Publications from The Sainsbury Laboratory
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Frontiers in Plant Sci: Strategies for transferring resistance into wheat: from wide crosses to GM cassettes (2014)

Frontiers in Plant Sci: Strategies for transferring resistance into wheat: from wide crosses to GM cassettes (2014) | Publications from The Sainsbury Laboratory | Scoop.it
The domestication of wheat in the Fertile Crescent 10,000 years ago led to a genetic bottleneck. Modern agriculture has further narrowed the genetic base by introducing extreme levels of uniformity...
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The domestication of wheat in the Fertile Crescent 10,000 years ago led to a genetic bottleneck. Modern agriculture has further narrowed the genetic base by introducing extreme levels of uniformity on a vast spatial and temporal scale. This reduction in genetic complexity renders the crop vulnerable to new and emerging pests and pathogens. The wild relatives of wheat represent an important source of genetic variation for disease resistance. For nearly a century farmers, breeders, and cytogeneticists have sought to access this variation for crop improvement. Several barriers restricting interspecies hybridization and introgression have been overcome, providing the opportunity to tap an extensive reservoir of genetic diversity. Resistance has been introgressed into wheat from at least 52 species from 13 genera, demonstrating the remarkable plasticity of the wheat genome and the importance of such natural variation in wheat breeding. Two main problems hinder the effective deployment of introgressed resistance genes for crop improvement: (1) the simultaneous introduction of genetically linked deleterious traits and (2) the rapid breakdown of resistance when deployed individually. In this review, we discuss how recent advances in molecular genomics are providing new opportunities to overcome these problems.

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Curr Opin Plant Biol: Regulation of pattern recognition receptor signalling by phosphorylation and ubiquitination (2018)

Curr Opin Plant Biol: Regulation of pattern recognition receptor signalling by phosphorylation and ubiquitination (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Our understanding of how plant innate immunity is triggered and regulated has seen tremendous progress over the last decade, with many important players identified in the model systems Arabidopsis thaliana and Oryza sativa (rice). Identification of these components has come from both genetic screens as well as from proteomics approaches. While genetic approaches are powerful tools of discovery to identify key components in a signalling pathway, the application of genetics is limited when dealing with redundancy or when mutations cause lethal phenotypes. This is where the complementary strength of proteomics has brought major advances. With the advancement in technology in the field of proteomics, not only the proteins involved in innate immune signalling and responses have been identified, but also the posttranslational modifications (PTMs) that these proteins carry have been mapped in more intricate detail and shown to be functionally relevant in both genetic and biochemical terms. Here we discuss the most recent progress in pattern recognition receptor (PRR) signalling with a focus on phosphorylation and ubiquitination.

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Nature Plants: Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen (2018)

Nature Plants: Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Accelerated adaptive evolution is a hallmark of plant–pathogen interactions. Plant intracellular immune receptors (NLRs) often occur as allelic series with differential pathogen specificities. The determinants of this specificity remain largely unknown. Here, we unravelled the biophysical and structural basis of expanded specificity in the allelic rice NLR Pik, which responds to the effector AVR-Pik from the rice blast pathogen Magnaporthe oryzae. Rice plants expressing the Pikm allele resist infection by blast strains expressing any of three AVR-Pik effector variants, whereas those expressing Pikp only respond to one. Unlike Pikp, the integrated heavy metal-associated (HMA) domain of Pikm binds with high affinity to each of the three recognized effector variants, and variation at binding interfaces between effectors and Pikp-HMA or Pikm-HMA domains encodes specificity. By understanding how co-evolution has shaped the response profile of an allelic NLR, we highlight how natural selection drove the emergence of new receptor specificities. This work has implications for the engineering of NLRs with improved utility in agriculture.

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BMC Evol Biol: Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (2018)

BMC Evol Biol: Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186–194, 2012; Kupferschmidt K, Science 337:636–638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335–345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591–11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans.

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Sci Signal: The plant cell wall integrity maintenance and immune signaling systems cooperate to control stress responses in Arabidopsis thaliana (2018)

Sci Signal: The plant cell wall integrity maintenance and immune signaling systems cooperate to control stress responses in Arabidopsis thaliana (2018) | Publications from The Sainsbury Laboratory | Scoop.it
When plant cell walls are damaged by mechanical or biochemical means, the cells initiate adaptive responses to repair the walls and prevent infection. Whereas the cell wall integrity (CWI) maintenance mechanism monitors the status of the cell wall and initiates adaptive cellular responses to damage, pattern-triggered immunity (PTI) induces both cellular and systemic responses that limit infection. Engelsdorf et al . found that osmosensitive alterations in the mechanical properties of the cell wall were important for inducing the adaptive responses to cell wall damage. The receptor-like kinases THE1 and FEI2 and the ion channel MCA1 were required for stimulating CWI-dependent responses to damage. Cell wall damage also induced the expression of host defense peptides that promoted PTI and dampened CWI-dependent processes. The CWI mechanism still elicited damage responses even when PTI was impaired, suggesting that it serves as a failsafe to protect plants even if the immune response is compromised.
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bioRxiv: TTL proteins scaffold brassinosteroid signaling components at the plasma membrane to optimize signal transduction in plant cells (2018)

bioRxiv: TTL proteins scaffold brassinosteroid signaling components at the plasma membrane to optimize signal transduction in plant cells (2018) | Publications from The Sainsbury Laboratory | Scoop.it
Brassinosteroids (BRs) form a group of steroidal hormones essential for plant growth, development and stress responses. Here, we report that plant-specific TETRATRICOPEPTIDE THIOREDOXIN-LIKE (TTL) proteins are positive regulators of BR signaling functioning as scaffold for BR signaling components in Arabidopsis. TTL3 forms a complex with all core components involved in BR signaling, including the receptor kinase BRASSINOSTEROID INSENSITIVE1 (BRI1), the transcription factor BRASSINAZOLE RESISTANT1 (BZR1) and the phosphatase BRI1-SUPPRESSOR1 (BSU1), but excluding the co-receptor BAK1. TTL3 is mainly localized in the cytoplasm, but BR treatment increases its localization at the plasma membrane, where it strengthens the association with BR signaling components. Consistent with a role in BR signaling, mutations in TTL3 and related TTL1 and TTL4 genes cause reduced BR responsiveness. We propose a mechanistic model for BR signaling, in which cytoplasmic/nuclear BR components bound to TTL proteins are recruited to the plasma membrane upon BR perception, which in turn allows the assembly of a BR signaling complex, leading to the de-phosphorylation and nuclear accumulation of the transcription factors BZR1 and BES1.
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Phytopathology: Transgenic expression of EFR and Bs2 genes for field management of bacterial wilt and bacterial spot of tomato (2018)

Phytopathology: Transgenic expression of EFR and Bs2 genes for field management of bacterial wilt and bacterial spot of tomato (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Field trials were conducted at two locations in Florida to evaluate transgenic tomatoes expressing the EFR gene from Arabidopsis thaliana, the Bs2 gene from pepper, or both Bs2/EFR for managing bacterial wilt caused by Ralstonia solanacearum and bacterial spot caused by Xanthomonas perforans. Expression of EFR or Bs2/EFR, in the susceptible genotype, Fla. 8000, significantly reduced bacterial wilt incidence (50-100%) and increased total yield (57-114%) relative to lines expressing only Bs2 or non-transformed Fla. 8000 control, although the marketable yield was not significantly affected. Following harvest, surviving symptomatic and non-symptomatic plants were assessed for colonization by R. solanacearum. There were no significant differences in the population at the lower stem. Interestingly, in the middle stem, no bacteria could be recovered from EFRor Bs2/EFR lines, but viable bacterial populations were recovered from Bs2 and non-transformed control lines at 102-105 colony forming units (CFU) per gram of stem tissue. In growth chamber experiments, the EFR transgenic tomato lines were found to be effective against seven different R. solanacearum strains isolated from the southeastern U.S, indicating utility across southeast U.S. In all the bacterial spot trials, EFR and Bs2/EFRlines had significantly reduced disease severity (22-98%) compared to Fla. 8000 control. The marketable and total yield of Bs2/EFR were significantly higher (43-170%) than Fla. 8000 control in three out of four field trials. These results demonstrate for the first time the potential of using the EFR gene for field management of bacterial wilt and bacterial spot diseases of tomato.

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Stud Mycol: Two different R gene loci co-evolved with Avr2 of Phytophthora infestans and confer distinct resistance specificities in potato (2018)

Stud Mycol: Two different R gene loci co-evolved with Avr2 of Phytophthora infestans and confer distinct resistance specificities in potato (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating disease in potato. For sustainable management of this economically important disease, resistance breeding relies on the availability of resistance (R) genes. Such R genes against P. infestans have evolved in wild tuber-bearing Solanum species from North, Central and South America, upon co-evolution with cognate avirulence (Avr) genes. Here, we report how effectoromics screens with Avr2 of P. infestans revealed defense responses in diverse Solanum species that are native to Mexico and Peru. We found that the response to AVR2 in the Mexican Solanum species is mediated by R genes of the R2 family that resides on a major late blight locus on chromosome IV. In contrast, the response to AVR2 in Peruvian Solanum species is mediated by Rpi-mcq1, which resides on chromosome IX and does not belong to the R2 family. The data indicate that AVR2 recognition has evolved independently on two genetic loci in Mexican and Peruvian Solanum species, respectively. Detached leaf tests on potato cultivar ‘Désirée’ transformed with R genes from either the R2 or the Rpi-mcq1 locus revealed an overlapping, but distinct resistance profile to a panel of 18 diverse P. infestans isolates. The achieved insights in the molecular R – Avr gene interaction can lead to more educated exploitation of R genes and maximize the potential of generating more broad-spectrum, and potentially more durable control of the late blight disease in potato.

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Cell Res: (Research Highlight) Plant G-protein activation: connecting to plant receptor kinases

Cell Res: (Research Highlight) Plant G-protein activation: connecting to plant receptor kinases | Publications from The Sainsbury Laboratory | Scoop.it

Plant heterotrimeric G-proteins function in important signaling pathways mediated by plant receptor kinases (RKs), however, the unique biochemical properties of Gα subunits have complicated our understanding of their regulation in plants. In their new paper in Cell Research, Liang et al. reveal that phosphorylation of the Gα regulator, RGS1, is critical for triggering G-protein signaling downstream of RK activation.

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Plant Biotechnol J: Using CRISPR/Cas9 genome editing in tomato to create a gibberellin‐responsive dominant dwarf DELLA allele (2018)

Plant Biotechnol J: Using CRISPR/Cas9 genome editing in tomato to create a gibberellin‐responsive dominant dwarf DELLA allele (2018) | Publications from The Sainsbury Laboratory | Scoop.it

The tomato PROCERA gene encodes a DELLA protein, and loss‐of‐function mutations derepress growth. We used CRISPR/Cas9 and a single guide RNAs (sgRNA) to target mutations to the PROCERA DELLA domain, and recovered several loss‐of‐function mutations and a dominant dwarf mutation that carries a deletion of one amino acid in the DELLA domain. This is the first report of a dominant dwarf PROCERA allele. This allele retains partial responsiveness to exogenously applied gibberellin (GA). Heterozygotes show an intermediate phenotype at the seedling stage, but adult heterozygotes are as dwarfed as homozygotes.

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Nat Ecol Evol: The ash dieback invasion of Europe was founded by two genetically divergent individuals (2018)

Nat Ecol Evol: The ash dieback invasion of Europe was founded by two genetically divergent individuals (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen that has been moving across continents and hosts from Asian to European ash. Most European common ash trees (Fraxinus excelsior) are highly susceptible to H.fraxineus, although a minority (~5%) have partial resistance to dieback. Here, we assemble and annotate a H.fraxineus draft genome, which approaches chromosome scale. Pathogen genetic diversity across Europe and in Japan, reveals a strong bottleneck in Europe, though a signal of adaptive diversity remains in key host interaction genes. We find that the European population was founded by two divergent haploid individuals. Divergence between these haplotypes represents the ancestral polymorphism within a large source population. Subsequent introduction from this source would greatly increase adaptive potential of the pathogen. Thus, further introgression of H.fraxineus into Europe represents a potential threat and Europe-wide biological security measures are needed to manage this disease.

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BMC Bioinformatics: nQuire: a statistical framework for ploidy estimation using next generation sequencing (2018)

BMC Bioinformatics: nQuire: a statistical framework for ploidy estimation using next generation sequencing (2018) | Publications from The Sainsbury Laboratory | Scoop.it
Intraspecific variation in ploidy occurs in a wide range of species including pathogenic and nonpathogenic eukaryotes such as yeasts and oomycetes. Ploidy can be inferred indirectly - without measuring DNA content - from experiments using next-generation sequencing (NGS). We present nQuire, a statistical framework that distinguishes between diploids, triploids and tetraploids using NGS. The command-line tool models the distribution of base frequencies at variable sites using a Gaussian Mixture Model, and uses maximum likelihood to select the most plausible ploidy model. nQuire handles large genomes at high coverage efficiently and uses standard input file formats. We demonstrate the utility of nQuire analyzing individual samples of the pathogenic oomycete Phytophthora infestans and the Baker’s yeast Saccharomyces cerevisiae. Using these organisms we show the dependence between reliability of the ploidy assignment and sequencing depth. Additionally, we employ normalized maximized log- likelihoods generated by nQuire to ascertain ploidy level in a population of samples with ploidy heterogeneity. Using these normalized values we cluster samples in three dimensions using multivariate Gaussian mixtures. The cluster assignments retrieved from a S. cerevisiae population recovered the true ploidy level in over 96% of samples. Finally, we show that nQuire can be used regionally to identify chromosomal aneuploidies. nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuire under the MIT license.
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Mol. Plant: Pm21 from Haynaldia villosa Encodes a CC-NBS-LRR that Confers Powdery Mildew Resistance in Wheat (2018)

Mol. Plant: Pm21 from Haynaldia villosa Encodes a CC-NBS-LRR that Confers Powdery Mildew Resistance in Wheat (2018) | Publications from The Sainsbury Laboratory | Scoop.it
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Nature Plants: An apoplastic peptide activates salicylic acid signalling in maize (2018)

Nature Plants: An apoplastic peptide activates salicylic acid signalling in maize (2018) | Publications from The Sainsbury Laboratory | Scoop.it
Localized control of cell death is crucial for the resistance of plants to pathogens. Papain-like cysteine proteases (PLCPs) regulate plant defence to drive cell death and protection against biotrophic pathogens. In maize (Zea mays), PLCPs are crucial in the orchestration of salicylic acid (SA)-dependent defence signalling. Despite this central role in immunity, it remains unknown how PLCPs are activated, and which downstream signals they induce to trigger plant immunity. Here, we discover an immune signalling peptide, Z. mays immune signalling peptide 1 (Zip1), which is produced after salicylic acid (SA) treatment. In vitro studies demonstrate that PLCPs are required to release bioactive Zip1 from its propeptide precursor. Conversely, Zip1 treatment strongly elicits SA accumulation in leaves. Moreover, transcriptome analyses revealed that Zip1 and SA induce highly overlapping transcriptional changes. Consequently, Zip1 promotes the infection of the necrotrophic fungus Botrytis cinerea, while it reduces virulence of the biotrophic fungus Ustilago maydis. Thus, Zip1 represents the previously missing signal that is released by PLCPs to activate SA defence signalling.
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bioRxiv: DeepStomata: Facial Recognition Technology for Automated Stomatal Aperture Measurement (2018)

bioRxiv: DeepStomata: Facial Recognition Technology for Automated Stomatal Aperture Measurement (2018) | Publications from The Sainsbury Laboratory | Scoop.it
Stomata are an attractive model for studying the physiological responses of plants to various environmental stimuli. Of the morphological parameters that represent the degree of stomatal opening, the length of the minor axis of the stomatal pore (the stomatal aperture) has been most commonly used to dissect the molecular basis of its regulation. Measuring stomatal apertures is time consuming and labour intensive, preventing their use in large-scale studies. Here, we completely automated this process by developing a program called DeepStomata, which combines stomatal region detection and pore isolation by image segmentation. The former, which comprises histograms of oriented gradients (HOG)-based stomatal detection and the convolutional neural network (CNN)-based classification of open/closed-state stomata, acts as an efficient conditional branch in the workflow to selectively quantify the pores of open stomata. An analysis of batches of images showed that the accuracy of our automated aperture measurements was equivalent to that of manual measurements, however had higher sensitivity (i,e., lower false negative rate ) and the process speed was at least 80 times faster. The outstanding performance of our proposed method for automating a laborious and repetitive task will allow researchers to focus on deciphering complex phenomena.
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Ann Rev Phytopath: CRISPR Crops: Plant Genome Editing Toward Disease Resistance (2018)

Ann Rev Phytopath: CRISPR Crops: Plant Genome Editing Toward Disease Resistance (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Genome editing by sequence-specific nucleases (SSNs) has revolutionized biology by enabling targeted modifications of genomes. Although routine plant genome editing emerged only a few years ago, we are already witnessing the first applications to improve disease resistance. In particular, CRISPR-Cas9 has democratized the use of genome editing in plants thanks to the ease and robustness of this method. Here, we review the recent developments in plant genome editing and its application to enhancing disease resistance against plant pathogens. In the future, bioedited disease resistant crops will become a standard tool in plant breeding.

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GigaScience: A workflow for simplified analysis of ATAC-cap-seq data in R (2018)

GigaScience: A workflow for simplified analysis of ATAC-cap-seq data in R (2018) | Publications from The Sainsbury Laboratory | Scoop.it

ATAC-cap-seq is a high-throughput sequencing method that combines ATAC-seq with targeted nucleic acid enrichment of precipitated DNA fragment. There are increased analytical difficulties arising from working with a set of regions of interest that may be small in number and biologically dependent. Common statistical pipelines for RNAseq might be assumed to apply but can give misleading results on ATAC-cap-seq data. A tool is needed to allow a non-specialist user to quickly and easily summarise data and apply sensible and effective normalisation and analysis.

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Dagdas et al: Host autophagy machinery is diverted to the pathogen interface to mediate focal defense responses against the Irish potato famine pathogen (2018)

Dagdas et al: Host autophagy machinery is diverted to the pathogen interface to mediate focal defense responses against the Irish potato famine pathogen (2018) | Publications from The Sainsbury Laboratory | Scoop.it

During plant cell invasion, the oomycete Phytophthora infestans remains enveloped by host-derived membranes whose functional properties are poorly understood. P. infestans secretes a myriad of effector proteins through these interfaces for plant colonization. Recently we showed that the effector protein PexRD54 reprograms host-selective autophagy by antagonising antimicrobial-autophagy receptor Joka2/NBR1 for ATG8CL binding (Dagdas, 2016). Here, we show that during infection, ATG8CL/Joka2 labelled defense-related autophagosomes are diverted toward the perimicrobial host membrane to restrict pathogen growth. PexRD54 also localizes to autophagosomes across the perimicrobial membrane, consistent with the view that the pathogen remodels host-microbe interface by co-opting the host autophagy machinery. Furthermore, we show that the host-pathogen interface is a hotspot for autophagosome biogenesis. Notably, overexpression of the early autophagosome biogenesis protein ATG9 enhances plant immunity. Our results implicate selective autophagy in polarized immune responses of plants and point to more complex functions for autophagy than the widely known degradative roles.

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Science: Receptor networks underpin plant immunity (2018)

Science: Receptor networks underpin plant immunity (2018) | Publications from The Sainsbury Laboratory | Scoop.it
Plants are attacked by a multitude of pathogens and pests, some of which cause epidemics that threaten food security. Yet a fundamental concept in plant pathology is that most plants are actively resistant to most pathogens and pests. Plants fend off their innumerable biotic foes primarily through innate immune receptors that detect the invading pathogens and trigger a robust immune response. The conceptual basis of such interactions was elegantly articulated by Harold H. Flor, who, in 1942, proposed the hypothesis that single genes in plants and pathogens define the outcome of their interactions; that is, a plant harboring a specific gene displays resistance against a pathogen that carries an interacting virulence gene ( 1 ). This gene-for-gene model was hugely insightful and influential—it has helped to guide applied and basic research on disease resistance. However, recent findings are taking the field beyond this simplified binary view of plant-pathogen interactions. Plants carry extremely diverse and dynamic repertoires of immune receptors that are interconnected in complex ways. Conversely, plant pathogens secrete a diversity of virulence proteins and metabolites called effectors, and pathogen genomics has revealed hundreds of effector genes in many species. These effectors have evidently evolved to favor pathogen infection and spread, but a subset of them inadvertently activate plant immune receptors. The emerging paradigm is that dynamic webs of genetic and biochemical networks underpin the early stages of plant-pathogen interactions.
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Phytopathology: Detection of race-specific resistance against Puccinia coronata f. sp. avenae in Brachypodium species (2018)

Phytopathology: Detection of race-specific resistance against Puccinia coronata f. sp. avenae in Brachypodium species (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Oat crown rust caused by Puccinia coronata f. sp. avenae is the most destructive foliar disease of cultivated oat. Characterization of genetic factors controlling resistance responses to Puccinia coronata f. sp. avenae in non-host species could provide new resources for developing disease protection strategies in oat. We examined symptom development and fungal colonization levels of a collection of Brachypodium distachyon and B. hybridum accessions infected with three North American P. coronata f. sp. avenae isolates. Our results demonstrated that colonization phenotypes are dependent on both host and pathogen genotypes, indicating a role for race-specific responses in these interactions. These responses were independent of the accumulation of reactive oxygen species. Expression analysis of several defense-related genes suggested that salicylic acid and ethylene-mediated signaling, but not jasmonic acid are components of resistance reaction to P. coronata f. sp. avenae. Our findings provide the basis to conduct a genetic inheritance study to examine if effector-triggered immunity contributes to non-host resistance to P. coronata f. sp. avenae in Brachypodium species.

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Plant Cell: Receptor-like Cytoplasmic Kinases Directly Link Diverse Pattern Recognition Receptors to the Activation of Mitogen-activated Protein Kinase Cascades in Arabidopsis (2018)

Plant Cell: Receptor-like Cytoplasmic Kinases Directly Link Diverse Pattern Recognition Receptors to the Activation of Mitogen-activated Protein Kinase Cascades in Arabidopsis (2018) | Publications from The Sainsbury Laboratory | Scoop.it
Plants deploy numerous cell surface-localized pattern-recognition receptors (PRRs) to perceive host- and microbe-derived molecular patterns that are specifically released during infection and activate defense responses. The activation of the mitogen-activated protein kinases MPK3, MPK4 and MPK6 (MPK¾/6) is a hallmark of immune system activation by all known PRRs and is crucial for establishing disease resistance. The MAP kinase kinase kinase (MAPKKK) MEKK1 controls MPK4 activation, but the MAPKKKs responsible for MPK3/6 activation downstream of diverse PRRs and how the perception of diverse molecular patterns leads to the activation of MAPKKKs remain elusive. Here we show that two highly related MAPKKKs, MAPKKK3 and MAPKKK5, mediate MPK3/6 activation by at least four PRRs and confer resistance to bacterial and fungal pathogens in Arabidopsis thaliana. The receptor-like cytoplasmic kinases VII (RLCK VII), which act downstream of PRRs, directly phosphorylate MAPKKK5 Ser599, which is required for pattern-triggered MPK3/6 activation, defense gene expression, and disease resistance. Surprisingly, MPK6 further phosphorylates MAPKKK5 Ser682 and Ser692 to enhance MPK3/6 activation and disease resistance, pointing to a positive feedback mechanism. Finally, MEKK1 Ser603 is phosphorylated by both RLCK VII and MPK4, which is required for pattern-triggered MPK4 activation. These findings illustrate central mechanisms by which multiple PRRs activate MAPK cascades and disease resistance.
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Cell Res: (Research Highlight) Deadlier than the malate (2018)

Cell Res: (Research Highlight) Deadlier than the malate (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Plant and animal cells share similar malate-mediated cell death processes, but plants have evolved a unique intracellular communication between organelles in regulating programmed cell death in response to specific photoperiods.

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Phytopathology: A new resistance gene in combination with Rmg8 confers strong resistance against Triticum isolates of Pyricularia oryzae in a common wheat landrace (2018)

Phytopathology: A new resistance gene in combination with Rmg8 confers strong resistance against Triticum isolates of Pyricularia oryzae in a common wheat landrace (2018) | Publications from The Sainsbury Laboratory | Scoop.it

The wheat blast fungus (Triticum pathotype of Pyricularia oryzae) first arose in Brazil in 1985 and has recently spread to Asia. Resistance genes against this new pathogen are very rare in common wheat populations. We screened 520 local landraces of common wheat collected worldwide with Br48, a Triticum isolate collected in Brazil, and found a highly resistant, unique accession, GR119. When F2 seedlings derived from a cross between GR119 and Chinese Spring (CS, susceptible control) were inoculated with Br48, resistant and susceptible seedlings segregated in a 15:1 ratio, suggesting that GR119 carries two resistance genes. When the F2 seedlings were inoculated with Br48△A8 carrying a disrupted allele of AVR-Rmg8 (an avirulence gene corresponding to a previously reported resistance gene, Rmg8), however, the segregation fitted a 3:1 ratio. These results suggest that one of the two genes in GR119 was Rmg8. The other, new gene was tentatively designated as RmgGR119. GR119 was highly resistant to all Triticum isolates tested. Spikes of GR119 were highly resistant to Br48, moderately resistant to Br48△A8 and a hybrid culture carrying avr-Rmg8 (nonfunctional allele), and highly resistant to its transformant carrying AVR-Rmg8. The strong resistance of GR119 was attributed to the combined effects of Rmg8 and RmgGR119.

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mBio: The Blast Fungus Decoded: Genomes in Flux (2018)

mBio: The Blast Fungus Decoded: Genomes in Flux (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Plant disease outbreaks caused by fungi are a chronic threat to global food security. A prime case is blast disease, which is caused by the ascomycete fungus Magnaporthe oryzae (syn. Pyricularia oryzae), which is infamous as the most destructive disease of the staple crop rice. However, despite its Linnaean binomial name, M. oryzae is a multihost pathogen that infects more than 50 species of grasses. A timely study by P. Gladieux and colleagues (mBio 9:e01219-17, 2018, https://doi.org/10.1128/mBio.01219-17) reports the most extensive population genomic analysis of the blast fungus thus far. M. oryzae consists of an assemblage of differentiated lineages that tend to be associated with particular host genera. Nonetheless, there is clear evidence of gene flow between lineages consistent with maintaining M. oryzae as a single species. Here, we discuss these findings with an emphasis on the ecologic and genetic mechanisms underpinning gene flow. This work also bears practical implications for diagnostics, surveillance, and management of blast diseases.

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Curr Opin Plant Biol: The coming of age of EvoMPMI: evolutionary molecular plant–microbe interactions across multiple timescales (2018)

Curr Opin Plant Biol: The coming of age of EvoMPMI: evolutionary molecular plant–microbe interactions across multiple timescales (2018) | Publications from The Sainsbury Laboratory | Scoop.it
Plant–microbe interactions are great model systems to study co-evolutionary dynamics across multiple timescales. However, mechanistic research on plant–microbe interactions has often been conducted with little consideration of evolutionary concepts and methods. Conversely, evolutionary research has rarely integrated the range of mechanisms and models from the molecular plant–microbe interactions field. In recent years, the incipient field of evolutionary molecular plant–microbe interactions (EvoMPMI) has emerged to bridge this gap. Here, we report on some of the recent advances in EvoMPMI. In particular, we highlight new systems to study microbe interactions with early diverging land plants, and new findings from studies of adaptive evolution in pathogens and plants. By linking mechanistic and evolutionary research, EvoMPMI promises to expand our understanding of plant–microbe interactions.
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Theor. Appl. Genet.: Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species Solanum verrucosum through DNA capture technologies (2...

Theor. Appl. Genet.: Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species Solanum verrucosum through DNA capture technologies (2... | Publications from The Sainsbury Laboratory | Scoop.it
Key message
A broad-spectrum late blight disease-resistance gene from Solanum verrucosum has been mapped to potato chromosome 9. The gene is distinct from previously identified-resistance genes.

Abstract
We have identified and characterised a broad-spectrum resistance to Phytophthora infestans from the wild Mexican species Solanum verrucosum. Diagnostic resistance gene enrichment (dRenSeq) revealed that the resistance is not conferred by previously identified nucleotide-binding, leucine-rich repeat genes. Utilising the sequenced potato genome as a reference, two complementary enrichment strategies that target resistance genes (RenSeq) and single/low-copy number genes (Generic-mapping enrichment Sequencing; GenSeq), respectively, were deployed for the rapid, SNP-based mapping of the resistance through bulked-segregant analysis. Both approaches independently positioned the resistance, referred to as Rpi-ver1, to the distal end of potato chromosome 9. Stringent post-enrichment read filtering identified a total of 64 informative SNPs that corresponded to the expected ratio for significant polymorphisms in the parents as well as the bulks. Of these, 61 SNPs are located on potato chromosome 9 and reside within 27 individual genes, which in the sequenced potato clone DM locate to positions 45.9 to 60.9 Mb. RenSeq- and GenSeq-derived SNPs within the target region were converted into allele-specific PCR-based KASP markers and further defined the position of the resistance to a 4.3 Mb interval at the bottom end of chromosome 9 between positions 52.62–56.98 Mb.
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