Integrated Multi-Omics Analysis of the Response of Lycium barbarum ‘Ningqi-1’ to Powdery Mildew Infection and Functional Characterization of LbMLO6

Powdery mildew severely constrains the production of Lycium barbarum L., yet the molecular mechanisms underlying its response to infection remain poorly understood. Here, ‘Ningqi-1’ plants were inoculated with the powdery mildew pathogen and sampled at 0, 12, 24, and 48 hpi for integrated transcriptomic, proteomic, and metabolomic analyses. Quantitative PCR and CRISPR/Cas9-mediated gene editing were further used to evaluate the candidate susceptibility gene LbMLO6. Infection induced extensive molecular reprogramming, yielding 1299 differentially expressed genes with sustained changes, 75 DAPs shared across all three time points, and 127 shared differentially accumulated metabolites. These molecules were mainly enriched in plant–pathogen interaction, plant hormone signal transduction, MAPK signaling, phenylpropanoid biosynthesis, and α-linolenic acid metabolism pathways, suggesting coordinated roles for Ca2+ signaling, reactive oxygen species, defense-related proteins, and secondary metabolism in the host response. Integrated multi-omics analysis identified LbMLO6 as a candidate gene associated with powdery mildew susceptibility, its expression was markedly induced from 24 hpi onward. CRISPR/Cas9-edited LbMLO6 lines showed reduced fungal development compared with the control, particularly during the early stages of infection. These findings provide preliminary evidence that LbMLO6 may be associated with powdery mildew susceptibility in L. barbarum.