Breed-specific meat quality and flavor characteristics of Wannan and Chinese Simmental cattle revealed by whole transcriptome and metabolome analysis

Deciphering the genetic and metabolic factors influencing meat quality and flavor is crucial for enhancing beef industry productivity and meeting consumer demands. This study aimed to explore the effects of different breeds on meat quality and flavor characteristics of Wannan and Chinese Simmental cattle through analysis of myofiber traits, fatty acid and amino acid contents, whole transcriptomics, and metabolomics. Results revealed that Wannan cattle had markedly smaller myofiber diameter ( P < 0.01) and higher myofiber density ( P < 0.05) than Chinese Simmental cattle. Wannan cattle also exhibited significantly higher contents of umami−/sweet-related amino acids (aspartic acid and glycine) ( P < 0.05), and unsaturated fatty acids (C15:1, C16:1, and C18:2n6c) ( P < 0.05), as well as higher levels of total unsaturated (UFAs), monounsaturated (MUFAs), and polyunsaturated fatty acids (PUFAs) ( P < 0.05). We identified key genes involved in fatty acid metabolism ( FADS6 , PLB1 , ELOVL6 , HACD2 ) and amino acid metabolism ( ADSS2 , GSTA2 , SLC36A4 ), as well as core signaling pathways including PI3K-Akt, AMPK, and PPAR. Additionally, lncRNA/circRNA-mediated potential competing endogenous RNA regulatory networks were constructed, represented by LOC112449549/miR-424/ELOVL6, circ_015602/miR-2285/HACD2, and circ_035929/miR-194-3p/SLC36A4 axes. Further, key metabolites in fatty acid metabolism (16:0 PC, 16:1 (Δ9-Cis) PC, 18:1 Dimethyl PE) and amino acid metabolism (gamma-Glu-Cys, 1-methyl-L-histidine, l -glutamine) were identified, and an mRNA-metabolite regulatory network was established. The findings are expected to contribute to the genetic improvement of local cattle breeds and promote the development of high-quality beef production in China.