Integrating Transcriptomics and Metabolomics to Unravel the Molecular Mechanisms of Meat Quality: A Systematic Review

Meat quality serves as a pivotal determinant of consumer purchasing behavior and of the economic viability of the livestock industry; as such, research into its regulatory mechanisms is of critical significance for the development of modern agriculture. Traditional investigations into meat quality have predominantly centered on sensory and physicochemical assessments of ultimate phenotypic traits, thereby facing inherent limitations in systematically deciphering the intricate molecular regulatory networks underlying meat quality formation. By contrast, an integrated analysis of the transcriptome and metabolome effectively connects the cascade of “gene transcription—metabolic regulation—phenotypic determination,” which has emerged as a core methodological paradigm in contemporary research on the molecular mechanisms governing meat quality. This review systematically delineates the evolutionary trajectory and principal technological frameworks of meat quality evaluation systems, with a focused synthesis of recent advances achieved through combined transcriptomic and metabolomic analyses in the field of meat quality regulation. The scope of this review encompasses core transcriptional regulatory networks associated with meat quality attributes, pivotal metabolic pathways, signal transduction mechanisms, and protein degradation dynamics. Furthermore, the regulatory impacts exerted by genetic variation among breeds, nutritional modulation, rearing environments, and stress responses on meat quality characteristics are comprehensively elucidated. Integrative analysis reveals that combined transcriptome–metabolome approaches transcend the inherent limitations of single-omics investigations, systematically unraveling the hierarchical regulatory mechanisms governing fundamental meat quality traits, such as muscle fiber type differentiation, postmortem glycolytic progression, intramuscular fat deposition, and flavor compound accumulation. Such integrative strategies have facilitated the identification of functional genes and metabolic biomarkers with potential utility for the early prediction of meat quality outcomes. Concurrently, this review acknowledges persistent challenges confronting the field, including the absence of standardized protocols for multi-omics data integration, insufficient functional causal validation, and a discernible disconnect between research discoveries and practical industrial implementation. Building upon this comprehensive assessment, prospective directions for future multi-omics research in meat quality are proposed, accompanied by the formulation of an integrated end-to-end improvement framework spanning fundamental research, technological innovation, and industrial application. Collectively, this review provides a systematic theoretical foundation for the in-depth elucidation of mechanisms that determine meat quality and the precision-oriented regulation of quality-determining traits in livestock production practices, thereby offering substantial scientific guidance for quality improvement initiatives within the animal husbandry sector.