Objective To investigate the differential components existing in the roots of Puerariae lobata, a plant with both medicinal and edible properties, at growth stages of one-year, biennial and three-year-old. Methods By comprehensively applying metabolomics and label-free quantitative proteomics, a comparative analysis was conducted of metabolite accumulation dynamics and protein expression profiles in samples from different growth years. Results Metabolic profiling revealed significant differences in flavonoid composition across developmental stages. Comparative analysis identified 236 significantly differentially accumulated metabolites between one-year-old and two-year-old plants, of which 205 were up-accumulated and 31 down-accumulated; between two-year-old and three-year-old plants, the number decreased markedly to 25 differentially accumulated metabolites (14 up-accumulated, 11 down-accumulated); and between one-year-old and three-year-old plants, 83 differentially accumulated metabolites were detected (70 up-accumulated, 13 down-accumulated). Subsequent compound classification, correlation analysis, and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis of these metabolites identified five pathways significantly enriched in flavonoid-related metabolism. Parallel proteomic profiling yielded 2 764 significantly differentially expressed proteins (FC ≥ 1.5 or ≤ 0.67, P < 0.05). Across the three pairwise comparisons, upregulated proteins numbered 1 565, 1 437, and 193, respectively, while downregulated proteins totaled 931, 817, and 260, respectively. Functional annotation via gene ontology (GO) and KEGG pathway analyses further demonstrated significant enrichment of these proteins in biological processes and pathways central to flavonoid biosynthesis, pyruvate metabolism, and amino acid biosynthesis. Conclusion Metabolite accumulation and proteomic variations across different growth years of P. lobata are predominantly enriched in the biosynthetic pathways of phenylpropanoids, flavonoids, and other plant secondary metabolites. Flavonoid constituents from P. lobata are closely associated with pharmacological activities including anti&8209;inflammatory, lipid&8209;regulating and hypoglycemic effects.This study establishes a foundational framework for both the rational development and utilization of P. lobata resources and the mechanistic understanding of its growth and developmental regulation at the molecular level.

Pueraria lobata (Willd.) Ohwi  /  growth ages  /  metabolomics  /  proteomics  /  differential metabolic pathways  /  flavonoids