Integrated transcriptome and metabolomics analysis reveals that phenylpropanoid metabolism drives resistance of Lycium barbarum to root rot

Wolfberry root rot is a prevalent soil-borne vascular fungal disease that seriously impairs wolfberry yield and quality. In this study, resistant ‘Ganqi No.2’ and susceptible ‘Ningqi No.7’ were artificially inoculated with Fusarium solani , the dominant pathogen of wolfberry root rot. Combined with phenotypic surveys, physiological assays and integrated transcriptome-metabolome analysis, we systematically dissected wolfberry’s defensive mechanisms against root rot. The results showed that after inoculation with F. solani , ‘Ganqi No.2’ exhibited a significant resistance advantage, with both the Incidence rate (46.7%) and disease index (16.1) at 35 days being significantly lower than those of ‘Ningqi No.7’ (80%, 38.9). During the late infection stage, the superoxide dismutase activity in the roots of ‘Ganqi No.2’ was significantly enhanced, effectively inhibiting the accumulation of hydrogen peroxide and malondialdehyde. Meanwhile, the early induction of salicylic acid and sustained high levels of chitinase and β-1,3-glucanase activities in later stages formed a multi-layered defense barrier. Notably, the activation of phenylpropane metabolism plays a pivotal role in disease resistance responses. In the roots of ‘Ganqi No.2’, the activity of phenylalanine ammonia-lyase continuously increases, promoting significant accumulation of flavonoids, total phenols, and lignin content. Integrated transcriptomic and metabolomic analyses further reveal that varietal differential regulation primarily concentrates on phenylalanine metabolism and its downstream phenylpropane metabolic pathways. Upregulated expression of genes such as PAL5 , 4CL , and CCOAOMT collectively drives differential accumulation of metabolites like rutin and coniferaldehyde. In conclusion, ‘Ganqi No.2’ exhibits significantly superior resistance to root rot compared to ‘Ningqi No.7’. The multi-omics integrated analysis system elucidated the molecular mechanism by which ‘Ganqi No.2’ enhances resistance to root rot through regulating the phenylpropanoid metabolic network, providing a theoretical basis for the breeding of disease-resistant wolfberry germplasm and green prevention and control of root rot.