Common bean viruses in Tanzania
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PROVIDER: PRJEB23835 | ENA |
REPOSITORIES: ENA
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Project description:We report how phosphate deficiency early rhizobia-induced genes in Phaseolus vulgaris (common bean)
2018-11-14 | GSE118968 | GEO
Project description:Phaseolus vulgaris was inoculated with water, and Pseudomonas syringae pv phasiolicola R5 (avirulent) and R8 (virulent) and sampled 24 h later. Tags 126, 127N, and 128C were assigned to water-treated control replicates; tags 129C, 130N, and 131 were assigned to R8-inoculated (susceptible) replicates; and tags 127C, 128N and 130C were assigned to R5-inoculated (resistant) replicates.
2019-12-19 | MSV000084725 | MassIVE
Project description:A wide range of environmental stresses lead to an elevated production of reactive oxygen species (ROS) in plant cells thus resulting in oxidative stress. The biological nitrogen fixation in the legume - Rhizobium symbiosis is at high risk of damage from oxidative stress. Common bean (Phaseolus vulgaris) active nodules exposed to the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) that generates ROS accumulation, showed a reduced nitrogenase activity and ureide content. We analyzed the global gene response of stressed nodules using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). A total of 4,280 ESTs were differentially expressed in oxidative stressed bean nodules; of these 2,218 were repressed. These genes were grouped in 44 different biological processes as defined by Gene Onthology. Analysis with the PathExpress bioinformatic tool, adapted for bean, identified five significantly repressed metabolic path
2012-07-01 | GSE37638 | GEO
Project description:A wide range of environmental stresses lead to an elevated production of reactive oxygen species (ROS) in plant cells thus resulting in oxidative stress. The biological nitrogen fixation in the legume - Rhizobium symbiosis is at high risk of damage from oxidative stress. Common bean (Phaseolus vulgaris) active nodules exposed to the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) that generates ROS accumulation, showed a reduced nitrogenase activity and ureide content. We analyzed the global gene response of stressed nodules using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). A total of 4,280 ESTs were differentially expressed in oxidative stressed bean nodules; of these 2,218 were repressed. These genes were grouped in 44 different biological processes as defined by Gene Onthology. Analysis with the PathExpress bioinformatic tool, adapted for bean, identified five significantly repressed metabolic path This work presents the transcriptional profile of bean nodules, induced by strain Rhizobium tropici CIAT 899, under oxidative stress, generated experimentally by adding the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) for 48 hours. We analyzed the transcript profile, via microarray hybridization, using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). A total of 4,280 ESTs were differentially expressed in oxidative stressed bean nodules; of these 2,218 were repressed.
2012-06-30 | E-GEOD-37638 | biostudies-arrayexpress
Project description:Common bean (Phaseolus vulgaris L.) is a relevant crop cultivated over the world, largely in water insufficiency vulnerable areas. Since drought is the main environmental factor restraining worldwide crop production, efforts have been invested to amend drought tolerance in commercial common bean varieties. However, scarce molecular data are available for those cultivars of P. vulgaris with drought tolerance attributes. As a first approach, Pinto Saltillo (PS), Azufrado Higuera (AH), and Negro Jamapa Plus (NP) were assessed phenotypically and physiologically to determine the outcome in response to drought on these common bean cultivars. Based on this, a Next-generation sequencing approach was applied to PS, which was the most drought-tolerant cultivar to determine the molecular changes at the transcriptional level. The RNA-Seq analysis revealed that numerous PS genes are dynamically modulated by drought. In brief, 1005 differentially expressed genes (DEGs) were identified, from which 645 genes were up-regulated by drought stress, whereas 360 genes were down-regulated. Further analysis showed that the enriched categories of the up-regulated genes in response to drought fit to processes related to carbohydrate metabolism (polysaccharide metabolic processes), particularly genes encoding proteins located within the cell periphery (cell wall dynamics). In the case of down-regulated genes, heat shock-responsive genes, mainly associated with protein folding, chloroplast, and oxidation-reduction processes were identified. Our findings suggest that secondary cell wall (SCW) properties contribute to P. vulgaris L. drought tolerance through alleviation or mitigation of drought-induced osmotic disturbances, making cultivars more adaptable to such stress. Altogether, the knowledge derived from this study is significant for a forthcoming understanding of the molecular mechanisms involved in drought tolerance on common bean, especially for drought-tolerant cultivars such as PS.
2019-12-31 | GSE123381 | GEO
Project description:P. syringae pv. phaseolicola is the causal agent of the halo blight disease of beans (Phaseolus vulgaris L). The disease attacks both foliage and pods of plant host. Many genes involve in pathogenicity and virulence are induced only in plant or in the presence of host components. In this work we investigated the effect of bean pod extract on the transcriptomic profile of the bacterium, when grown at low temperature in minimal medium with or without bean pod extract.
2009-03-03 | GSE14625 | GEO
Project description:The goal of this study was to detemine the genes responsible of the pod indehiscence in Phaseolus vulgaris by comparing 4 accesions with total, middle and null dehiscence transcriptomes of three stages of pod develoment of Phaseolus vulgaris
2022-04-16 | GSE179985 | GEO
Project description:To understand the molecular basis for differences of common bean wild-type and mutant in sulphur amino acid content, transcripts were profiled at four developmental stages of seeds from wild-type SARC1 and major seed storage protein-deficient line SMARC1N-PN1 using a CustomArray 90K array. Microarray data confirmed that transcripts of storage and sulphur-rich proteins and sulphur-metabolism related genes were differentially expressed between the lines. The common bean (Phaseolus vulgaris) mutant line, SMARC1N-PN1 and its wild type, SARC1 used in the microarray experiment were grown in the field in London, ON, in 2009. Four developmental stages of seeds, based on fresh seed weight, were harvested. The stages of seeds used are Stage IV M-bM-^@M-^S cotyledon, 25 mg seed weight; Stage V M-bM-^@M-^S cotyledon, 50 mg seed weight; Stage VI M-bM-^@M-^S maturation, 150 mg seed weight, corresponding to the most active phase of reserve accumulation; and Stage VIII M-bM-^@M-^S maturation, 380 mg seed weight, corresponding to the onset of desiccation, were harvested for total RNA extraction. Four biological replicates for Stage IV and V and 3 biological replicates for Stage VI and VIII.
2012-11-06 | E-GEOD-34233 | biostudies-arrayexpress
Project description:Virus diseases are among the main biotic factors constraining common bean (Phaseolus vulgaris L.) production in Tanzania. Disease management requires information on types, distribution, incidence, and genetic variation of the causal viruses, which is currently limited. Thus, a countrywide comprehensive survey was conducted. Use of a next-generation sequencing technique enabled simultaneous detection of 15 viruses belonging to 11 genera. De novo assembly resulted in many contigs, including complete or nearly complete sequences of Bean common mosaic virus (BCMV), Bean common mosaic necrosis virus (BCMNV), and Southern bean mosaic virus (SBMV). Some viruses (for example, SBMV and Tomato leaf curl Uganda virus-related begomovirus) were detected for the first time in common bean in Tanzania. Visually assessed virus-like disease incidence ranged from 0 to 98% but reverse-transcription polymerase chain reaction-based incidence of BCMV and BCMNV (7,756 samples) was mostly less than 40%. The Sanger-based nucleotide sequences encoding coat proteins of BCMV and BCMNV isolates were 90.2 to 100% and 97.1 to 100% identical to each other, respectively. Phylogenetic analysis showed that BCMV isolates were more diverse than BCMNV isolates. The information generated in this study will contribute to the development of molecular diagnostic tools and strategies for management of virus diseases nationally and internationally. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
| S-EPMC7779967 | biostudies-literature
Project description:Exploring the native habitat and wild relatives of common bean (Phaseolus vulgaris) for ‘missing plant microbes’
| PRJEB26084 | ENA