Multiomics profiling identifies molecular signatures of meat quality in sika deer cuts

Sika deer ( Cervus nippon hortulorum ) meat is increasingly recognized for its nutritional and culinary value, yet the molecular mechanisms underlying its quality traits remain poorly understood. In this study, we performed integrated transcriptomic, proteomic, and metabolomic profiling of six representative muscle cuts from farmed sika deer ( n = 12). Intercostal and trapezius muscles exhibiting enriched features related to tenderness, marbling, and flavor. Weighted gene co-expression network analysis identified two convergent multi-omics regulatory axes, in which transcriptional programs represented by ME6_trans and ME7_trans were linked to protein modules involved in muscle structural organization and contractile metabolism (ME3_protein), ultimately reflected in metabolite clusters associated with lipid utilization and energy homeostasis (ME2_metab). These coordinated transcription-to-protein-to-metabolite relationships suggest integrated regulation of extracellular matrix remodeling, muscle fiber functional properties, and lipid metabolic adaptation underlying region-dependent molecular variation in sika deer muscle. In addition, RT–qPCR and Western blot validation of selected key factors demonstrated expression patterns consistent with the multi-omics analyses, supporting the robustness of the identified molecular features. This study represents the first integrative multi-omics characterization of molecular variation across major muscle cuts in farmed sika deer, providing preliminary systems-level insights into coordinated metabolic and structural features associated with meat quality-related traits.