Transcriptome and metabolome integration in sheep meat quality: a systematic review of molecular mechanisms, key pathways, and candidate biomarkers

Sheep meat quality, including tenderness, intramuscular fat content, flavour, and colour, is determined by complex transcriptional and metabolic networks in muscle tissue.While integrated omics profiling is increasingly used to investigate these mechanisms, the available literature has not yet been systematically synthesised.This review examined 27 studies (2016-2026) employing transcriptomic and metabolomic analyses to investigate sheep muscle characteristics and identify genes, metabolites, and pathways reported in multiple studies rather than relying on results from individual works.The most common findings involved peroxisome proliferator-activated receptor (PPAR) signalling (6 studies), glycolysis, and oxidative phosphorylation.However, the same genes were rarely identified in different studies.Only PPARGC1A, FABP4, and PLIN1 were reported in more than one study, whereas most genes were identified in only a single study.Metabolites showed greater consistency across studies, with arachidonic acid and purine nucleotides each reported in three studies.Only one article included functional validation beyond gene expression analysis.Although lipid metabolism, energy regulation, and amino acid pathways were associated with meat quality traits, including intramuscular fat (IMF) deposition and flavour, the evidence remains insufficient to establish specific genes or metabolites as reliable biomarkers.The field is limited by inconsistent reporting thresholds and a lack of data sharing.Further progress requires standardised criteria for identifying significant changes, full data availability, and functional experiments.Without these steps, no gene or metabolite can be considered a validated biomarker of sheep meat quality.