Integrated Volatilomics, Metabolomics, and Transcriptomics Implicate PLD–PA–LPAR Signaling in Rabbit Meat Flavor Divergence

Chinese indigenous rabbit breeds are highly prized for their unique meat flavor, yet the molecular mechanisms underlying breed-specific flavor profiles remain incompletely understood. This study characterized the longissimus dorsi muscle of two indigenous Chinese black rabbit breeds, Laiwu Black (LW) and Minxinan Black (MX), through integrated analysis of volatilomics (HS-SPME-GC-MS), nontargeted metabolomics (LC-MS/MS), and transcriptomics (RNA-seq). LW rabbits displayed significantly increased intramuscular fatty acid content, characterized by elevated levels of de novo lipogenesis markers and polyunsaturated fatty acids (PUFAs), including linoleic acid (C18:2n6). In contrast, MX rabbits exhibited higher concentrations of elongation products such as C22:5n3 and C22:5n6. ROAV analysis identified hexanal, the primary oxidation product of linoleic acid (C18:2n6), as the most discriminative key odorant between breeds. Transcriptomic profiling revealed 2747 differentially expressed genes, with KEGG pathway analysis identifying PPAR signaling, phospholipase D signaling, and cAMP signaling as significantly enriched pathways. This study employed multi-omics integration through O2PLS analysis, Pearson correlation, and KEGG co-enrichment to identify a central molecular discriminator: the PLD–PA–LPAR lipid signaling axis. Key regulatory genes such as PLA2G7, PLD2, and LPAR family members were found to connect glycerophospholipid metabolism with breed-specific fatty acid partitioning. These findings identify a gene–lipid–volatile network in which PPAR signaling-mediated lipogenesis is associated with polyunsaturated fatty acid (PUFA) substrates for hexanal generation, while PLD–PA–LPAR signaling may influence the allocation of fatty acyl-CoA between phospholipid turnover and triacylglycerol storage. Together, these mechanisms are associated with the breed-specific aroma profiles in rabbit meat.