Pectin induced transcriptome of a Rhizoctonia solani strain causing sheath blight disease in rice reveals insights on key genes and RNAi machinery for development of pathogen derived resistance

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

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Not AvailableThe 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.Not Availabl

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Not AvailableSheath 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.Not Availabl

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Not AvailableRice tungro disease, one of the major constraints to rice production in South and Southeast Asia, is caused by a combination of two viruses: Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV). The present study was undertaken to determine the genetic variation of RTSV population present in tungro endemic states of Indian subcontinent. Phylogenetic analysis based on coat protein sequences showed distinct divergence of Indian RTSV isolates into two groups; one consisted isolates from Hyderabad (Andhra Pradesh), Cuttack (Orissa), and Puducherry and another from West Bengal, Coimbatore (Tamil Nadu), and Kanyakumari (Tamil Nadu). The results obtained from phylogenetic study were further supported with the SNPs (single nucleotide polymorphism), INDELs (insertion and deletion) and evolutionary distance analysis. In addition, sequence difference count matrix revealed 2–68 nucleotides differences among all the Indian RTSV isolates taken in this study. However, at the protein level these differences were not significant as revealed by Ka/Ks ratio calculation. Sequence identity at nucleotide and amino acid level was 92–100% and 97–100%, respectively, among Indian isolates of RTSV. Understanding of the population structure of RTSV from tungro endemic regions of India would potentially provide insights into the molecular diversification of this virus.Not Availabl

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Occurrence of a new necrosis viral disease of blackgram (Vigna mungo) and identification using electron microscopy and ELISA technique

A new necrosis viral disease was observed in blackgram, showed brown necrotic rings along with veinal and stem necrosis. The virus was mechanically inoculated on the local lesion host, cowpea cv. 152 and maintained in the local lesion host throughout the study. Yield studies under pot culture experiment showed 10- to 30-day-old plants were highly susceptible and the yield became almost nil. By using Transmission Electron Microscope (TEM) and indirect Direct Antigen Coated-Enzyme Linked Immuno-Sorbent Assay (DAC-ELISA) studies the virus was identified as Tobacco streak virus (TSV). The ultraviolet absorbance of the purified virus was measured and the ratio of A260/A280 was determined as 1.41. Polyclonal antiserum was raised against blackgram necrosis virus in New Zealand white rabbit and the titre value was determined as 1: 200. Direct antigen coating-ELISA was used to detect the virus concentration in various plant parts and stem portion recorded maximum virus concentration. TSV in blackgram was not transmitted through seeds

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Not AvailableBacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae (Xoo), remains a major production constraint in rice cultivation especially in irrigated and rainfed lowland ecosystems in India. The pathogen is highly dynamic in nature and knowledge on pathotype composition among the Xoo population is imperative for designing a scientific resistance breeding program. In this study, four hundred isolates of Xoo collected from diverse rice growing regions of India were analyzed for their virulence and genetic composition. Virulence profiling was carried out on a set of differentials consisting of 22 near isogenic lines (NILs) of IR24 possessing different BB resistance genes and their combinations along with the checks. It was observed that different NILs possessing single BB resistance gene were susceptible to about 59–94% of the Xoo isolates except IRBB 13 (containing BB resistance gene xa13), which showed susceptibility to about 35% of the isolates. Based on the reaction of the Xoo isolates on the differentials, they were categorized into 22 pathotypes. Among the 22 pathotypes, IXoPt-1 and IXoPt-2 were least virulent and IXoPt # 18–22 were highly virulent. Pathotype IXoPt-19 which was virulent on all single BB resistance genes except xa13 constituted the major pathotype (22.5% isolates) and was widely distributed throughout India (16 states). This was followed by pathotype IXoPt-22 (17.25%) which was virulent on all the NILs possessing single BB resistance genes. Molecular analysis was carried out using two outwardly directed primers complementary to sequence of IS1112, a repetitive element of Xoo. A high level of genetic polymorphism was detected among these isolates and the isolates were grouped into 12 major clusters. The data indicated complex nature of evolution of the Xoo pathotypes and there was no strong correlation between pathotypes and genetic clusters as each genetic cluster was composed of Xoo isolates belonging to different pathotypes. The study indicated that none of the single BB resistance genes can provide broad spectrum resistance in India. However, two-gene combinations like xa5 + xa13 and different 3 or 4 genes combination like Xa4 + xa5 + xa13, Xa4 + xa13 + Xa21, xa5 + xa13 + Xa21 and Xa4 + xa5 + xa13 + Xa21 are broadly effective throughout India.Department of Biotechnology, Government of Indi

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Not AvailableBacterial 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.Not Availabl

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Not AvailableSheath 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 fieldresistance, 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.Not Availabl