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PLOS ONE: Comparative Transcriptome Profiling of the Early Response to Magnaporthe oryzae in Durable Resistant vs Susceptible Rice (Oryza sativa L.) Genotypes

PLOS ONE: Comparative Transcriptome Profiling of the Early Response to Magnaporthe oryzae in Durable Resistant vs Susceptible Rice (Oryza sativa L.) Genotypes | Rice Blast | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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Rice Blast
Scientific articles on rice blast and wheat blast 20 new articles each month !
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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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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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Transcriptome sequencing of infected wheat samples collected during the wheat blast epidemic in Bangladesh in 2017 and release of raw sequence data on OpenWheatBlast website with open access

Transcriptome sequencing of infected wheat samples collected during the wheat blast epidemic in Bangladesh in 2017 and release of raw sequence data on OpenWheatBlast website with open access | Rice Blast | Scoop.it
Wheat fields in Bangladesh were again infected by wheat blast fungus (Magnaporthe oryzae) in 2017 growing season, following the epidemic of 2016. Infected wheat samples were collected by Tofazzal Islam and team, and sent to the Sainsbury Laboratory for RNA extraction and sequencing. Library preparation and RNA-Seq sequencing runs were performed on Illumina HiSeq-2500 machines at the Earlham Institute to produce paired-end reads with ~267 bp average insert size. Here we report the release of these data to general public with open access on OpenWheatBlast website.
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Accumulation of Azole Drugs in the Fungal Plant Pathogen Magnaporthe oryzae Is the Result of Facilitated Diffusion Influx

Magnaporthe oryzae is an agricultural mold that causes disease in rice, resulting in devastating crop losses. Since rice is a world-wide staple food crop, infection by M. oryzae poses a serious global food security threat. Fungicides, including azole antifungals, are used to prevent and combat M. oryzae plant infections. The target of azoles is CYP51, an enzyme localized on the endoplasmic reticulum (ER) and required for fungal ergosterol biosynthesis. However, many basic drug-pathogen interactions, such as how the azole gets past the fungal cell wall and plasma membrane, and is transported to the ER, are not understood. In addition, reduced intracellular accumulation of antifungals has consistently been observed as a drug resistance mechanism in many fungal species. Studying the basic biology of drug-pathogen interactions may elucidate uncharacterized mechanisms of drug resistance and susceptibility in M. oryzae and potentially other related fungal pathogens. We characterized intracellular accumulation of azole drugs in M. oryzae using a radioactively labeled fluconazole uptake assay to gain insight on whether azoles enter the cell by passive diffusion, active transport, or facilitated diffusion. We show that azole accumulation is not ATP-dependent, nor does it rely on a pH-dependent process. Instead there is evidence for azole drug uptake in M. oryzae by a facilitated diffusion mechanism. The uptake system is specific for azole or azole-like compounds and can be modulated depending on cell phase and growth media. In addition, we found that co-treatment of M. oryzae with ‘repurposed’ clorgyline and radio-labeled fluconazole prevented energy-dependent efflux of fluconazole, resulting in an increased intracellular concentration of fluconazole in the fungal cell.
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Tpc1 is an important Zn(II)2Cys6 transcriptional regulator required for polarized growth and virulence in the rice blast fungus

Tpc1 is an important Zn(II)2Cys6 transcriptional regulator required for polarized growth and virulence in the rice blast fungus | Rice Blast | Scoop.it
The establishment of polarity is a critical process in pathogenic fungi, mediating infection-related morphogenesis and host tissue invasion. Here, we report the identification of TPC1 (Transcription factor for Polarity Control 1), which regulates invasive polarized growth in the rice blast fungus Magnaporthe oryzae. TPC1 encodes a putative transcription factor of the fungal Zn(II)2Cys6 family, exclusive to filamentous fungi. Tpc1-deficient mutants show severe defects in conidiogenesis, infection-associated autophagy, glycogen and lipid metabolism, and plant tissue colonisation. By tracking actin-binding proteins, septin-5 and autophagosome components, we show that Tpc1 regulates cytoskeletal dynamics and infection-associated autophagy during appressorium-mediated plant penetration. We found that Tpc1 interacts with Mst12 and modulates its DNA-binding activity, while Tpc1 nuclear localisation also depends on the MAP kinase Pmk1, consistent with the involvement of Tpc1 in this signalling pathway, which is critical for appressorium development. Importantly, Tpc1 directly regulates NOXD expression, the p22phox subunit of the fungal NADPH oxidase complex via an interaction with Mst12. Tpc1 therefore controls spatial and temporal regulation of cortical F-actin through regulation of the NADPH oxidase complex during appressorium re-polarisation. Consequently, Tpc1 is a core developmental regulator in filamentous fungi, linking the regulated synthesis of reactive oxygen species and the Pmk1 pathway, with polarity control during host invasion.

Via Philip Carella
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New findings on phosphodiesterases, MoPdeH and MoPdeL in Magnaporthe oryzae revealed by structure analysis

New findings on phosphodiesterases, MoPdeH and MoPdeL in Magnaporthe oryzae revealed by structure analysis | Rice Blast | Scoop.it
The cyclic AMP signaling pathway mediates signal communication and sensing during infection-related morphogenesis in eukaryotes. Many studies have implicated cAMP as a critical mediator of appressorium development in the rice blast fungus, Magnaporthe oryzae. The cyclic AMP phosphodiesterases, MoPdeH and MoPdeL, as key regulators of intracellular cAMP levels, play pleiotropic roles in cell wall integrity, cellular morphology, appressorium formation, and infectious growth in M. oryzae. Here, we analyzed the roles of domains of MoPdeH and MoPdeL separately or in chimeras. The results indicated that the HD and EAL domains of MoPdeH are indispensable for its phosphodiesterase activity and function. Replacement of the MoPdeH HD domain with the L1 and L2 domains of MoPdeL, either singly or together, resulted in decreased cAMP hydrolysis activity of MoPdeH. All of the transformants exhibited phenotypes similar to the ΔMopdeH mutant, but also revealed that EAL and L1 play additional roles in conidiation, and that L1 is involved in infectious growth. We further found that the intracellular cAMP level is important for surface signal recognition and hyphal autolysis. The intracellular cAMP level negatively regulates Mps1-MAPK and positively regulates Pmk1-MAPK in the rice blast fungus. Our results provide new information to better understand the cAMP signaling pathway in the development, differentiation, and plant infection of the fungus. This article is protected by copyright. All rights reserved.
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MoMon1 is required for vacuolar assembly, conidiogenesis and pathogenicity in the rice blast fungus Magnaporthe oryzae

MoMon1 is required for vacuolar assembly, conidiogenesis and pathogenicity in the rice blast fungus Magnaporthe oryzae | Rice Blast | Scoop.it
The Pseudomonas fluorescens strain used in this work (Aur 6) has demonstrated its ability to improve fitness of different plant species upon biotic and abiotic stress conditions. Random mutants of this strain were constructed with the Tn5 transposon technology, and biological tests to evaluate loss of salt protection were conducted with all the mutants (104 mutants) on rice seedlings. Mutant 33 showed an evident reduction in its ability to protect plants upon salt stress challenge, whereas mutant 19 was more effective than the wild type. Enzymes related with oxidative stress were studied in both mutants and wild type. Enzyme activities were decreased with mutant 33 with regard to wild type, whereas mutant 19 did not produce important changes suggesting involvement of redox balance associated to the observed modifications in these antioxidant enzymes as one of the probable mechanisms used by these strains. Data of malondialdehyde (MDA) were consistent with this fact. Mutants also affected accumulation of proline, the most common osmolyte in plants. A second experiment to evaluate the ability of both mutants and wild type to stimulate growth on tomato plants was conducted, as this feature was previously demonstrated by wild type. Similar results were obtained in growth of both species, suggesting that mutations of both mutants are related with the capacities of the wild type to stimulate growth. To reveal mutated genes, both mutants were mapped. Three mutated genes were found in mutant 33. A gene related with a general secretion pathway protein D, a gene related with a putative two-component system sensor kinase (ColS), and a gene related with flagellar motor switch protein (FliG). In mutant 19, two mutated genes were found. One gene related with heavy metal efflux pump Czca family, and other gene of 16s rRNA.
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Identification of resistant germplasm containing novel resistance genes at or tightly linked to the Pi2/9 locus conferring broad-spectrum resistance against rice blast

The newly developed marker Pi2/9-RH could be used as a potentially diagnostic marker for the quick identification of resistant donors containing functional Pi2/9 alleles or unknown linked R genes. The three new monogenic lines containing the Pi2/9 introgression segment could be used as valuable materials for disease assessment and resistance donors in breeding program
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Expression of HopAI interferes with MAP kinase signaling in Magnaporthe oryzae

Expression of HopAI interferes with MAP kinase signaling in Magnaporthe oryzae | Rice Blast | Scoop.it
The Pmk1 and Mps1 MAP kinases are essential for appressorium formation and plant infection in Magnaporthe oryzae. However, their exact roles during invasive growth are not clear because pmk1 and mps1 mutants are defective in penetration. To further characterize their functions after penetration, in this study we expressed the Pseudomonas syringae effector HopAI known to inactivate plant MAP kinases in M. oryzae. Constitutive expression of HopAI with the RP27 or TrpC promoter resulted in defects in hyphal growth, conidiation, appressorium penetration, and pathogenicity, which is similar to the phenotype of the mps1 mutant. HopAI interacted strongly with Mps1 in vivo and expression of dominant active MKK2 partially suppressed the defects of PRP27-HopAI transformants, which were significantly reduced in Mps1 phosphorylation. When the infection-specific MIR1 (Magnaporthe-infection-related gene-1) promoter was used to express HopAI, PMIR1-HopAI transformants were defective in the spreading of invasive hyphae and elicited strong defense responses in penetrated plant cells. Expression of HopAI in Fusarium graminearum also mainly affected the activation of Mgv1, an Mps1 ortholog. Taken together, our results showed that Mps1 id the major intracellular target of HopAI when it is overexpressed, and MAP kinase signaling is important for cell-to-cell movement of invasive hyphae in M. oryzae. This article is protected by copyright. All rights reserved.
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Identification of a three-base deletion in the Pi2 locus, and development of functional marker for marker-assisted resistance selection

Identification of a three-base deletion in the Pi2 locus, and development of functional marker for marker-assisted resistance selection | Rice Blast | Scoop.it
Rice blast causes huge losses of rice and is the limiting factor in rice production. Host resistance improvement using marker-assisted selection (MAS) is considered to be the most economic and effective way to overcome rice blast. In this study, an allele mining strategy was used to find variation of the Pi2 blast-resistance gene from different rice varieties. In some varieties, there was an out-of-frame deletion of 3 base-pairs (bp) at the 1543–1545 site of the Pi2 gene (the “deletion” allele). Deletion of these 3 bp causes the loss of cysteine–arginine and their replacement with glycine in the protein product. As a consequence the predicted protein structure is changed, especially in the LRR region which is important to plant blast resistance. Plants with the deletion allele showed poor resistance compared to those with the non-deletion variant. Haplotype analysis showed that the deletion of these 3 bp was common only in indica rice, and the rice varieties with 3 bp deletion perform poor rice blast resistance, which indicates that the deletion allele variant of Pi2 occurred recently and was artificially selected. We developed a functional molecular marker Pi2-1, spanning base pairs 1543–1545 of the Pi2 gene, which clearly distinguished between rice varieties with good or inferior blast resistance. Finally, Pi2-1 was used for rice blast MAS in the Huazhan/R900 F2 segregation population, and excellent plants with good rice blast resistance were selected.
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PKA activity is essential for relieving the suppression of hyphal growth and appressorium formation by MoSfl1 in Magnaporthe oryzae

PKA activity is essential for relieving the suppression of hyphal growth and appressorium formation by MoSfl1 in Magnaporthe oryzae | Rice Blast | Scoop.it
The cAMP-PKA signaling pathway plays a critical role in regulating various cellular processes in eukaryotic cells in response to extracellular cues. In the rice blast fungus, this important pathway is involved in surface recognition, appressorium morphogenesis, and infection. However, the exact role of PKA is not clear due to the functional redundancy of two PKA catalytic subunits CPKA and CPK2. To further characterize their functions in growth and pathogenesis, in this study we generated and characterized the cpkA cpk2 double mutant and its suppressor strains. Unlike the single mutants, cpkA cpk2 mutant had severe defects in growth and conidiation and was defective in appressorium formation and plant infection. Interestingly, the double mutant was unstable and produced fast-growing suppressors. In two suppressor strains, mutations were identified in a transcription factor gene orthologous to SFL1, a downstream target of PKA in yeast. Deletion of the entire or C-terminal 93 residues of MoSFL1 could suppress the growth defect of cpkA cpk2. Furthermore, the terminal region of MoSfl1 was found to be essential for its interaction with the MoCyc8 co-repressor, which may be negatively regulated by PKA. Therefore, loss-of-function mutations in MoSFL1 can bypass PKA activity to suppress the growth defect of cpkA cpk2.
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A genome Tree of Life for the Fungi kingdom

A genome Tree of Life for the Fungi kingdom | Rice Blast | Scoop.it
Fungi belong to one of the largest and most diverse groups of living organisms. The evolutionary kinship within a fungal population has so far been inferred mostly from the gene-information–based trees (“gene trees”) constructed using a small number of genes. Since each gene evolves under different evolutionary pressure and time scale, it has been known that one gene tree for a population may differ from other gene trees for the same population, depending on the selection of the genes. We present whole-genome information-based trees (“genome trees”) using a variation of a computational algorithm developed to find plagiarism in two books, where we represent a whole-genomic information of an organism as a book of words without spaces.

Abstract
Fungi belong to one of the largest and most diverse kingdoms of living organisms. The evolutionary kinship within a fungal population has so far been inferred mostly from the gene-information–based trees (“gene trees”), constructed commonly based on the degree of differences of proteins or DNA sequences of a small number of highly conserved genes common among the population by a multiple sequence alignment (MSA) method. Since each gene evolves under different evolutionary pressure and time scale, it has been known that one gene tree for a population may differ from other gene trees for the same population depending on the subjective selection of the genes. Within the last decade, a large number of whole-genome sequences of fungi have become publicly available, which represent, at present, the most fundamental and complete information about each fungal organism. This presents an opportunity to infer kinship among fungi using a whole-genome information-based tree (“genome tree”). The method we used allows comparison of whole-genome information without MSA, and is a variation of a computational algorithm developed to find semantic similarities or plagiarism in two books, where we represent whole-genomic information of an organism as a book of words without spaces. The genome tree reveals several significant and notable differences from the gene trees, and these differences invoke new discussions about alternative narratives for the evolution of some of the currently accepted fungal groups.

Via Steve Marek, Francis Martin, Ronny Kellner
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Steve Marek's comment, August 17, 12:55 PM
I would have liked to have seen how this approach places Fungi in the broader eukaryotic tree of life; first within the opisthokonts (w/ Metazoa and Amoebozoa) and then with representatives of the other main euk lineages.
Bridget Barker's comment, August 17, 1:02 PM
Good point Steve, I think that is the major issue with the analysis. I'm going to look into the scripts closer too. I think it's an interesting idea, and I'm always open to new approaches that can lead us to a better understanding of deeper phylogenetic relationships. But yeah, I won't be changing my FTOL slide just yet ;)
WillistonPlantPath's comment, August 17, 5:00 PM
Intuitively I think it makes more sense to use the whole proteome or genome to construct phylogenetic trees rather than single genes, or even a few genes in combination. Whether this is the best way to go about it remains to be seen.
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Origin of rice (Oryza sativa L.) domestication genes

Origin of rice (Oryza sativa L.) domestication genes | Rice Blast | Scoop.it
A number of genes that contribute to the domestication traits of cultivated rice have been identified. These include Sh4, Rc, PROG1 and LABA1, which are associated with non-shattering rachis, white pericarp, erect growth and barbless awns, respectively. The mutations giving rise to the “domestication alleles” of these genes are either invariable in cultivated rice, or have variability that is strictly associated with the phenotypic trait. This observation forms the basis to those current rice domestication models that envisage a single origin for the domesticated phenotype. Such models assume that the domestication alleles are absent or rare in wild rice, emerged under cultivation and spread across all rice groups by introgressive hybridization. We examined whole-genome sequencing datasets for wild and cultivated rice to test the former two assumptions. We found that the rc and laba1 alleles occur in wild rice with broad geographical distribution, and reach frequencies as high as 13 and 15%, respectively. These results are in agreement with previous observations of the prog1 and sh4 domestication alleles in wild populations. We also show that the diversity of the genomic regions surrounding the rc, laba1, prog1 and sh4 alleles in wild accessions is greater than that in cultivated rice, suggesting that these alleles emerged prior to domestication. Our findings indicate that the possibility that independent rice groups obtained identical domestication alleles directly from the wild population needs to be considered.
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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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Genotyping-by-Sequencing-Based Genetic Analysis of African Rice Cultivars and Association Mapping of Blast Resistance Genes Against Magnaporthe oryzae Populations in Africa

Genotyping-by-Sequencing-Based Genetic Analysis of African Rice Cultivars and Association Mapping of Blast Resistance Genes Against Magnaporthe oryzae Populations in Africa | Rice Blast | Scoop.it
Understanding the genetic diversity of rice germplasm is important for the sustainable use of genetic materials in rice breeding and production. Africa is rich in rice genetic resources that can be utilized to boost rice productivity on the continent. A major constraint to rice production in Africa is rice blast, caused by the hemibiotrophic fungal pathogen Magnaporthe oryzae. In this report, we present the results of a genotyping-by-sequencing (GBS)-based diversity analysis of 190 African rice cultivars and an association mapping of blast resistance (R) genes and quantitative trait loci (QTLs). The 190 African cultivars were clustered into three groups based on the 184K single nucleotide polymorphisms generated by GBS. We inoculated the rice cultivars with six African M. oryzae isolates. Association mapping identified 25 genomic regions associated with blast resistance (RABRs) in the rice genome. Moreover, PCR analysis indicated that RABR_23 is associated with the Pi-ta gene on chromosome 12. Our study demonstrates that the combination of GBS-based genetic diversity population analysis and association mapping is effective in identifying rice blast R genes/QTLs that contribute to resistance against African populations of M. oryzae. The identified markers linked to the RABRs and 14 highly resistant cultivars in this study will be useful for rice breeding in Africa.
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Genome assemblies of Magnaporthe oryzae isolated from Bangladesh in 2016 and 2017

Genome assemblies of Magnaporthe oryzae isolated from Bangladesh in 2016 and 2017 | Rice Blast | Scoop.it
Genomic DNA from nineteen isolates of Magnaporthe oryzae sampled from barley, wheat and torpedo grass in Bangladesh were sequenced using Illumina HiSeq 2500 producing 125 base paired-end reads. Reads were assembled ‘de novo’ using Spades.
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Genome re-sequencing analysis uncovers pathogenecity-related genes undergoing positive selection in Magnaporthe oryzae

Rice blast caused by Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases, which causes significant rice yield losses and affects global food security. To better understand genetic variations among different isolates of M. oryzae in nature, we re-sequenced the genomes of two field isolates, CH43 and Zhong-10-8-14, which showed distinct pathogenecity on most of the rice cultivars. Genome-wide genetic variation analysis reveals that ZHONG-10-8-14 exhibits higher sequence variations than CH43. Structural variations (SVs) detection shows that the sequence variations primarily occur in exons and intergenic regions. Bioinformatics analysis for gene variations reveals that many pathogenecity-related pathways are enriched. In addition, 193 candidate effectors with various DNA polymorphisms were identified, including two known effectors AVR-Pik and AVR-Pita1. Comparative polymorphism analysis of thirteen randomly selected effectors suggests that the genetic variations of effectors are under positive selection. The expression pattern analysis of several pathogenecity-related variant genes indicates that these genes are differentially regulated in two isolates, with much higher expression levels in Zhong-10-8-14 than CH43. Our data demonstrate that the genetic variations of effectors and pathogenecity-related genes are under positive selection, resulting in the distinct pathogenicities of CH43 and Zhong-10-8-14 on rice.
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Genetic Structure of the Rice Blast Pathogen (Magnaporthe oryzae) over a Decade in North Central California Rice Fields

Rice blast, caused by the ascomycete Magnaporthe oryzae, is one of the most destructive rice diseases worldwide. Even though the disease has been present in California since 1996, there is no data for the pathogen population biology in the state. Using amplified fragment length polymorphisms and mating-type markers, the M. oryzae population diversity was investigated using isolates collected when the disease was first established in California and isolates collected a decade later. While in the 1990 samples, a single multilocus genotype (MLG) was identified (MLG1), over a decade later, we found 14 additional MLGs in the 2000 isolates. Some of these MLGs were found to infect the only rice blast-resistant cultivar (M-208) available for commercial production in California. The same samples also had a significant decrease of MLG1. MLG1 was found infecting the resistant rice cultivar M-208 on one occasion whereas MLG7 was the most common genotype infecting the M-208. MLG7 was identified in the 2000 samples, and it was not present in the M. oryzae population a decade earlier. Our results demonstrate a significant increase in genotypic diversity over time with no evidence of sexual reproduction and suggest a recent introduction of new virulent race(s) of the pathogen. In addition, our data could provide information regarding the durability of the Pi-z resistance gene of the M-208. This information will be critical to plant breeders in developing strategies for deployment of other rice blast resistance genes/cultivars in the future.
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WRKY45 phosphorylation at threonine 266 acts negatively on WRKY45-dependent blast resistance in rice

WRKY45 is a central regulator of disease resistance mediated by salicylic acid signaling in rice and its activation involves phosphorylation by OsMPK6. OsMPK6 phosphorylates WRKY45 at Thr266, Ser294, and Ser299 in vitro. Phosphorylation of Ser294 and/or Ser299 is required for full activation of WRKY45, but the importance of Thr266 phosphorylation has remained unknown. Here, we report on the characterization of Thr266 phosphorylation of WRKY45 in rice. Transient expression of mutant WRKY45 revealed that Thr266 is phosphorylated in vivo, together with Ser294/299. Replacement of Thr266 by Asn did not affect the enhanced Magnaporthe oryzae resistance afforded by WRKY45 overexpression. By contrast, replacement by Asp negated the enhancement of M. oryzae resistance. These results suggest that Thr266 phosphorylation acts negatively on WRKY45-dependent disease resistance.
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Panicle blast 1 (Pb1) resistance is dependent on at least four QTLs in the rice genome

Panicle blast 1 (Pb1) resistance is dependent on at least four QTLs in the rice genome | Rice Blast | Scoop.it
We clarified how the K209 cultivar is vulnerable to the blast disease despite possessing Pb1 and found the DNA marker responsible for the quantitative resistance of Pb1. We identified the QTL loci required for Pb1-mediated resistance to rice panicle blast. Pb1 was negatively dependent on at least three QTLs, 7, 9 and 11, and positively dependent on one, QTL 8, in the K209 genome. This finding paves the way for creating a line to select optimal QTLs in order to make use of Pb1-mediated resistance more effectively.
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Marker-assisted breeding of Chinese elite rice cultivar 9311 for disease resistance to rice blast and bacterial blight and tolerance to submergence

Marker-assisted breeding of Chinese elite rice cultivar 9311 for disease resistance to rice blast and bacterial blight and tolerance to submergence | Rice Blast | Scoop.it
Rice (Oryza sativa L.) is the staple food crop for more than half of the world’s population. The development of hybrid rice is a practical approach to increase rice production. However, rice production was frequently affected by biotic and abiotic stresses. Rice blast and bacterial blight are two major diseases in rice growing regions. Rice plantation is also frequently affected by short-term submergence or seasonal floods in wet seasons and drought in dry seasons. The utilization of natural disease resistance (R) genes and stress tolerance genes in rice breeding is the most economic and efficient way to combat or adapt to these biotic and abiotic stresses. Rice cultivar 9311 is widely planted rice variety, either as inbred rice or the paternal line of two-line hybrid rice. Here, we report the pyramiding of rice blast R gene Pi9, bacterial blight R genes Xa21 and Xa27, and submergence tolerance gene Sub1A in 9311 genetic background through backcrossing and marker-assisted selection. The improved rice line, designated as 49311, theoretically possesses 99.2% genetic background of 9311. 49311 and its hybrid rice, GZ63S/49311, conferred disease resistance to rice blast and bacterial blight and showed tolerance to submergence for over 18 days without significant loss of viability. 49311 and its hybrids had similar agronomic traits and grain quality to 9311 and the control hybrid rice, respectively. The development of 49311 provides an improved paternal line for two-line hybrid rice production with disease resistance to rice blast and bacterial blight and tolerance to submergence.
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Methylmalonate‐Semialdehyde Dehydrogenase Mediated Metabolite Homeostasis Essentially Regulate Conidiation, Polarized Germination and Pathogenesis in Magnaporthe oryzae

Methylmalonate‐Semialdehyde Dehydrogenase Mediated Metabolite Homeostasis Essentially Regulate Conidiation, Polarized Germination and Pathogenesis in Magnaporthe oryzae | Rice Blast | Scoop.it
Plants generate multitude of aldehydes under abiotic and biotic stress conditions. Ample demonstrations have shown that rice-derived aldehydes enhance the resistance of rice against the rice-blast fungus Magnaporthe oryzae. However, how the fungal pathogen nullifies the inhibitory effects of host aldehydes to establish compatible interaction remains unknown. Here we identified and evaluated the in vivo transcriptional activities of M. oryzae aldehyde dehydrogenase (ALDH) genes.

Transcriptional analysis of M. oryzae ALDH genes revealed that the acetylating enzyme Methylmalonate-Semialdehyde Dehydrogenase (MoMsdh/MoMmsdh) elevated activities during host invasion and colonization of the fungus. We further examined the pathophysiological importance of MoMSDH by deploying integrated functional genetics, and biochemical approaches. MoMSDH deletion mutant ΔMomsdh exhibited germination defect, hyper-branching of germ tube and failed to form appressoria on hydrophobic and hydrophilic surface. The MoMSDH disruption caused accumulation of small branch-chain amino acids, pyridoxine and AMP/cAMP in the ΔMomsdh mutant and altered Spitzenkörper organisation in the conidia.

We concluded that MoMSDH contribute significantly to the pathogenesis of M. oryzae by regulating the mobilization of Spitzenkörper during germ tube morphogenesis, appressoria formation by acting as metabolic switch regulating small branch-chain amino acids, inositol, pyridoxine and AMP/cAMP homeostasis. This article is protected by copyright. All rights reserved.
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The Magnaporthe oryzae Alt A 1-like protein MoHrip1 binds to the plant plasma membrane

The Magnaporthe oryzae Alt A 1-like protein MoHrip1 binds to the plant plasma membrane | Rice Blast | Scoop.it

MoHrip1 was both present in the secretome and abundant in the fungal cell wall.
MoHrip1 was able to bind to the tobacco and rice plant plasma membrane.
MoHrip1 caused rapid morphological changes at the cellular level.
MoHrip1 can be detected by the plant immune system as a MAMP.
It is the first study on an AA1 family protein that can bind to the protoplasts.

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The cyclic lipopeptide orfamide induces systemic resistance in rice to Cochliobolus miyabeanus but not to Magnaporthe oryzae

The cyclic lipopeptide orfamide induces systemic resistance in rice to Cochliobolus miyabeanus but not to Magnaporthe oryzae | Rice Blast | Scoop.it
Diverse natural products produced by beneficial Pseudomonas species have the potential to trigger induced systemic resistance (ISR) in plants, and thus may contribute to control of diseases in crops. Some beneficial Pseudomonas spp. can produce cyclic lipopeptides (CLPs), amphiphilic molecules composed of a fatty acid tail linked to an oligopeptide which is cyclized. CLPs can have versatile biological functions, but the capacity of Pseudomonas-derived CLPs in triggering ISR responses has barely been studied. Pseudomonas protegens and related species can produce orfamide-type CLPs. Here we show that in rice, orfamides can act as ISR elicitors against the necrotrophic fungus Cochliobolus miyabeanus, the causal agent of brown spot disease, but are not active against the blast fungus Magnaporthe oryzae. Orfamide A can trigger early defensive events and activate transcripts of defense-related genes in rice cell suspension cultures, but does not cause cell death. Further testing in rice cell suspension cultures and rice plants showed that abscisic acid signaling, the transcriptional activator OsWRKY4 and pathogenesis-related protein PR1b are triggered by orfamide A and may play a role in the ISR response against C. miyabeanus.
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Expression-based genotyping of the rice blast resistance genes in the elite maintainer line Yixiang1B

Expression-based genotyping of the rice blast resistance genes in the elite maintainer line Yixiang1B | Rice Blast | Scoop.it
Rice blast caused by Magnaporthe oryzae poses a major threat to rice production worldwide. Utilization of resistance is the most effective and economic means to control the disease. An elite maintainer line Yixiang1B (Y1B) has been widely exploited in three-line hybrid rice breeding. However, it remains unclear which blast resistance gene or genes contribute to its resistant phenotype. In this work, we found that a novel functional Pid2 allele is critical for the Y1B’s resistance against rice blast pathogen. First, we confirmed that Y1B is resistant to a number of M. oryzae isolates, with a resistance frequency of 65%. Then, we exploited expression-based approach to genotype the cloned rice blast resistance genes. Transcripts from Pid2, Pid3, Pib, Pi36, Pi5 and Pia were readily detected in Y1B upon M. oryzae infection. Sequencing analyses detected many SNPs in these genes, except that Pib had no substitution and Pid2 contained two tandem base-pair mutations at the nucleotide positions 1997 and 1998 leading to the H666R substitution. Knocking-down Pid2_Y1B via RNAi in Y1B resulted in susceptibility. In contrast, over-expression of Pid2_Y1B in a blast-susceptible accession led to enhanced resistance to M. oryzae. Therefore, Pid2_Y1B is the main contributor to the rice blast resistance in Y1B. Taken together, we identified a functional resistance allele of Pid2 that can be utilized as a resource in rice blast resistant breeding programs.
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Genome wide re-sequencing of newly developed Rice Lines from common wild rice (Oryza rufipogon Griff.) for the identification of NBS-LRR genes

Genome wide re-sequencing of newly developed Rice Lines from common wild rice (Oryza rufipogon Griff.) for the identification of NBS-LRR genes | Rice Blast | Scoop.it
Common wild rice (Oryza rufipogon Griff.) is an important germplasm for rice breeding, which contains many resistance genes. Re-sequencing provides an unprecedented opportunity to explore the abundant useful genes at whole genome level. Here, we identified the nucleotide-binding site leucine-rich repeat (NBS-LRR) encoding genes by re-sequencing of two wild rice lines (i.e. Huaye 1 and Huaye 2) that were developed from common wild rice. We obtained 128 to 147 million reads with approximately 32.5-fold coverage depth, and uniquely covered more than 89.6% (> = 1 fold) of reference genomes. Two wild rice lines showed high SNP (single-nucleotide polymorphisms) variation rate in 12 chromosomes against the reference genomes of Nipponbare (japonica cultivar) and 93–11 (indica cultivar). InDels (insertion/deletion polymorphisms) count-length distribution exhibited normal distribution in the two lines, and most of the InDels were ranged from -5 to 5 bp. With reference to the Nipponbare genome sequence, we detected a total of 1,209,308 SNPs, 161,117 InDels and 4,192 SVs (structural variations) in Huaye 1, and 1,387,959 SNPs, 180,226 InDels and 5,305 SVs in Huaye 2. A total of 44.9% and 46.9% genes exhibited sequence variations in two wild rice lines compared to the Nipponbare and 93–11 reference genomes, respectively. Analysis of NBS-LRR mutant candidate genes showed that they were mainly distributed on chromosome 11, and NBS domain was more conserved than LRR domain in both wild rice lines. NBS genes depicted higher levels of genetic diversity in Huaye 1 than that found in Huaye 2. Furthermore, protein-protein interaction analysis showed that NBS genes mostly interacted with the cytochrome C protein (Os05g0420600, Os01g0885000 and BGIOSGA038922), while some NBS genes interacted with heat shock protein, DNA-binding activity, Phosphoinositide 3-kinase and a coiled coil region. We explored abundant NBS-LRR encoding genes in two common wild rice lines through genome wide re-sequencing, which proved to be a useful tool to exploit elite NBS-LRR genes in wild rice. The data here provide a foundation for future work aimed at dissecting the genetic basis of disease resistance in rice, and the two wild rice lines will be useful germplasm for the molecular improvement of cultivated rice.
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