Integrated Transcriptomic and Metabolomic Analyses Revealed That Exogenous 24-Epibrassinolide Application Modulated Lignin Biosynthesis in Cold-Stressed Zizania latifolia

During cold storage, water bamboo (Zizania latifolia) is susceptible to lignification. This study employed quality evaluation, transcriptomics, and metabolomics to elucidate the mechanisms by which exogenous 24-epibrassinolide (EBR) delays lignification in water bamboo during cold storage. EBR-treated (1 mg/L) water bamboo was stored at 4 °C for 28 d, followed by additional storage at 25 °C for 3 d. The results indicate that EBR treatment effectively delays postharvest decay in water bamboo while retarding changes in weight loss, hardness, color, and total soluble solids (TSS). Transcriptomic analyses revealed that EBR treatment downregulated the expression of key genes involved in lignin biosynthesis, including peroxidase (POD) and cinnamoyl-CoA reductase (CCR). Simultaneously, EBR suppressed the expression of cell wall degradation-related genes, such as β-glucosidase (β-BGL). Within the lignin biosynthetic diversion pathway, EBR also reduced the expression of UDP-glycosyltransferase 92A1 (UGT92A1), a gene family typically involved in monolignol glycosylation leading to lignin formation. Metabolomic profiling indicated that EBR inhibited the synthesis of metabolites in the phenylalanine biosynthetic precursor pathway, including quinic acid, phenylpyruvic acid, shikimic acid, L-phenylalanine, and (E)-ferulic acid. These findings suggest that EBR prevents lignification and preserves fruit quality in water bamboo by downregulating lignin biosynthesis genes and suppressing phenylpropanoid precursor metabolites.