Multi-Omics Analyses Identify Candidate Genes Associated With Stage-Specific Quality Formation in Mulching-Treated Moso Bamboo Shoots

Bamboo shoots are nutrient-rich edible resources, and organic mulching promotes earlier shoot emergence and increases yield. However, the molecular mechanisms regulating mulching-treated shoot (MtS) development remain unclear. Field experiments across three Moso bamboo forests, combined with biochemical profiling, metabolomics, and transcriptomics, examine MtS development. Mulching induces stage-specific shoot quality formation (MtS1-MtS4) and increases shoot size, yield, biochemical traits, and market value compared with spring shoots (SS) and winter shoots (WS). MtS increases soluble sugars, phenolics, tannins, and alkaloid-related metabolites and reduces water content and antioxidant capacity. Metabolite profiling identifies 2029 metabolites and reveals stage-dependent shifts in amino acid, carbohydrate, lipid, flavonoid, tricin-related, and cell-wall modification pathways. Transcriptome analysis identifies 13 691-18 038 differentially expressed genes across SS vs MtS comparisons. KEGG enrichment highlights sugar metabolism, lignin and cellulose synthesis, and hormone signalling. Transcription factor families, including bHLH, MYB, NAC, bZIP, C2H2, and SPL, show stage-dependent expression. O2PLS analysis reveals covariance between metabolite and transcriptome profiles. WGCNA identifies 16 stage-associated modules and candidate genes, including SPL18, NID1, PIF3L6, ATH1L, and TOM6. Alternative splicing indicates widespread post-transcriptional regulation. Protein-protein interaction analysis reveals interactions among AS-O2PLS-prioritised genes. These results show that mulching reshapes stage-specific shoot quality formation through coordinated physiological, metabolic, transcriptional, and post-transcriptional changes.