Rice Blast
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Scientific articles on rice blast and wheat blast 20 new articles each month !
Curated by Elsa Ballini
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Gene flow between divergent cereal- and grass-specific lineages of the rice blast fungus Magnaporthe oryzae

Gene flow between divergent cereal- and grass-specific lineages of the rice blast fungus Magnaporthe oryzae | Rice Blast | Scoop.it
Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity, and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multi-host pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for 76 M. oryzae isolates sampled from 12 grass and cereal genera to infer the population structure of M. oryzae, and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously-used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis tritici). Inference of population subdivisions revealed multiple divergent lineages within M. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages within M. oryzae. These findings provide greater understanding of the eco-evolutionary factors that underlie the diversification of M. oryzae and highlight the practicality of genomic data for epidemiological surveillance in this important multi-host pathogen.
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Dynamic Changes in the Rice Blast Population in the United States Over Six Decades | Molecular Plant-Microbe Interactions

Dynamic Changes in the Rice Blast Population in the United States Over Six Decades | Molecular Plant-Microbe Interactions | Rice Blast | Scoop.it
Rice blast disease caused by Magnaporthe oryzae is one of the most destructive diseases of rice. Field isolates of M. oryzae rapidly adapt to their hosts and climate. Tracking the genetic and pathogenic variability of field isolates is essential to understand how M. oryzae interacts with hosts and environments. In this study, a total of 1,022 United States field isolates collected from 1959 to 2015 were analyzed for pathogenicity toward eight international rice differentials. A subset of 457 isolates was genotyped with 10 polymorphic simple sequence repeat (SSR) markers. The average polymorphism information content value of markers was 0.55, suggesting that the SSR markers were highly informative to capture the population variances. Six genetic clusters were identified by both STRUCTURE and discriminant analysis of principal components methods. Overall, Nei’s diversity of M. oryzae in the United States was 0.53, which is higher than previously reported in a world rice blast collection (0.19). The observed subdivision was associated with collection time periods but not with geographic origin of the isolates. Races such as IC-17, IE-1, and IB-49 have been identified across almost all collection periods and all clusters; races such as IA-1, IB-17, and IH-1 have a much higher frequency in certain periods and clusters. Both genomic and pathogenicity changes of United States blast isolates were associated with collection year, suggesting that hosts are a driving force for the genomic variability of rice blast fungus.

Via Niklaus Grunwald
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Stunted growth caused by blast disease in rice seedlings is associated with changes in phytohormone signaling pathways

Stunted growth caused by blast disease in rice seedlings is associated with changes in phytohormone signaling pathways | Rice Blast | Scoop.it
In response to pathogen attack, plants prioritize defense reactions generally at the expense of plant growth. In this work, we report that changes in phytohormone signaling pathways are associated with the stunted plant growth caused by blast disease in rice seedlings. Infection of rice seedlings with blast fungus Magnaporthe oryzae (race 007.0) at the four-leaf stage (three true leaves) resulted in considerable inhibition of the growth of the upper uninfected distal leaves; the length of leaf blade and leaf sheath of the sixth and seventh leaf was reduced by 27% and 82%, and 88% and 72%, respectively, compared to that in the uninoculated plant control. Interestingly, cutting off the blast-infected fourth leaf within 2 days post inoculation (dpi) significantly rescued the inhibition of leaf growth, implying that an inhibitory substance(s) and/or signal was generated in the blast-infected leaves (fourth leaf) and transmitted to the upper distal leaves (sixth and seventh) during the 2-dpi period that induced growth inhibition. Expression analysis of marker genes for phytohormone pathways revealed acute activation of the jasmonate (JA) and abscisic acid (ABA) signaling pathways, and repression of auxin, gibberellic acid (GA) and salicylic acid (SA) signaling pathways, in the sixth leaf. The genes related to cell wall expansion were also significantly downregulated. In the blast-infected fourth leaf, JA pathway was activated within 2 dpi, followed by activation of ABA pathway 3 dpi. Further, leaf inhibition caused by blast infection was partially rescued in the rice mutant line coleoptile photomorphogenesis 2 (cpm2), which is defective in the gene encoding allene oxide cyclase (OsAOC). These results indicate that the JA signaling pathway is at least partly involved in the growth inhibition processes. Collectively, our data suggest that, upon pathogen attack, rice seedlings prioritize defense reactions against the infecting pathogen by temporarily ceasing plant growth through the systemic control of phytohormone pathways.

Via Philip Carella
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Review of combinations of experimental and computational techniques to identifyand understand genes involved in innate immunity and effector-triggered defence

Review of combinations of experimental and computational techniques to identifyand understand genes involved in innate immunity and effector-triggered defence | Rice Blast | Scoop.it
The innate immune system includes a first layer of defence that recognises conserved pathogen-associated molecular patterns that are essential for microbial fitness. Resistance (R) gene-based recognition of pathogen effectors, which function in modulation or avoidance of host immunity, activates a second layer of plant defence. In this review, experimental and computational techniques are considered to improve understanding of the plant immune system. Biocomputation contributes to discovery of the molecular genetic basis of host resistance against pathogens. Sequenced genomes have been used to identify R genes in plants. Resistance gene enrichment sequencing based on conserved protein domains has increased the number of R genes with nucleotide-binding site and leucine-rich repeat domains. Network analysis will contribute to an improved understanding of the innate immune system and identify novel genes for partial disease resistance. Machine learning algorithms are expected to become important in defining aspects of the immune system that are less well characterised, including identification of R genes that lack conserved protein domains.
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Chitin-deacetylase activity induces appressorium differentiation in the rice blast fungus Magnaporthe oryzae

Chitin-deacetylase activity induces appressorium differentiation in the rice blast fungus Magnaporthe oryzae | Rice Blast | Scoop.it
The rice blast fungus Magnaporthe oryzae differentiates a specialized infection structure called an appressorium to invade rice cells. In this report, we show that CBP1, which encodes a chitin-deacetylase, is involved in the induction phase of appressorium differentiation. We demonstrate that the enzymatic activity of Cbp1 is critical for appressorium formation. M. oryzae has six CDA homologues in addition to Cbp1, but none of these are indispensable for appressorium formation. We observed chitosan localization at the fungal cell wall using OGA488. This observation suggests that Cbp1-catalysed conversion of chitin into chitosan occurs at the cell wall of germ tubes during appressorium differentiation by M. oryzae. Taken together, our results provide evidence that the chitin deacetylase activity of Cbp1 is necessary for appressorium formation.
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Molecular Plant Pathology: Rmg8 and Rmg7, wheat genes for resistance to the wheat blast fungus, recognize the same avirulence gene AVR‐Rmg8 (2017)

Molecular Plant Pathology: Rmg8 and Rmg7, wheat genes for resistance to the wheat blast fungus, recognize the same avirulence gene AVR‐Rmg8 (2017) | Rice Blast | Scoop.it

Rmg8 and Rmg7 are genes for resistance to the wheat blast fungus (Pyricularia oryzae) located on 2B chromosome in hexaploid wheat and 2A chromosome in tetraploid wheat, respectively. AVR-Rmg8, an avirulence gene corresponding to Rmg8, was isolated from a wheat blast isolate through map-based strategy. The cloned fragment encoded a small protein containing a putative signal peptide. AVR-Rmg8 was recognized not only by Rmg8 but also by Rmg7, suggesting that these two resistance genes are equivalent to a single gene from the viewpoint of resistance breeding. This article is protected by copyright. All rights reserved.


Via Kamoun Lab @ TSL
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Status of Global Pearl Millet Breeding Programs and the Way Forward

Status of Global Pearl Millet Breeding Programs and the Way Forward | Rice Blast | Scoop.it
Pearl millet [Pennisetum glaucum (L.) R. Br.] is a warm-season, C4 annual cereal primarily grown in Africa and India for food and fodder. It is also grown in the United States, mainly as a forage crop on a limited area. It is the sixth most important cereal crop in the world. More than 90 million people around the world rely on it as a food grain. It is known for its drought and heat tolerance to reliably produce crops in arid environments. This review is meant to assess the current status of pearl millet breeding and its future prospects globally, with major emphasis on breeding efforts in the United States and India. The topics discussed relate to improvements in plant stature, maturity, photoperiod insensitivity, discovery of cytoplasmic male sterility (CMS), and transfer of apomixis from wild relatives. These improvements have led to increased grain and forage yields, nutritional quality, and enhanced disease resistance. Hybrids developed using CMS reportedly have an average of 50% higher grain yield than open-pollinated cultivars. We discuss important genetic and breeding achievements in pearl millet for different traits and their implications for further improvement as a potential crop. Additional research is needed to enhance its productivity, early stand establishment, drought tolerance, and nutritional quality for growing it as a grain crop in moisture-limited areas. The application of advanced genomics and marker-assisted selection tools is needed to accelerate pearl millet breeding and accomplish targeted breeding goals.
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Genomic study shows endemic and pandemic rice blast lineages and lineages between rice and setaria infecting gene pools. Book of Abstracts of the 12th European Fondation for Plant Pathology (EFPP) ...

The rice blast fungus Magnaporthe oryzae is the most damaging rice pathogen, and a textbook example of widely distributed, rapidly adapting pathogen, despite limited genetic diversity. The aim of our study was to elucidate the factors and evolutionary changes underlying the emergence, diversification and spread of M. oryzae on rice. Analyses of population structure based on Infinium-genotyping of 5300 SNPs for 970 isolates collected on rice on the five continents identified 13 lineages within M. oryzae. Three lineages were pandemic in multiple continents and one of them was the only lineage detected in Europe. Multiple lineages with more restricted distributions in sub-Saharan Africa and Asia were also identified. Whole genome resequencing of a subset of 80 rice-infecting isolates combined with 12 isolates collected on Setaria millet revealed several lineages with intermediate positions between the previously identified rice- and Setariainfecting gene pools, questioning the Setaria origin of rice-infecting M. oryzae and suggesting that the emergence of rice blast may be more recent than previously thought. Because the sequenced isolates were collected between 1973 and 2009 and recombination is limited, we will use dated tips to calibrate tree nodes within a phylogenetic framework to elucidate the timing of emergence and global dispersal of M. oryzae. Most lineages were highly clonal, but we found evidence for recombination in a widely distributed lineage infecting upland rice in Yunnan, Laos and Thailand. We will use genome scans for genetic exchanges to test the hypothesis that recombining lineages are more likely to receive genetic material from other lineages. Our work provides a population-level genomic framework for defining molecular markers to assist in the control of rice blast and for investigating the molecular underpinnings of phenotypic and fitness differences between divergent lineages
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Diverse rice landraces of North East India enables the identification of novel genetic resources for Magnaporthe resistance

North-East (NE) India, the probable origin of rice has diverse genetic resources. Many rice landraces of NE India were not yet characterized for blast resistance. A set of 232 landraces of NE India, were screened for field resistance at two different hotspots of rice blast viz., IIRR-UBN, Hyderabad and ICAR-NEH, Manipur in two consecutive seasons. The phenotypic evaluation as well as gene profiling for twelve major blast resistance genes (Pitp, Pi33, Pi54, Pib, Pi20, Pi38, Pita2, Pi1, Piz, Pi9, Pizt and Pi40) with linked as well as gene-specific markers, identified 84 resistant landraces possessing different gene(s) either in singly or in combinations and also identified seven resistant landraces which do not have the tested genes, indicating the valuable genetic resources for blast resistance. To understand the molecular diversity existing in the population, distance and model based analysis were performed using 120 SSR markers. Results of both analyses are highly correlated by forming two distinct subgroups and the existence of high diversity (24.9% among the subgroups; 75.1% among individuals of each subgroup) was observed. To practically utilize the diversity in the breeding programme, a robust core set having an efficiency index of 0.82 which consists of 33 landraces were identified through data of molecular, blast phenotyping and important Agro-morphological traits. The association of eight novel SSR markers was revealed through genome-wide association analysis. This also consists of important agronomic traits including leaf and neck blast resistance. The current study focuses on identifying novel resources having field resistance to blast as well as markers which can be explored in rice improvement programmes. It also entails the development of a core set which can aid in representing the entire diversity for efficiently harnessing its properties to broaden the gene pool of rice.
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bioRxiv: Coexistence of multiple endemic and pandemic lineages of the rice blast pathogen (2017)

bioRxiv: Coexistence of multiple endemic and pandemic lineages of the rice blast pathogen (2017) | Rice Blast | Scoop.it

The rice blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae) causes the most damaging rice disease. Yet, little is known about the genetic makeup of this important system for plant pathology. Using whole genome resequencing of a worldwide collection of isolates, we identified four major M. oryzae lineages mainly associated with Japonica or Indica rice, including one pandemic lineage on each rice subspecies. Tip-dating calibration indicated that M. oryzae lineages separated about a millenium ago, much later than the initial domestication of rice. The major lineage endemic to Southeast continental Asia displayed signatures of sexual recombination and evidence for having received DNA from multiple lineages. Tests of weak selection revealed that the pandemic spread of clonal lineages entailed an evolutionary 'cost', in terms of an accumulation of deleterious mutations. Our work reveals the coexistence of multiple endemic and pandemic lineages with contrasting population and genetic characteristics within a widely distributed pathogen.


Via Kamoun Lab @ TSL, Elsa Ballini
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Sorting nexin (MoVps17) is required for fungal development and plant infection by regulating endosome dynamics in the rice blast fungus

Sorting nexin (MoVps17) is required for fungal development and plant infection by regulating endosome dynamics in the rice blast fungus | Rice Blast | Scoop.it
Vps17 is a sorting nexin (SNX) and a component of the retromer, a protein complex mediating retrograde vesicle transport between endosomes and the trans-Golgi network. However, its role in the development and pathogenicity of filamentous fungi such as the rice blast fungus (Magnaporthe oryzae) remains unclear. We investigate the functional relationship between the SNX and the cargo-selective complex (CSC) of the fungal retromer by genetic analysis, live cell imaging and immunological assay. Our data show that the MoVps17 null mutation causes defects in growth, development, and pathogenicity in M. oryzae. MoVps17 is localized to endosomes depending on the activity of phosphatidylinositol 3-kinase (PI3K), a key enzyme for fungal development and infection. Both PX and BAR domains of MoVps17 are essential for its endosomal localization and function. Furthermore, our yeast two-hybrid assaysshow that MoVps17 and MoVps5 can interact . Lastly, live cell imaging suggests that MoVps17 can regulate early endosome fusion and budding as well as endocytosis. Taken together, our results suggest that MoVps17 specifically functions as a retromer component with CSC and also plays a distinct role in the regulation of endosome dynamics during fungal development and plant infection. This article is protected by copyright. All rights reserved.
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Broad-spectrum blast resistance: harnessing a natural allele of a transcription factor in rice

Broad-spectrum blast resistance: harnessing a natural allele of a transcription factor in rice | Rice Blast | Scoop.it
The model illustrates that a mutation in Bsr-d1 promoter in ‘Digu’ recruits a transcriptional repressor MYBS1, which suppresses BSR-D1 expression, leading to  decreased peroxidase expression and higher H2O2 levels after M. oryzae infection in the  blast-resistant rice variety (‘Digu’) compared with a susceptible variety (‘LTH’).

Via Philip Carella
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Wheat Production and Consumption Dynamics in an Asian Rice Economy: The Bangladesh Case

Wheat consumption in Asia’s major rice economies has been increasing over the decades. Bangladesh is no exception, despite being the world’s fourth largest rice-producing and the largest rice-consuming country. In Bangladesh, wheat consumption has doubled from 1961 to 2013, and now stands at 17.5 kg per capita, about a ninth of the rice consumption. Densely populated Bangladesh has achieved rice self-sufficiency, but relies on imports to top up modest domestic wheat production. This study assesses the prospects for Bangladesh to expand its wheat production. The rice–wheat production system offers good prospects to expand wheat production in Bangladesh and respond to increasing domestic demand. Based on the findings, this study urges the expansion of wheat production in the seasonally fallow land, particularly in southern Bangladesh. Also, this study calls for further investments in wheat research and development to ensure local adaptation, comparative advantage, and sustainable intensification.
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COST | Glossary | STSM

COST | Glossary | STSM | Rice Blast | Scoop.it

Phenotyping is an emerging science that characterizes plant behaviour and quantifies features such as growth and stress tolerance in a precise and reproducible manner that allows linking to genetic and environmental control. As a highly interdisciplinary research area, phenotyping covers a wide range of methodological approaches from whole plant phenotyping (characterization of morphological and physiological plant features), over molecular phenotyping approaches on a cellular level (transcriptomics, proteomics, metabolomics) to computational methods for image analysis, plant growth modeling and statistical data analysis and data integration.


Short-Term Scientific Missions - These Missions (Inter-laboratory Exchange Visits) aim at strengthening the existing COST Actions by allowing scientists to go to an institution or laboratory in another COST country to foster collaboration, to learn a new technique or to take measurements using instruments and/or methods not available in their own institution/laboratory. They are particularly intended for Early Stage Researchers.

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Identification of long non-coding RNA in rice lines resistant to Rice blast pathogen Maganaporthe oryzae

Identification of long non-coding RNA in rice lines resistant to Rice blast pathogen Maganaporthe oryzae | Rice Blast | Scoop.it

Rice blast disease caused by a fungus Magnaporthae oryzae is one of the most important biotic factors that severely damage the rice crop. Several molecular approaches are now being applied to tackle this issue in rice. It is of interest to study long non-coding RNA (lncRNA) in rice to control the disease. lncRNA, a non-coding transcript that does not encode protein, is known to play an important role in gene regulation of various biological processes. Here we describe a computational pipeline to identify lncRNA from a resistant rice line. The number of lncRNA found in resistant line was 1429, 1927 and 1981 in mock and M. oryzae (ZB13 and Zhong) inoculated samples, respectively. Functional classification of these lncRNA reveals a higher number of long intergenic non-coding RNA compared to antisense lncRNA in both mock and M. oryzae inoculated resistant rice lines. Many intergenic lncRNA candidates were identified from resistant rice line and their role to regulate the resistance mechanism in rice during M. oryzae invasion is implied.

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Allelic variation of the rice blast resistance gene Pid3 in cultivated rice worldwide

Allelic variation of the rice blast resistance gene Pid3 in cultivated rice worldwide | Rice Blast | Scoop.it
In this study, the re-sequencing data from 3,000 rice genomes project (3 K RGP) was used to analyze the allelic variation at the rice blast resistance (R) Pid3 locus. A total of 40 haplotypes were identified based on 71 nucleotide polymorphic sites among 2621 Pid3 homozygous alleles in the 3k genomes. Pid3 alleles in most japonica rice accessions were pseudogenes due to premature stop mutations, while those in most indica rice accessions were identical to the functional haplotype Hap_6, which had a similar resistance spectrum as the previously reported Pid3 gene. By sequencing and CAPS marker analyzing the Pid3 alleles in widespread cultivars in China, we verified that Hap_6 had been widely deployed in indica rice breeding of China. Thus, we suggest that the priority for utilization of the Pid3 locus in rice breeding should be on introducing the functional Pid3 alleles into japonica rice cultivars and the functional alleles of non-Hap_6 haplotypes into indica rice cultivars for increasing genetic diversity.
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Increased metabolite production by deletion of an HDA1‐type histone deacetylase in the phytopathogenic fungi, Magnaporthe oryzae (Pyricularia oryzae) and Fusarium asiaticum

Histone deacetylases (HDACs) play an important role in the regulation of chromatin structure and gene expression. We found that dark pigmentation of Magnaporthe oryzae (anamorph Pyricularia oryzae) ΔMohda1, a mutant strain in which an ortholog of the yeast HDA1 was disrupted by double cross-over homologous recombination, was significantly stimulated in liquid culture. Analysis of metabolites in a ΔMohda1 mutant culture revealed that the accumulation of shunt products of the 1,8-dihydroxynaphthalene melanin and ergosterol pathways were significantly enhanced compared to the wild-type strain. Northern blot analysis of the ΔMohda1 mutant revealed transcriptional activation of three melanin genes that are dispersed throughout the genome of M. oryzae. The effect of deletion of the yeast HDA1 ortholog was also observed in Fusarium asiaticum from the Fusarium graminearum species complex; the HDF2 deletion mutant produced increased levels of nivalenol-type trichothecenes. These results suggest that histone modification via HDA1-type HDAC regulates the production of natural products in filamentous fungi.
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2018 Journal of Fungi Travel Award for postdocs and Phd Students

2018 Journal of Fungi Travel Award for postdocs and Phd Students | Rice Blast | Scoop.it

On behalf of Prof. Dr. David S. Perlin, Editor-in-Chief of Journal of Fungi, we are pleased to inform you that we will be offering a 2018 JoF Travel Award to PhD graduate students and postdoctoral fellows involved in mycology research to attend a conference of their choice in 2018.


Candidates’ Requirements: Applicants must be PhD graduate students and postdoctoral fellows involved in mycology research. Applicants will attend an international conference related to mycology research in 2018 and present their research (poster or oral presentation) during the event.

After the meeting, the awardee is requested to provide a copy of the page in the conference program showing the abstract/presentation and meeting badge that verifies his/her attendance

The awarded applicant will receive 800 Swiss Francs and an Award Certificate. The fees can be used for registration, travel, or accommodation.

 If you would like to nominate someone for this award, please go directly to 2018 JoF Travel Award page (http://www.mdpi.com/journal/jof/awards) and submit the application to us (jof@mdpi.com or bernice.li@mdpi.com). The application deadline is 15 December 2017. The winner will be announced by the end of January 2018.
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bioRxiv: Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions (2017)

bioRxiv: Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions (2017) | Rice Blast | Scoop.it
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The Sainsbury Lab's curator insight, August 29, 3:39 AM
The plant immune system is innate, encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that plant immune receptors are able to recognize pathogen effectors through the acquisition of exogenous protein domains from other plant genes. We showed that plant immune receptors with integrated domains are distributed unevenly across their phylogeny in grasses. Using phylogenetic analysis, we uncovered a major integration clade, whose members underwent repeated independent integration events producing diverse fusions. This clade is ancestral in grasses with members often found on syntenic chromosomes. Analyses of these fusion events revealed that homologous receptors can be fused to diverse domains. Furthermore, we discovered a 43 amino acids long motif that was associated with this dominant integration clade and was located immediately upstream of the fusion site. Sequence analysis revealed that DNA transposition and/or ectopic recombination are the most likely mechanisms of NLR-ID formation. The identification of this subclass of plant immune receptors that is naturally adapted to new domain integration will inform biotechnological approaches for generating synthetic receptors with novel pathogen baits.
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Effect of Blast Disease on Seed Vigor Parameters in Rice

Blast (Magnaporthe oryza) is considered as one of the most important biotic stresses limiting rice production. In the recent years due to uncertain climatic factors blast is affecting even the popular landraces known to be resistant over a period of time. Present study is focused on the effect of the disease on seed germination and growth rate. The pool consists of 85 varieties, which include 38 released varieties, 43 landraces and four check varieties (Tadukan and Tetep- Resistant checks, HR-12 and CO- 39 susceptible). The experiment was laid out in Completely Randomized Design (CRD) with three replications. Results showed that 12 varieties showed minimal influence of blast disease. Five varieties- BI-33, Sannamullu, Mysur sanna, Ugibhatta and Jeerigesanna were susceptible under field condition but found with minimum losses in germination and seedling growth test. Therefore, the results clearly indicate that minimum to moderate influence can be observed by blast disease during germination and seedling growth stages.
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Towards agroecological management of rice blast disease in Madagascar Highlands. Book of Abstracts of the 12th European Fondation for Plant Pathology (EFPP) and the 10th French Society for Plant Pa...

Rice is the staple crop and food in Madagascar. Since the 1980s, a joint breeding program conducted by CIRAD and Fofifa, has led to the creation of new varieties adapted to the high altitude and at the same time to rainfed cropping environment (Raboin et al., 2014). But the first released varieties rapidly became susceptible to rice blast, a fungal disease caused by Magnaporthe oryzae, and had to be abandoned. In the 2000 and 2010s, new varieties tolerant to blast were proposed to farmers. Upland rice cropping system has become an important complement to irrigated rice, and a way to improve self-sufficiency in rice and food security. Rice blast, a fungal disease caused by Magnaporthe oryzae, is a major constraint for rice particularly in upland cropping conditions. In developing countries like in Madagascar, no chemical solution can be considered, so there is a crucial importance to find out agroecological solutions to limit the risk of epidemics. The interactions between upland rice and blast epidemics have then been studied in a multidisciplinary team in the highlands of Madagascar for more than 10 years. Conservation agriculture cropping systems were studied (Sester et al., 2014, Dusserre et al., in press) and showed an interesting impact on rice susceptibility to blast. Complementary field experiments showed that rice susceptibility was affected by soil origin and crop density and that infested crop residues appeared as sources of primary inoculum (Raveloson et al., 2013). Experiments on cultivar mixtures showed promising results to control blast epidemics (Raboin et al., 2012). These data were measured in field experiments and integrated together in a simulation model at the landscape scale (Sester et al., 2016)
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PacBio Sequencing Reveals Transposable Element as a Key Contributor to Genomic Plasticity and Virulence Variation in Magnaporthe oryzae

PacBio Sequencing Reveals Transposable Element as a Key Contributor to Genomic Plasticity and Virulence Variation in Magnaporthe oryzae | Rice Blast | Scoop.it
We deployed single molecule real-time (SMRT) sequencing developed by Pacific BioSciences (PacBio), to generate near complete genome assembly for M. oryzae field isolates FJ81278 and Guy11, and evaluated the possible contribution of TEs to genomic variation events such as chromosomal translocation, gene presence/absence in LS regions and virulence-associated secreted proteins (SPs) polymorphism.

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bioRxiv: Coexistence of multiple endemic and pandemic lineages of the rice blast pathogen (2017)

bioRxiv: Coexistence of multiple endemic and pandemic lineages of the rice blast pathogen (2017) | Rice Blast | Scoop.it

The rice blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae) causes the most damaging rice disease. Yet, little is known about the genetic makeup of this important system for plant pathology. Using whole genome resequencing of a worldwide collection of isolates, we identified four major M. oryzae lineages mainly associated with Japonica or Indica rice, including one pandemic lineage on each rice subspecies. Tip-dating calibration indicated that M. oryzae lineages separated about a millenium ago, much later than the initial domestication of rice. The major lineage endemic to Southeast continental Asia displayed signatures of sexual recombination and evidence for having received DNA from multiple lineages. Tests of weak selection revealed that the pandemic spread of clonal lineages entailed an evolutionary 'cost', in terms of an accumulation of deleterious mutations. Our work reveals the coexistence of multiple endemic and pandemic lineages with contrasting population and genetic characteristics within a widely distributed pathogen.


Via Kamoun Lab @ TSL
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Construction and application of functional gene modules to regulatory pathways in rice

Construction and application of functional gene modules to regulatory pathways in rice | Rice Blast | Scoop.it
Signal transduction and transcriptional regulation pathways are key elements in the control of diverse physiological responses and agronomic traits in plants. The regulatory roles of more than 1,000 known genes have been functionally characterized in rice, a model crop plant, and many of them are associated with transcriptional regulation and signal transduction pathways. In this study, we collected and analyzed 417 known genes associated with regulatory pathways, about 40% of the known genes, using the regulation overview installed in the MapMan toolkit. Connecting novel genes to current knowledge about regulatory pathways can elucidate their molecular functions and inspire ideas for further applications. We have summarized the functions of known regulatory genes in the areas of transcriptional regulation, epigenetic regulation, protein modification, protein degradation, signaling and hormone metabolism, also we have emphasized the unique features of several gene families in these classes, including MADS box families, which are strongly associated with the regulation of floral organ identity and flowering time. In addition, our construction of functional modules in four agronomic categories, morphological, physiological, biotic stress and abiotic stress, suggests a basic framework for expanding current knowledge about regulatory pathways to enhance agronomic traits in rice. We also provide a quick illustration of the positive and negative regulatory relationships of the target gene to manipulate agronomic trait by using genome-wide transcriptome data of knockout or overexpression mutations of genes of interest in each functional module
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Regulatory Mechanism of Mycotoxin Tenuazonic Acid Production in Pyricularia oryzae

Regulatory Mechanism of Mycotoxin Tenuazonic Acid Production in Pyricularia oryzae | Rice Blast | Scoop.it
Tenuazonic acid (TeA) is a mycotoxin produced by the rice blast fungus Pyricularia oryzae and some plant pathogenic fungi. We previously demonstrated that TeA is biosynthesized in P. oryzae by TeA synthetase 1 (TAS1), and that its production is induced by osmo-sensory MAPK-encoding gene (OSM1) deletion or the addition of 1% DMSO to cultures; however, the regulatory mechanisms of TeA production were unknown. Here, we identified a Zn(II)2-Cys6-type transcription factor in the upstream region of TAS1, which is encoded by TAS2 and regulates TeA production. We also found PoLAE1, which is an homolog of LaeA, a regulator of fungal secondary metabolism. Analysis of PoLAE1 deletion and overexpression strains indicated that PoLAE1 drives TeA production. We also demonstrated that 2 TeA-inducing signals, 1% DMSO addition and OSM1 deletion, were transmitted through PoLAE1. Our results indicate that TeA production is regulated by 2 specific regulators, TAS2 and PoLAE1, in P. oryzae.
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Nutrients and host attributes modulate the abundance and functional traits of phyllosphere microbiome in rice - ScienceDirect

Nutrients and host attributes modulate the abundance and functional traits of phyllosphere microbiome in rice - ScienceDirect | Rice Blast | Scoop.it
The abundance of phyllosphere bacterial communities of seven genotypes of rice ADT- 38, ADT-43, CR-1009, PB-1, PS-5, P-44, and PB-1509 was investigated, in relation to nutrient dynamics of rhizosphere and leaves. P-44 genotype recorded highest pigment accumulation, while genotypes CR-1009 and P-44 exhibited most number of different bacterial morphotypes, Colony forming units in two media (Nutrient agar and R2A) varied significantly and ranged from 106-107 per g plant tissues. Among the selected 60 distinct morphotypes, IAA and siderophore producers were the dominant functional types. Biocontrol activity against Drechslera oryzae was shown by 38 isolates, while 17 and 9 isolates were potent against Rhizoctonia solani and Magnaporthe oryzae respectively. Principal Component Analysis (PCA) illustrated the significant effects of selected soil and leaf nutrients of seven rice varieties on the culturable phyllospheric population (log CFU), particularly in the R2A medium. Eigen values revealed that 83% of the variance observed could be assigned to Leaf-Fe, Leaf-Mn, chlorophyll b and soil organic carbon (OC). Quantitative PCR analyses of abundance of bacteria, cyanobacteria and archaebacteria revealed a host-specific response, with CR-1009 showing highest number of 16S rRNA copies of bacterial members, while both P-44 and PS-5 had higher cyanobacterial abundance, but lowest number of those belonging to archaebacteria. Nutritional aspects of leaf and soil influenced the abundance of bacteria and their functional attributes; this is of interest for enhancing the efficacy of foliar inoculants, thereby, improving plant growth and disease tolerance.
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