Transcriptome-assisted SNP marker discovery late blight resistance in tomato breeding.
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB59344 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR10814969.fastq.gz | Fastqsanger.gz | |||
| ERR10814970.fastq.gz | Fastqsanger.gz | |||
| ERR10814971.fastq.gz | Fastqsanger.gz | |||
| ERR10814972.fastq.gz | Fastqsanger.gz | |||
| ERR10814973.fastq.gz | Fastqsanger.gz |
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Project description:Late blight, caused by the oomycete Phytophthora infestans, is one of the most damaging potato diseases. Genetic resistance is one of the most effective means to control the destruction caused by this pathogen. Transgenic potato lines harboring a resistance gene, RB, confer broad-spectrum, rate-reducing late blight resistance. A microarray approach was used to understand what genes are manipulated in the potato background after the addition of the RB gene that contribute to the late blight resistant phenotype. Keywords: Time course, disease state analysis CRD (3x2x2) Split-Split Plot: 3 sampling time points after inoculation (2, 5, 10 hours), Two genotypes (Katahdin with and without the RB gene), Inoculation with P. infestans or mock inoculation with water. 48 arrays were hybridized in total; 12 in each biological replicate. Each genotype with the mock and late blight inoculated samples was hybridized on two arrays using a dye-swap procedure. Each genotype had a total of 6 arrays across the three sampling time points.
2010-05-22 | E-GEOD-13341 | biostudies-arrayexpress
Project description:Late blight, caused by the oomycete Phytophthora infestans, is one of the most damaging potato diseases. Genetic resistance is one of the most effective means to control the destruction caused by this pathogen. Transgenic potato lines harboring a resistance gene, RB, confer broad-spectrum, rate-reducing late blight resistance. A microarray approach was used to understand what genes are manipulated in the potato background after the addition of the RB gene that contribute to the late blight resistant phenotype. Keywords: Time course, disease state analysis
2009-10-01 | GSE13341 | GEO
Project description:Much of the pathogenic success of Phytophthora infestans, the potato and tomato late blight agent, relies on its ability to generate from mycelia large amounts of sporangia, which release zoospores that encyst and form infection structures. To better understand these critical stages, Affymetrix GeneChips based on 15,650 unigenes were designed and used to profile the life cycle, through an analysis of RNA from hyphae, sporangia, cleaving sporangia, motile zoospores, and germinated zoospore cysts. Keywords: Developmental study
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Project description:To effectively manage resources, regulatory cross-talk between biological processes within an organism is essential. An emerging area in plant research focuses on antagonism between regulatory systems controlling growth/development and those governing immunity. Such crosstalk represents a point of vulnerability for pathogens to exploit. Here we show that the notorious potato blight pathogen Phytophthora infestans promotes a growth and development pathway in order to antagonise plant immunity. AVR2, an effector protein secreted by P. infestans, has been shown to interact with potato BSL1, a putative phosphatase implicated in brassinosteroid hormone signalling. Plants expressing AVR2 exhibit transcriptional and phenotypic overlaps with an over-active brassinosteroid signalling pathway, and have compromised immunity. The activity of AVR2 leads to up-regulation of a functional orthologue of AtHBI1, known to facilitate cross-talk between the brassinosteroid pathway and immune signalling in Arabidopsis. Transient expression of potato HBI1-like compromises immunity and enhances leaf colonisation by P. infestans. Knowledge of how pathogens manipulate regulatory cross-talk governing resource allocation in plants will inform crop breeding efforts of the future; helping to maximise both yield and resistance to ensure food security as pressure on our agricultural systems increases.
2017-03-01 | E-MTAB-3854 | biostudies-arrayexpress
Project description:Oomycetes are filamentous organisms that cause notorious diseases, several of which with high economic impact. Well known is Phytophthora infestans, the causal agent of potato late blight. Previously, in silico analyses of the genome and transcriptome of P. infestans resulted in the annotation of a large number of genes encoding proteins with an N-terminal signal peptide. This set is collectively referred to as the secretome and comprises proteins involved in, for example, cell wall growth and modification, proteolytic processes and the promotion of successful invasion of plant cells. So far, proteomic profiling in oomycetes was primarily focussed on subcellular, intracellular or cell wall fractions; the extracellular proteome has not been studied systematically. Here we present the first comprehensive characterization of the in vivo secretome and extracellular proteome of P. infestans. We have used mass spectrometry to analyse P. infestans proteins present in seven different growth media with mycelial cultures and this resulted in the consistent identification of over two hundred proteins. Gene ontology classification pinpointed proteins involved in cell wall modifications, pathogenesis, defense responses and proteolytic processes. Moreover, we found members of the RXLR and CRN effector families as well as several proteins lacking an obvious signal peptide. The latter were confirmed to be bona fide extracellular proteins and this suggests that, similar to other organisms, oomycetes exploit non-conventional secretion mechanisms to transfer certain proteins to the extracellular environment.
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Project description:Plant diseases are a major cause for yield losses and new strategies to control them without harming the environment are urgently needed. Plant-associated bacteria contribute to their host’s health in diverse ways, among which the emission of disease-inhibiting volatile organic compounds (VOCs). We have previously reported that VOCs emitted by potato-associated bacteria caused strong in vitro growth inhibition of the late blight causing agent Phytophthora infestans. This work focuses on sulfur-containing VOCs (sVOCs) and demonstrates the high in planta protective potential of S-methyl methane thiosulfonate (MMTS), which fully prevented late blight disease in potato leaves and plantlets without phytotoxic effects, in contrast to other sVOCs. Short exposure times were sufficient to protect plants against infection and MMTS also displayed curative effects. We further show that MMTS’s protective activity was not mediated by the plant immune system but lied in its anti-oomycete activity. Using quantitative proteomics, we determined that different sVOCs caused specific proteome changes in P. infestans, highlighting sulfur metabolism, protein translation and redox balance as main targets. This work brings new perspectives for sustainable protection against the devastating Irish Famine pathogen, while opening new research avenues on the role of sVOCs in the interaction between plants and their microbiome.
2020-01-07 | PXD014455 | Pride
Project description:Much of the pathogenic success of Phytophthora infestans, the potato and tomato late blight agent, relies on its ability to generate from mycelia large amounts of sporangia, which release zoospores that encyst and form infection structures. To better understand these critical stages, Affymetrix GeneChips based on 15,650 unigenes were designed and used to profile the life cycle, through an analysis of RNA from hyphae, sporangia, cleaving sporangia, motile zoospores, and germinated zoospore cysts. Keywords: Developmental study Gene expression in non-sporulating hyphae, asexual sporangia, sporangia undergoing cleavage, swimming zoospores, and germinated cysts containing appressoria were characterized using isolate 88069. Several strategies controlled for experimental error. Firstly, two replicate hybridizations were used for each tissue type. Secondly, RNAs for the two replicates were prepared by research groups in North America and/or Europe. Thirdly, RNA for each hybridization was pooled from two or three independent cultures made by that group. Finally, before using an RNA sample in an experiment the expression of selected well-characterized genes was measured to ensure that the tissue was properly prepared.
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Project description:Infection of a nonhost plant by Albugo laibachii enables full colonization by Phytophthora infestans
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Project description:Tomato crops suffer attacks of various pathogens that cause large production losses. Late blight caused by Phytophthora infestans is a devastating disease in tomatoes because of its difficultly to control. Here, we applied metabolomics based on liquid chromatography–mass spectrometry (LC-MS) and metabolic profiling by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) in combination with multivariate data analysis in the early detection of late blight on asymptomatic tomato plants and to discriminate infection times of 4, 12, 24, 36, 48, 60, 72 and 96 h after inoculation (hpi). MALDI-MS and LC-MS profiles of metabolites combined with multivariate data analysis are able to detect early-late blight-infected tomato plants, and metabolomics based on LC-MS discriminates infection times in asymptomatic plants. We found the metabolite tomatidine as an important biomarker of infection, saponins as early infection metabolite markers and isocoumarin as early and late asymptomatic infection marker along the post infection time. MALDI-MS and LC-MS analysis can therefore be used as a rapid and effective method for the early detection of late blight-infected tomato plants, offering a suitable tool to guide the correct management and application of sanitary defense approaches. LC-MS analysis also appears to be a suitable tool for identifying major metabolites of asymptomatic late blight-infected tomato plants.
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