Morpho-cultural and molecular variability in Rhizoctonia solani isolates from rice-vegetable cropping alluvial zone of West Bengal

Intensified rice based cropping practices in alluvial zone of West Bengal (WB), include Terai-Teesta alluvial, Gangetic alluvial, Vindhyan alluvial, provide continuous supply of inoculums for fresh infection in the host plants, which leads to yield reduction. A total of 38 Rhizoctonia sp. isolates, the incitant of sheath blight disease of rice, were isolated from the symptomatic plant samples of rice-vegetable based cropping system of WB for morpho-cultural characteristics. Significant variations in the key cultural (mycelia growth rate, growth pattern and colony colour) and morphological (length and diameter of hypha, and size and weight of sclerotia) parameters were observed among the isolates. Based on data of overall morphological and cultural parameters of all the isolates, three K-mean groups of the isolates were obtained. Growth rate (mm/h), hyphal width (µm), number of sclerotia, weight of sclerotia (mg), size of sclerotia (mm) and time of first sclerotia formation (T) were found significantly important characters towards grouping of the isolates. Isolates of all the 37 Rhizoctonia species and Rhizoctonia solani were found similar in taxonomic characteristics, i.e., right angular branching pattern of hypha, constriction near branching point and delimitation near branching, however, the remaining one isolate, i.e., Krc9, had similarity with Ceratobasidium oryzae sativae. Nineteen compatibility groups were obtained among the 38 isolates. Species identification was performed for 30 isolates by sequencing of rDNA-Internal Transcribed Spacer (ITS) region. The size of amplified DNA bands obtained from PCR with ITS1 and ITS4 primer ranged from 700 to 750 bp in all the isolates. ITS sequences of 21 isolates shared 99–100% identity with R. solani AG1-IA and eight isolates shared 99.84–100% identity with R. solani AG1-ID and Krc9 shared 100% identity with Ceratobasidium oryzae sativae. Genetic variation was also analysed and fingerprint patterns were generated for each isolate by using eight Universal primers (UP-PCR). All the isolates were classified into eight groups based on analysis of the DNA fingerprint patterns generated by UP-PCR.