Morpho-molecular diversity and avirulence genes distribution among the diverse isolates of Magnaporthe oryzae from Southern India.

AIMS: To investigate the diversity of eco-distinct isolates of Magnaporthe oryzae for their morphological, virulence and molecular diversity and relative distribution of five Avr genes. METHODS AND RESULTS: Fifty-two M. oryzae isolates were collected from different rice ecosystems of southern India. A majority of them (n = 28) formed a circular colony on culture media. Based on the disease reaction on susceptible cultivar (cv. HR-12), all 52 isolates were classified in to highly virulent (n = 28), moderately virulent (n = 11) and less-virulent (13) types. Among the 52 isolates, 38 were selected for deducing internal transcribed spacer (ITS) sequence diversity. For deducing phylogeny, another set of 36 isolates from other parts of the world was included, which yielded two distinct phylogenetic clusters. We identified eight haplotype groups and 91 variable sites within the ITS sequences, and haplotype-group-2 (Hap_2) was predominant (n = 24). The Tajima's and Fu's Fs neutrality tests exhibited many rare alleles. Furthermore, PCR analysis for detecting the presence of five Avr genes in the different M. oryzae isolates using Avr gene-specific primers in PCR revealed that Avr-Piz-t, Avr-Pik, Avr-Pia and Avr-Pita were present in 73.68%, 73.68%, 63.16% and 47.37% of the isolates studied, respectively; whereas, Avr-Pii was identified only in 13.16% of the isolates. CONCLUSIONS: Morpho-molecular and virulence studies revealed the significant diversity among eco-distinct isolates. PCR detection of Avr genes among the M. oryzae population revealed the presence of five Avr genes. Among them, Avr-Piz-t, Avr-Pik and Avr-Pia were more predominant. SIGNIFICANCE AND IMPACT OF THE STUDY: The study documented the morphological and genetic variability of eco-distinct M. oryzae isolates. This is the first study demonstrating the distribution of the Avr genes among the eco-distinct population of M. oryzae from southern India. The information generated will help plant breeders to select appropriate resistant gene/s combinations to develop blast disease-resistant rice cultivars.

Thymol-a plant-based monoterpenoid phenol compound of an essential oil for the management of sheath blight disease of rice.

Sheath blight of rice is a global disease that significantly reduces rice yield. This study reports the antifungal activity of an active compound of essential oil, thymol, at different concentrations against Rhizoctonia solani (strain RS-Gvt). In vitro assay results indicated that thymol concentrations (0.5 mg mL-1 and 0.25 mg mL-1) completely inhibited (100%) the mycelial growth of RS-Gvt (p ≤ 0.01). Microscopic observations of thymol-treated mycelium of RS-Gvt at 0.0312 mg mL-1 and above concentrations, revealed a distorted mycelial morphology with deformed hyphae. Hyphae showed a bead-like appearance, reduction in size, and constriction of the hyphae at uneven points with increased hyphal density often entangling with each other. Further, an on-field experiment was conducted to study the field bio-efficacy of thymol for two consecutive Kharif seasons of 2022 and 2023 using a factorial RCBD design. The disease severity was measured as the percent disease index (PDI), and the results of two seasons were pooled. Pathogen (RS-Gvt) and thymol were inoculated in different combinations/methods as main treatments (M1-M3), and concentrations of thymol (0.0625-1.0 mg ML-1) as sub-treatments. The results indicated that all two factors significantly (P = 0.05) influenced the PDI and grain yield. The pooled data of two seasons indicated a significant difference between the main treatments (M1: RS-Gvt + thymol together; M2: thymol sprayed first followed by RS-Gvt; M3: RS-Gvt first followed by thymol spray) on PDI (53.39-59.67) and grain yield (4.16-4.75 t ha-1). M1 exhibited a lower PDI (53.39) and a higher grain yield (4.75 t ha-1) compared to M2 and M3, indicating a protective mode of action of thymol against sheath blight disease of rice. The sub-treatments have shown significant variation in PDI and grain yield. The PDI and grain yield ranged from 33.70 (at 1 mg mL-1) to 66.21 (at 0.0625 mg mL-1) and 4.18 (at 1 mg mL-1) to 5.26 (at 0.0625 mg mL-1) t ha-1, respectively, among the thymol concentrations. This indicates that increasing concentrations of thymol have negatively influenced the PDI and positively impacted the yield. Therefore, the spray of 1 mg mL-1 of thymol at the potential disease-infection stage is most effective in controlling the sheath blight disease of rice. This study provides an alternative green bioactive compound for controlling the sheath blight disease, and thymol can be included in developing eco-friendly integrated disease management practices. © 2024 Society of Chemical Industry.

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.