Integrated Transcriptome and Metabolome Analysis Reveals Candidate Genes and Regulatory Pathways Shaping Duck Meat Color

Meat color is the most intuitive measure of meat quality and has a significant impact on consumer preference. To explore the molecular mechanisms affecting duck pectoralis meat color, the phenotypic traits of Cherry Valley duck (CV, eight males and eight females) and Huai Fu duck (HF, eight males and eight females) were compared; three males and three females of each variety were later selected for transcriptomic and metabolomic analyses to reveal key molecular processes. This study found that the expression level of CA3 (carbonic anhydride enzyme 3) is positively correlated with the meat color phenotype, suggesting that it may play a positive regulatory role in the formation of meat color. The expression trend of the ST13 gene is opposite to the phenotype, suggesting that it may play a negative regulatory role. With the participation of CA3 and NDUF family genes (such as NDUFC2, NDUFB2, etc.), the oxidative phosphorylation pathway plays a key role in meat color formation by regulating the oxygenation/deoxygenation state of myoglobin and intracellular pH value. Although the effects of these genes and pathways on meat color have been discovered, their specific genetic mechanisms and molecular functions still need further verification. This provides important clues for further understanding the molecular mechanism of meat color formation and may offer potential molecular targets for improving meat color or breeding new varieties.