Identification and characterization of multiple fungal pathogens associated with brown spot disease of rice in India

Brown spot (BS) disease causes significant losses to rice productivity. In this study, a roving survey in the Karnataka state of India revealed a wider distribution of BS with a percent disease index range of 20.56-50.74. From the symptomatic geo-distinct samples, pure cultures of 63 isolates were obtained. Based on the conidial morphology, 63 isolates were identified as Bipolaris oryzae (Bo) (n = 40), Curvularia lunata (Cl) (n = 15), and Exserohilum rostratum (Er) (n = 08). The taxonomic identity was further confirmed via ITS-sequencing. A pathogenicity assay on a BS-susceptible rice cultivar GNV-05-01 confirmed the pathogenicity of all three pathogens, which induces typical BS disease on test plants. Further, on PDA media, all isolates of three pathogens showed significant cultural diversity for mycelial color, colony type, and sporulation. We further studied the in-planta distribution of three pathogens on a randomly collected 600 BS spots from 10 different rice fields, which indicated that 77.83%, 17.33%, and 4.83% of the typical BS were produced by Bo, Cl, and Er, respectively. The ITS region was sequenced for selected 9, 7, and 3 isolates of Bo, Cl, and Er, respectively, and analyzed for their nucleotide and haplotype diversity, and phylogenetic relationships. A phylogenetic study identified the unique clustering patterns, and haplotyping indicated 3, 4, and 6 haplotypes. Tajima's D (D) test showed several rare alleles in the ITS regions. This is the first comprehensive study reporting the three fungal pathogens causing BS of rice and it is useful for re-designing the screening protocol for the host plant resistance breeding program.

The online version contains supplementary material available at 10.1007/s13205-024-04033-3.