The intensity of rice false smut disease in selected states of northwest and south India was studied. In northern Indian states as a whole, disease incidence (percentage of false smut-infected tillers) varied from 2% to 75%. In the state of Haryana, maximum infection was recorded on hybrids like PA 6444 and PA 6129 while in Punjab state, 10-20% disease incidence was recorded in popular inbred rice varieties like PR 114, PA 116 and PAU 201. In the southern state of Tamil Nadu, the disease incidence varied from 5% to 85%. A heavy incidence of the disease was noticed in variety BPT 5204 and due to this, the air above the infected field gave a black smoky appearance from a distance as a result of release of spore mass in the atmosphere. In severe cases the number of infected grains reached even more than 100 per panicle. The pathogen Ustilaginoidea virens was isolated in potato dextrose agar medium and was characterized by both pathogenicity test and molecular analysis. Under glasshouse conditions, when a conidial suspension of the pathogen was injected during boot leaf stage of the rice variety TN1, typical smut balls were observed. The identity of the pathogen was further confirmed through polymerase chain reaction (PCR) analysis using U. virens-specific internal transcribed spacer (ITS) primers. The primer pair US 1-5/US3-3 and US2-5/US4-3 amplified 380 bp and 232 bp product, respectively, which are typical for the U. virens fungus.

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Key message RNAi mediated silencing of pectin degrading enzyme of R. solani gives a high level of resistance against sheath blight disease of rice. Abstract Rice sheath blight disease caused by Rhizoctonia solani Kuhn (telemorph; Thanatephorus cucumeris) is one of the most devastating fungal diseases which cause severe loss to rice grain production. In the absence of resistant cultivars, the disease is currently managed through fungicides which add to environmental pollution. To explore the potential of utilizing RNA interference (RNAi)-mediated resistance against sheath blight disease, we identified genes encoding proteins and enzymes involved in the RNAi pathway in this fungal pathogen. The RNAi target genes were deciphered by RNAseq analysis of a highly virulent strain of the R. solani grown in pectin medium. Additionally, pectin metabolism associated genes of R. solani were analyzed through transcriptome sequencing of infected rice tissues obtained from six diverse rice cultivars. One of the key candidate gene AG1IA_04727 encoding polygalacturonase (PG), which was observed to be significantly upregulated during infection, was targeted through RNAi to develop disease resistance. Stable expression of PG-RNAi construct in rice showed efficient silencing of AG1IA_04727 and suppression of sheath blight disease. This study highlights important information about the existence of RNAi machinery and key genes of R. solani which can be targeted through RNAi to develop pathogen-derived resistance, thus opening an alternative strategy for developing sheath blight-resistant rice cultivars.

Bacterial blight (BB) in rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major global production constraint, particularly in irrigated and rain-fed lowland areas. Improved Samba Mahsuri (ISM) is an elite, high-yielding, fine-grain type, BB-resistant rice variety possessing three BB-resistant genes (Xa21, xa13 and xa5) and is highly popular in the southern parts of India. As the BB pathogen is highly dynamic and the evolution of pathogen virulence against the deployed resistance genes is common, we added a novel BB-resistant gene, Xa38, into ISM through marker-assisted backcross breeding (MABB) to increase the spectrum and durability of BB resistance. The breeding line PR 114 (Xa38) was used as the donor for Xa38, whereas ISM was used as the recurrent parent. Foreground selection was conducted using PCR-based gene-specific markers for the target genes, whereas background selection was conducted using a set of polymorphic SSR markers between the parents and backcrossing that continued until the third generation. Eighteen homozygous BC3F2 plants possessing all four BB-resistant genes in the homozygous state and with a recurrent parent genome (RPG) recovery of more than 92% were identified and advanced to the BC3F6 generation. These 18 backcross-derived lines (BDLs) exhibited very high level of resistance against multiple Xoo strains and displayed agro-morphological traits, grain qualities and yield levels similar to or better than those of the recurrent parent ISM.

Sheath blight disease of rice caused by Rhizoctonia solani is one of the most dreaded plant diseases faced by the rice farmers all over the world. None of the commercially cultivated rice varieties have sufficient level of field resistance, and the disease is presently being managed by chemical pesticides. In this study, 40 isolates of rice sheath blight pathogen, collected from diverse rice ecosystems from 12 different states of India, were characterized for their morphological, pathological and genetic variation. The isolates showed wide morphological variation in terms of size of sclerotia and abundance of sclerotia production. The virulence of each pathogen isolate was studied on four rice varieties, that is TN1, IR 64, Tetep and Swarnadhan in glasshouse, and observations were taken by measuring the relative lesion height. The relative lesion heights produced by these isolates on four different rice varieties varied widely. Genetic variation of the isolates was analysed using ISSR markers. The primers based on AG, GA, AC and CA repeats were informative and revealed polymorphism among the isolates. The polymorphism information content (PIC) of the primers ranged from 0.80 to 0.96, while the resolving power (Rp) ranged from 3.7 to 15.35. Largely, grouping of the isolates happened based on their geographical origin. One isolate from Titabar, Assam, and another from Adialabad, Telangana, were quite distinct from rest of the isolates.