Multi-Omics Insights into Rhizoctonia solani Variability and Resistance in Pulses

Rhizoctonia solani Kühn is a genetically heterogeneous, soil-borne fungal pathogenresponsible for substantial yield losses in legume crops, primarily through web blightand root rot. Among its diverse anastomosis groups (AGs), AG1-IA and AG-4 HGI arenotably aggressive. Although molecular tools such as ITS-based rDNA sequencing andAG-specific PCR facilitate classification, their application in legume pathosystemsremains limited.Recent developments in multi-omics technologies, encompassing genomics,transcriptomics, proteomics, and metabolomics have significantly advanced thecharacterization of R. solani in cereals; however, their integration into legume researchremains sparse. This review consolidates current knowledge on the phenotypic andmolecular variability of R. solani infecting legumes, emphasizing the need for AG-informed resistance strategies.We propose a systems biology framework that couples transcriptomic, proteomic andmetabolomic datasets with high-throughput phenotyping to identify molecular markersassociated with durable resistance. Key targets include effector genes, ROS-detoxifying enzymes, and secondary metabolites such as coumarins and flavonoids.Major research gaps are highlighted, including the lack of legume-specific secretomestudies. We recommend advanced approaches—such as dual RNA sequencing,weighted gene co-expression network analysis (WGCNA), and AG-targeted GWAS—toaccelerate resistance breeding. The integration of multi-omics with classical screeningis essential for developing broad-spectrum, durable resistance in legumes against thishighly adaptable pathogen.