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QTL-seq: Rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations - The Plant Journal

QTL-seq: Rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations - The Plant Journal | Rice Blast | Scoop.it

Here we report a rapid identification of plant QTL by whole genome resequencing of DNAs from two populations each composed of 20-50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We applied QTL-seq to rice recombinant inbred lines (RILs) and F2 populations and successfully identified QTL for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor.

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Rice Blast
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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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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Plantae: Taproot Episode 1, Season 1: Extreme Open Science and the Meaning of Scientific Impact (2017)

Plantae: Taproot Episode 1, Season 1: Extreme Open Science and the Meaning of Scientific Impact (2017) | Rice Blast | Scoop.it

In this episode, the hosts and Sophien discuss a recent collaborative paper (Islam et al., 2016, BMC Biology) that really embodies the concepts of open science. It addresses the source and characterization of a newly discovered wheat blast in Bangladesh. Wheat blast is a fungal disease that affects grasses that are a huge threat to food security. The authors report the geographical distribution of this new disease, characterize the disease symptoms of affected plants, and isolate and validate the causal fungus. Most strikingly, they performed RNA sequencing on symptomatic and asymptomatic leaves and show that RNA from these infected leaves aligns to the genome of a Brazilian wheat blast strain. They conclude that the Bangladesh isolate of wheat blast is phylogenetically related to the Brazilian wheat blast, rather than an unknown or new lineage.

 

Listen to this episode to hear Sophien, Ivan, and Liz discuss the science in this paper, how the project started, and how it developed into a peer-reviewed publication. Also discussed is the importance of redefining what is meant by scientific “impact”, and new ways to do science in the plant pathology community and beyond.


Via Kamoun Lab @ TSL
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PNAS: NLR network mediates immunity to diverse plant pathogens (2017)

PNAS: NLR network mediates immunity to diverse plant pathogens (2017) | Rice Blast | Scoop.it

Both plants and animals rely on nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins to respond to invading pathogens and activate immune responses. An emerging concept of NLR function is that “sensor” NLR proteins are paired with “helper” NLRs to mediate immune signaling. However, our fundamental knowledge of sensor/helper NLRs in plants remains limited. In this study, we discovered a complex NLR immune network in which helper NLRs in the NRC (NLR required for cell death) family are functionally redundant but display distinct specificities toward different sensor NLRs that confer immunity to oomycetes, bacteria, viruses, nematodes, and insects. The helper NLR NRC4 is required for the function of several sensor NLRs, including Rpi-blb2, Mi-1.2, and R1, whereas NRC2 and NRC3 are required for the function of the sensor NLR Prf. Interestingly, NRC2, NRC3, and NRC4 redundantly contribute to the immunity mediated by other sensor NLRs, including Rx, Bs2, R8, and Sw5. NRC family and NRC-dependent NLRs are phylogenetically related and cluster into a well-supported superclade. Using extensive phylogenetic analysis, we discovered that the NRC superclade probably emerged over 100 Mya from an NLR pair that diversified to constitute up to one-half of the NLRs of asterids. These findings reveal a complex genetic network of NLRs and point to a link between evolutionary history and the mechanism of immune signaling. We propose that this NLR network increases the robustness of immune signaling to counteract rapidly evolving plant pathogens.


Via Kamoun Lab @ TSL, Suayib Üstün
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Animal NLRs provide structural insights into plant NLR function

Animal NLRs provide structural insights into plant NLR function | Rice Blast | Scoop.it
This review provides an overview of the innate immune pathways in plants and animals, focusing on the available structural and biochemical information available for both plant and animal NLRs. We highlight the gap in knowledge between the animal and plant systems, in particular the lack of structural information for plant NLRs, with crystal structures only available for the N-terminal domains of plant NLRs and an integrated decoy domain, in contrast to the more complete structures available for animal NLRs. We assess the similarities and differences between plant and animal NLRs, and use the structural information on the animal NLR pair NAIP/NLRC4 to derive a plausible model for plant NLR activation.
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Bioinformatic approaches to understand RNA biology in the rice blast fungus - Archivo Digital UPM

The purpose of this thesis is to investigate various aspects of RNA metabolism in the rice blast fungus Magnaporthe oryzae using bioinformatic tools and approaches, and to attempt to extrapolate key features of the RNA life cycle over the whole fungal kingdom. In the first results chapter we conducted a bioinformatic analysis of a poly(A)-specific RNA-sequencing dataset obtained from a M. oryzae wild-type strain and knock-out mutants of two genes involved in the polyadenylation machinery, RBP35 and HRP1. This represents the first mapping of polyadenylation sites in the rice blast fungus, and it provided us with several insights regarding regulation of alternative polyadenylation. Alternative polyadenylation is a common feature in the M. oryzae transcriptome; it is a dynamic mechanism regulated by nutrient stresses such as carbon starvation, which provoke the selection of non-canonical poly(A) sites. Mutant analysis also indicate that Rbp35 and Hrp1 are involved in poly(A) site selection in a large number of genes. In the second results chapter we performed the small RNA sequencing of M. oryzae, using a novel library construction protocol. Genomic repetitive sequences such as retrotransposons and non-genomic invasive nucleic acids such as viruses display clear evidence of an RNA silencing mechanism acting in the M. oryzae cell. These same elements are also subject to an extensive post-transcriptional modification not observed in prior studies. We also provide confirmation that RBP35 and EXP5 (a karyopherin) genes are involved in small RNA regulation and possibly in some RNA silencing pathway. In the third results chapter we accomplish the molecular characterization of a novel ssRNA ourmia-like virus from M. oryzae, called MOLV1. This virus is specific to the strain Guy11. It is possibly polyadenylated, and contains a unique ORF coding for a putative RNA-dependent RNA polymerase. In the fourth chapter we carried out the proteome-wide ortholog prediction for approximately 700 RNA-related proteins, in 49 fungal species. The objective of this analysis was to provide a broader understanding of the conservation of RNA-associated processes in fungal species beyond M. oryzae. This evolutionary survey revealed an unexpected scenario; processes like mRNA translation and tRNA maturation are generally well conserved, while other processes like mRNA export and RNA silencing exhibit a variably degree of conservation among the selected fungal species.
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How filamentous plant pathogen effectors are translocated to host cells

How filamentous plant pathogen effectors are translocated to host cells | Rice Blast | Scoop.it
The interaction of microbes with “signature” plants is largely governed by secreted effector proteins, which serve to dampen plant defense responses and modulate host cell processes. Secreted effectors can function either in the apoplast or within plant cell compartments. How oomycetes and fungi translocate their effectors to plant cells is still poorly understood and controversial. While most oomycete effectors share a common ‘signature’ that was proposed to mediate their uptake via endocytosis, fungal effectors display no conserved motifs at the primary amino acid sequence level. Here we summarize current knowledge in the field of oomycete and fungal effector uptake and highlight emerging themes that may unite rather than set apart these unrelated filamentous pathogens.

Via Jonathan Plett, Yogesh Gupta, Prissana Aey
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Effects of agro-pedo-meteorological conditions on dynamics of temperate rice blast epidemics and associated yield and milling losses - ScienceDirect

Effects of agro-pedo-meteorological conditions on dynamics of temperate rice blast epidemics and associated yield and milling losses - ScienceDirect | Rice Blast | Scoop.it

A three-year experiment to assess rice blast disease impact on yield is presented.
Rice variety, nitrogen dose, year and site are tested factors of variability.
Leaf and panicle blast impacts on field and milling yield are distinctly considered.
Variety and year are the main sources of variability in blast disease progress curves.
Panicle blast is the symptomatology most correlated to field and milling yield losses.

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isrfg2017 September 25 to 28 2017 Suwon Korea

isrfg2017 September 25 to 28 2017 Suwon Korea | Rice Blast | Scoop.it

Rice is the major cereal food crop and an ideal species for studying mechanisms controlling various biological phenomena. During the past 15 years, International Symposium on Rice Functional Genomics brought together scientists from more than 30 countries to report research progress and exchange idea among scientists in rice community The fifteenth International Symposium on Rice Functional Genomics will be on September 25-28, 2017 in Suwon, Korea. The 2017 symposium will cover recent, exciting breakthroughs in structural, functional and evolutionary rice genome biology - pushing current scientific knowledge to address the need of sustainably increasing crop yields and global food security. Please join us for an exciting meeting to discuss cutting-edge science with many of the world's top scientists. Meet old friends, make new ones, and forge novel collaborations in the beautiful setting and hospitality of Suwon historical city.

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Which MAT gene? Pezizomycotina (Ascomycota) mating-type gene nomenclature reconsidered

Which MAT gene? Pezizomycotina (Ascomycota) mating-type gene nomenclature reconsidered | Rice Blast | Scoop.it

The current use of the fungal mating-type gene nomenclature system was reviewed.
Several inconsistencies were identified and remedial recommendations are made.
Suggestions to rename ten previously described mating-type genes are made.
Six new mating-type gene names are introduced.
A basic approach for identifying and naming Pezizomycotina MAT genes are provided.

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Direct and Tunable Modulation of Protein Levels in Rice and Wheat with a Synthetic Small Molecule

Direct and Tunable Modulation of Protein Levels in Rice and Wheat with a Synthetic Small Molecule | Rice Blast | Scoop.it
Direct control of protein level enables rapid and efficient analyses of gene functions in crops. Previously, we developed the RDDK-Shield1 (Shld1) system in the model plant Arabidopsis thaliana for direct modulation of protein stabilization using a synthetic small molecule. However, it was unclear whether this system is applicable to economically important crops. In this study we show that the RDDK-Shld1 system enables rapid and tunable control of protein levels in rice and wheat. Accumulation of RDDK-fusion proteins can be reversibly and spatio-temporally controlled by the synthetic small-molecule Shld1. Moreover, RDDK-Bar and RDDK-Pid3 fusions confer herbicide and rice blast resistance, respectively, in a Shld1-dependent manner. Therefore, the RDDK-Shld1 system provides a reversible and tunable technique for controlling protein functions and conditional expression of transgenes in crops.
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Prediction and analysis of three gene families related to leaf rust ( Puccinia triticina ) resistance in wheat ( Triticum aestivum L.)

Prediction and analysis of three gene families related to leaf rust ( Puccinia triticina ) resistance in wheat ( Triticum aestivum L.) | Rice Blast | Scoop.it
This study represents a comprehensive analysis of ABC, NLR and START genes in the hexaploid wheat genome and their physical relationships with QTLs for leaf rust resistance at seedling and adult stages. Our analysis suggests that the ABC (and START) genes are more likely to be co-located with QTLs for race-nonspecific, adult resistance whereas the NLR genes are more likely to be co-located with QTLs for race-specific resistance that would be often expressed at the seedling stage. Though our analysis was hampered by inaccurate or unknown physical positions of numerous QTLs due to the incomplete assembly of the complex hexaploid wheat genome that is currently available, the observed associations between (i) QTLs for race-specific resistance and NLR genes and (ii) QTLs for nonspecific resistance and ABC genes will help discover SNP variants for leaf rust resistance at seedling and adult stages. The genes containing nonsynonymous SNPs are promising candidates that can be investigated in future studies as potential new sources of leaf rust resistance in wheat breeding.
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Testing differences between pathogen compositions with small samples and sparse data

Testing differences between pathogen compositions with small samples and sparse data | Rice Blast | Scoop.it
The structure of pathogen populations is an important driver of epidemics affecting crops and natural plant communities. Comparing the composition of two pathogen populations consisting of assemblages of genotypes or phenotypes is a crucial, recurrent question encountered in many studies in plant disease epidemiology. Determining if there is a significant difference between two sets of proportions is also a generic question for numerous biological fields. When samples are small and data are sparse, it is not straightforward to provide an accurate answer to this simple question because routine statistical tests may not be exactly calibrated. To tackle this issue, we built a computationally-intensive testing procedure, namely the Generalized Monte Carlo Plug-In test with Calibration (GMCPIC test), which is implemented in an R package available at http://dx.doi.org/10.5281/zenodo.53996. A simulation study was carried out to assess the performance of the proposed methodology and to make a comparison with standard statistical tests. This study allows us to give advice on how to apply the proposed method, depending on the sample sizes. The proposed methodology was then applied to real datasets and the results of the analyses were discussed from an epidemiological perspective. The applications to real data sets deal with three topics in plant pathology: the reproduction of Magnaporthe oryzae, the spatial structure of Pseudomonas syringae, and the temporal recurrence of Puccinia triticina.
Elsa Ballini's insight:
GMCPIC (Generalized Monte Carlo plug-in test with calibration) is an R-package implementing a computer intensive procedure to test the equality of two unknown vectors of probabilities p1 and p2 based on two multinomial draws performed with these probabilities. The GMCPIC package was specifically developed to test differences between pathogen compositions with small samples and sparse data.
https://informatique-mia.inra.fr/biosp/gmcpic
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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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A HOPS protein, MoVps41, is essential for vacuolar morphogenesis, vegetative growth, reproductions and virulence in Magnaprothe oryzae

A HOPS protein, MoVps41, is essential for vacuolar morphogenesis, vegetative growth, reproductions and virulence in Magnaprothe oryzae | Rice Blast | Scoop.it
The homotypic fusion and protein sorting protein complex (HOPS) plays a key role in promoting homotypic vacuolar fusion, vacuolar biogenesis and endocytic trafficking in eukaryotes ranging from fungi to plants and animals. However, its physiological function in the economically destructive rice blast fungus M. oryzae has not been investigated. In this study, we have identified M. oryzae vacuolar protein sorting 41 (MoVps41), an accessory subunit of the HOPS complex, and generated MoVps41 knockout mutants to characterize its function in the growth, reproduction and infectious cycle of the rice blast fungus. Our data showed that MoVps41 is required for the vegetative growth of M. oryzae and depletion of MoVPS41 can abrogate the growth. Furthermore, MoVps41 deficiency can cause vacuolar fragmentation, compromised membrane integrity and reduced pathogenesis in the ΔMovps41 mutant. Our data also provide the first evidence that MoVps41 plays an essential role in the regulation of sexual and asexual reproduction of M. oryzae. In summary, our study provides insight into how MoVps41-mediated vacuolar fusion and biogenesis can have an impact on reproduction, pathogenesis, and vacuolar integrity in M. oryzae, and also underscores the need to investigate the whole HOPS complex in rice blast pathogen.

Via Philip Carella
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Phosphorylation-Mediated Regulatory Networks in Mycelia of Pyricularia oryzae Revealed by Phosphoproteomic Analyses

Phosphorylation-Mediated Regulatory Networks in Mycelia of Pyricularia oryzae Revealed by Phosphoproteomic Analyses | Rice Blast | Scoop.it
Protein phosphorylation is known to regulate pathogenesis, mycelial growth, conidiation and stress response in Pyricularia oryzae. However, phosphorylation mediated regulatory networks in the fungal pathogen remain largely to be uncovered. In this study, we identified 1621 phosphorylation sites of 799 proteins in mycelia of P. oryzae, including 899 new p-sites of 536 proteins and 47 new p-sites of 31 pathogenesis-relation proteins. From the sequences flanking the phosphorylation sites, 19 conserved phosphorylation motifs were identified. Notably, phosphorylation was detected in 7 proteins that function upstream of Pmk1, but not in Pmk1 and its downstream Mst12 and Sfl1 that have been known to regulate appressorium formation and infection hyphal growth of P. oryzae. Interestingly, phosphorylation was detected at the site Ser240 of Pmp1, which is a putative protein phosphatase highly conserved in filamentous fungi but not characterized. We thus generated Δpmp1 deletion mutants and dominant allele PMP1S240D mutants. Phenotyping analyses indicated that Pmp1 is required for virulence, conidiation and mycelial growth. Further, we observed that phosphorylation level of Pmk1 in mycelia was significantly increased in the Δpmp1 mutant, but decreased in the PMP1S240D mutant in comparison with the wild type, demonstrating that Pmp1 phosphorylated at Ser240 is important for regulating phosphorylation of Pmk1. To our surprise, phosphorylation of Mps1, another MAP kinase required for cell wall integrity and appressorium formation of P. oryzae, was also significantly enhanced in the Δpmp1 mutant, but decreased in the PMP1S240D mutant. In addition, we found that Pmp1 directly interacts with Mps1 and the region AA180-230 of Pmp1 is required for the interaction. In summary, this study shed new lights on the protein phosphorylation mediated regulatory networks in P. oryzae.
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The transcription factor PstSTE12 is required for virulence of Puccinia striiformis f. sp. tritici

The transcription factor PstSTE12 is required for virulence of Puccinia striiformis f. sp. tritici | Rice Blast | Scoop.it
Puccinia striiformis f. sp. tritici (Pst) is an obligate biotrophic fungus that causes extensive damage in wheat. The pathogen is now known to be a heteroecious fungus with an intricate life cycle containing sexual and asexual stages. Orthologs of the STE12 transcription factor that regulate mating and filamentation in Saccharomyces cerevisiae as well as virulence in other fungi has been extensively described. Because reliable transformation and gene disruption methods are lacking for Pst, knowledge about the function of its STE12 ortholog is limited. In this study, we identified a putative ortholog of STE12 from Pst in haustoria-enriched transcripts and designated it as PstSTE12. The gene encodes a protein of 879 amino acids containing three helices in the homeodomain, conserved phenylalanine and tryptophan sites, and two C2/H2-Zn2+ finger domains. Real-time RT-PCR analyses revealed that expression of PstSTE12 was highly induced during early infection stages and peaked during haustorium formation and the stage pycniospores in the aecial host barberry. Subcellular localization assays indicated that PstSTE12 is localized in the nucleus and functions as a transcriptional activator. Yeast one-hybrid assays revealed that PstSTE12 exhibits transcriptional activity, and that its C-terminus is necessary for the activation of transcription. PstSTE12 complemented the mating defect in α ste12 mutant of S. cerevisiae. In addition, it partially complemented the defects of the Magnaporthe oryzae mst12 mutant in plant infection. Knocking down PstSTE12 via host-induced gene silencing (HIGS) mediated by barley stripe mosaic virus (BSMV) resulted in a substantial reduction in the growth and spread of hyphae in Pst and weakened virulence of Pst on wheat. Our results suggest that PstSTE12 likely acts at an intersection participating in the invasion and the mating processes of Pst, and provide new insights toward comprehending the variation of virulence in cereal rust fungi. This article is protected by copyright. All rights reserved.
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Plant Cell: The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies (2017)

Plant Cell: The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies (2017) | Rice Blast | Scoop.it
The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa L. ssp. japonica), which completes its life cycle in 9 weeks. We sequenced 1,504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.

Via Nicolas Denancé
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Dorian Q Fuller's curator insight, July 14, 6:16 AM
fast moving genomics tools for rice!
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Accumulation of Azole Drugs in the Fungal Rice Pathogen Magnaporthe Oryzae is the Result of Facilitated Diffusion Influx | Microbiology

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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Caught in the jump

Caught in the jump | Rice Blast | Scoop.it
Microbial pathogens of plants typically cause disease on a limited number of host species. In nature, pathogens rarely become pathogenic to a new host. The underlying mechanisms of such host jumps are poorly understood but are thought to be linked to the capacity of the pathogen to undermine immunity of the former nonhost species (1). On page 80 of this issue, Inoue et al. (2) report a host jump mechanism of a notorious pathogenic fungus, Pyricularia oryzae, which causes blast disease in cereals.

The immune system of plants consists of two branches. First, surface-resident pattern recognition receptors (PRRs) detect microbial epitopes that are often conserved among many microbial taxa. Second, intracellular nucleotide-binding and leucinerich repeat proteins (NLRs) detect the actions of polymorphic pathogen-delivered and virulence-promoting proteins, called effectors. Recognized effectors are denoted avirulence genes (AVRs). Pathogen effectors often work by subverting signaling initiated by PRRs, facilitating host colonization and disease. The effector arsenal varies between strains of a pathogen species and is a major determinant for adaptation to specific hosts.

Via Francis Martin
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Dorian Q Fuller's curator insight, July 14, 6:18 AM
One of the poorly understood strands of the origins and spread of agriculture,is the origins of crop diseases, which must have be facilitated by the spread to new environments and the diversification of crop packages.
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Novel mastreviruses identified in Australian wild rice

First report of mastreviruses infecting Oryza sp.
Two novel mastreviruses species identified infecting wild rice.
22 genomes of rice latent virus 1 from nine sampling sites.
One genome rice latent virus 2 from one sampling site.

Elsa Ballini's insight:
There is considerable scientific interest in the wild species because of their potential to be used in rice breeding programs (Henry et al., 2010) but also because of the risks they pose to rice production by acting as reservoirs of pests and pathogens ( Khemmuk et al., 2016 ; Petrovic et al., 2013). The fungus Pyricularia oryzae, the cause of blast disease, is thought to have jumped from wild to domesticated rice in north Queensland, an event that has led to the temporary abandonment of cropping in parts of Cape York Peninsula until disease management strategies can be devised ( Khemmuk et al., 2016).
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Isolation and Characterization of Avirulence Genes in Magnaporthe oryzae | Jee | Borneo Journal of Resource Science and Technology

Isolation and Characterization of Avirulence Genes in Magnaporthe oryzae | Jee | Borneo Journal of Resource Science and Technology | Rice Blast | Scoop.it
Magnaporthe oryzae is a fungal pathogen contributing to rice blast diseases globally via their Avr (avirulence) gene. Although the occurrence of M. oryzae has been reported in Sarawak since several decades ago, however, none has focused specifically on Avr genes, which confer resistance against pathogen associated molecular pattern-triggered immunity (PTI) in host. The objective of this study is to isolate Avr genes from M. oryzae 7’ (a Sarawak isolate) that may contribute to susceptibility of rice towards diseases. In this study, AvrPiz-t, AVR-Pik, Avr-Pi54, and AVR-Pita1 genes were isolated via PCR and cloning approaches. The genes were then compared with set of similar genes from related isolates derived from NCBI. Results revealed that all eight Avr genes (including four other global isolates) shared similar N-myristoylation site and a novel motif. 3D modeling revealed similar β-sandwich structure in AvrPiz-t and AVR-Pik despite sequence dissimilarities. In conclusion, it is confirmed of the presence of these genes in the Sarawak (M. oryzae) isolate. This study implies that Sarawak isolate may confer similar avirulence properties as their counterparts worldwide. Further R/Avr gene-for-gene relationship studies may aid in strategic control of rice blast diseases in future.
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Rescooped by Elsa Ballini from Plant immunity and legume symbiosis
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OsBSK1-2, an Orthologous of AtBSK1, Is Involved in Rice Immunity

OsBSK1-2, an Orthologous of AtBSK1, Is Involved in Rice Immunity | Rice Blast | Scoop.it
The brassinosteroid-SIGNALING KINASE (BSK) belongs to the receptor-like cytoplasmic kinase XII subgroup. BSK1 regulates development and immunity in Arabidopsis. However, the function of rice (Oryza sativa) BSK1 is largely unknown. Here, we report that the expression level of OsBSK1-2 is induced after a chitin or fagellin22 (flg22) treatment. Silencing OsBSK1-2 in rice results in compromised responses to chitin- or flg22-triggered immunity and resistance to Magnaporthe oryzae, but does not alter the plant’s architecture nor reduce plant responses to brassinosteroid signaling. Our study reveals that OsBSK1-2 functions as a major regulator in rice plant immunity.

Via Christophe Jacquet
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Rescooped by Elsa Ballini from Wheat blast pathogen Magnaporthe oryzae Pathotype Triticum
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Evolution of the wheat blast fungus through functional losses in a host specificity determinant

Evolution of the wheat blast fungus through functional losses in a host specificity determinant | Rice Blast | Scoop.it

Wheat blast first emerged in Brazil in the mid-1980s and has recently caused heavy crop losses in Asia. Here we show how this devastating pathogen evolved in Brazil. Genetic analysis of host species determinants in the blast fungus resulted in the cloning of avirulence genes PWT3 and PWT4, whose gene products elicit defense in wheat cultivars containing the corresponding resistance genes Rwt3 and Rwt4. Studies on avirulence and resistance gene distributions, together with historical data on wheat cultivation in Brazil, suggest that wheat blast emerged due to widespread deployment of rwt3 wheat (susceptible to Lolium isolates), followed by the loss of function of PWT3. This implies that the rwt3 wheat served as a springboard for the host jump to common wheat.

 

Via Yogesh Gupta, Tofazzal Islam's Research Group
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