Spatial distribution and identification of potential risk regions to rice blast disease in different rice ecosystems of Karnataka.

Rice is a globally important crop and highly vulnerable to rice blast disease (RBD). We studied the spatial distribution of RBD by considering the 2-year exploratory data from 120 sampling sites over varied rice ecosystems of Karnataka, India. Point pattern and surface interpolation analyses were performed to identify the spatial distribution of RBD. The spatial clusters of RBD were generated by spatial autocorrelation and Ripley's K function. Further, inverse distance weighting (IDW), ordinary kriging (OK), and indicator kriging (IK) approaches were utilized to generate spatial maps by predicting the values at unvisited locations using neighboring observations. Hierarchical cluster analysis using the average linkage method identified two main clusters of RBD severity. From the Local Moran's I, most of the districts were clustered together (at I > 0), except the coastal and interior districts (at I < 0). Positive spatial dependency was observed in the Coastal, Hilly, Bhadra, and Upper Krishna Project ecosystems (p > 0.05), while Tungabhadra and Kaveri ecosystem districts were clustered together at p < 0.05. From the kriging, Hilly ecosystem, middle and southern parts of Karnataka were found vulnerable to RBD. This is the first intensive study in India on understanding the spatial distribution of RBD using geostatistical approaches, and the findings from this study help in setting up ecosystem-specific management strategies against RBD.

Multilocus sequence analysis and identification of mating-type idiomorphs distribution in Magnaporthe oryzae population of Karnataka state of India.

AIMS: To investigate the genetic diversity, population structure and mating-type distribution among the eco-distinct isolates of Magnaporthe oryzae from Karnataka, India. METHODS AND RESULTS: A set of 38 isolates of M. oryzae associated with leaf blast disease of rice were collected from different rice ecosystems of Karnataka, India, and analysed for their diversity at actin, ß-tubulin, calmodulin, translation elongation factor 1-α (TEF-1-α), and internal transcribed spacer (ITS) genes/region. The isolates were grouped into two clusters based on the multilocus sequence diversity, the majority being in cluster-IA (n = 37), and only one isolate formed cluster-IB. Population structure was analysed using 123 SNP data to understand the genetic relationship. Based on K = 2 and ancestry threshold of >70%, blast strains were classified into two subgroups (SG1 and SG2) whereas, based on K = 4 and ancestry threshold of >70%, blast strains were classified into four subgroups (SG1, SG2, SG3 and SG4). We have identified 13 haplotype groups where haplotype group 2 was predominant (n = 20) in the population. The Tajima's and Fu's Fs neutrality tests exhibited many rare alleles. Further, the mating-type analysis was also performed using MAT1 gene-specific primers to find the potentiality of sexual reproduction in different ecosystems. The majority of the isolates (54.5%) had MAT1-2 idiomorph, whereas 45.5% of the isolates possessed MAT1-1 idiomorph. CONCLUSIONS: The present study found the genetically homogenous population of M. oryzae by multilocus sequence analysis. Both mating types, MAT1-1 and MAT1-2, were found within the M. oryzae population of Karnataka. SIGNIFICANCE AND IMPACT OF STUDY: The study on the population structure and sexual mating behaviour of M. oryzae is important in developing region-specific blast-resistant rice cultivars. This is the first report of MAT1 idiomorphs distribution in the M. oryzae population in any Southern state of India.

Comparative genomics of rice false smut fungi Ustilaginoidea virens Uv-Gvt strain from India reveals genetic diversity and phylogenetic divergence.

False smut disease of rice caused by Ustilaginoidea virens, is an emerging threat to rice cultivation worldwide due to its detrimental effects on grain yield and quality. False smut disease severity was 4.44‒17.22% during a roving survey in Kharif 2016 in the four different rice ecosystems of Karnataka, India. Further, 15 pathogen isolates representing four different ecosystems were studied for their virulence and morphometric diversity. Among the 15 strains studied, most virulent strains Uv-Gvt was selected for whole genome sequencing in Illumina NextSeq 500 platform using 2 × 150 bp sequencing chemistry. The total assembled genome of Uv-Gvt was 26.96 Mb, which comprised of 9157 scaffolds with an N50 value of 15,934 bp and 6628 protein-coding genes. Next, the comparative genomic study revealed a similar gene inventory as UV-8b and MAFF 236576 strains reported from China and Japan, respectively. But, 1756 genes were unique to Uv-Gvt strain. The Uv-Gvt genome harbors 422 putative host-pathogen interacting genes compared to 359 and 520 genes in UV-8b and MAFF 236576 strains, respectively. The variant analysis revealed low genetic diversity (0.073‒0.088%) among U. virens strains. Further, phylogenetic analysis using 250 single copy orthologs genes of U. virens revealed a distinct phylogeny and an approximate divergence time. Our study, report the genomic resource of rice false smut pathogen from India, where the disease originated, and this information will have broader applicability in understanding the pathogen population diversity.