene to retinol, but significantly increases the content of lutein, which gives the yellow color to the breast muscle meat. Additionally, we also found that increase in yellow pigment production may promote fat deposition in breast muscle meat.