Bio-organic fertilizer affects secondary cell wall biosynthesis of Dendrocalamus farinosus by inhibiting the phenylpropanoid metabolic pathway

Abstract Bamboo, as a timber plant, holds significant environmental and economic value. Dendrocalamus farinosus is particularly valuable as it serves both as a source of bamboo shoots and timber, offering high yield, strong disease resistance, and superior fiber quality. Our previous study demonstrated that bio-organic fertilizers promoted the growth of D. farinosus and significantly altered the cellulose and lignin content, key components of the secondary cell wall in culms. However, the underlying regulatory mechanisms remain unclear. In this study, we used metabolomic and transcriptomic analyses to uncover the potential mechanisms by which bio-organic fertilizers affect the secondary cell wall biosynthesis in D. farinosus . A total of 1,437 metabolites were identified, with 20 differential metabolites significantly enriched in the phenylpropanoid metabolic pathway in bamboo shoots (7 upregulated; 13 downregulated). We identified 8,075 differentially expressed genes in bamboo shoots, including 72 genes potentially involved in lignin and flavonoid biosynthesis (6 upregulated; 66 downregulated). In internodes, we identified 5,324 differentially expressed genes, including 83 genes potentially involved in secondary cell wall biosynthesis (43 upregulated; 39 downregulated). Quantitative real-time PCR (qRT-PCR) validated the expression patterns of 8 key genes in internodes. The results suggest that bio-organic fertilizers may affect secondary cell wall biosynthesis in internodes by inhibiting the phenylpropanoid metabolic pathway in D. farinosus shoots. Our study offers insights into the efficient utilization of bamboo and lignocellulosic biomass, serving as a valuable resource for future research.