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. Two RNA samples were compared, one prepared from cells grown in minimal medium M9 and the other from cells grown in minimal medium supplemented with bean pod extract.To control de biological variation that might interfere with data interpretation, a minimum of three biological replicates and two technical replicates (swap) were prepared.

2010-05-22 | E-GEOD-14625 | biostudies-arrayexpress

Transcript Profiling of the Common Bean - Rhizobium Symbiosis under Oxidative Stress

2012-07-01 | GSE37638 | GEO

Transcript Profiling of the Common Bean - Rhizobium Symbiosis under Oxidative Stress

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

Nanoceria modulates kidney bean proteomic response and compromises its seed quality

Project description:There is inadequate understanding of the environmental fate and effects of engineered nanoparticles, including nanoceria. Also, knowledge about the influence of environmental factors on the bioavailability of these particles and resulting impacts on the nutritional quality of crops is limited. Alterations in mineral and macromolecular composition of some grains and fruits under nanoceria exposure have been reported recently; however, the cellular mechanisms associated with the effects are unknown. Here, we show that the impact of nanoceria at 62.5 to 500 mg/kg soil on kidney bean (Phaseolus vulgaris) productivity and seed quality are influenced by soil organic matter content. Seeds obtained from plants exposed to nanoceria at 125 mg/kg showed unique and contrasting response in terms of nutritional quality under varying soil organic matter content. Additionally, quantitative proteomic analysis provides evidence for dose-dependent down-regulation of some major proteins associated with nutrient storage and carbohydrate metabolism, including phaseolin and lectins in the exposed seeds. This study suggests that nCeO2 exposure negatively impacts the nutritional quality of kidney beans. This altered seed quality may have significant implications for food production and human health.

2019-02-21 | PXD002407 | Pride

Transcriptome Characterization of developing bean (Phaseolus vulgaris L.) pods from two genotypes with contrasting seed zinc concentrations.

Project description:Dry bean (Phaseolus vulgaris L.) seeds are a rich source of dietary zinc, especially for people consuming plant-based diets. Within P. vulgaris there is at least two-fold variation in seed Zn concentration. Genetic studies have revealed seed Zn differences to be controlled by a single gene in two closely related navy bean genotypes, Albion and Voyager. In this study, these two genotypes were grown under controlled fertilization conditions and the Zn concentration of various plant parts were determined. The two genotypes had similar levels of Zn in their leaves and pods but Voyager had 52% more Zn in its seeds than Albion. RNA was sequence from developing pods of both genotypes. Transcriptome analysis of these genotypes identified 27,198 genes in the developing bean pods, representing 86% of the genes in the P. vulgaris genome (v 1.0 DOE-JGI and USDA-NIFA). Expression was detected in 18,438 genes. A relatively small number of genes (381) were differentially expressed between Albion and Voyager. Differentially expressed genes included three genes potentially involved in Zn transport, including zinc-regulated transporter, iron regulated transporter like (ZIP), zinc-induced facilitator (ZIF) and heavy metal associated (HMA) family genes. In addition 12,118 SNPs were identified between the two genotypes. Of the gene families related to Zn and/or Fe transport, eleven genes were found to contain SNPs between Albion and Voyager.

2015-03-24 | GSE67121 | GEO

Genome wide gene-expression analysis of the spider mite Tetranychus urticae after long term host transfer from acyanogenic Phaseolus vulgaris cv. 'Prelude' bean plants to cyanogenic Phaseolus lunatus cv. '8078' bean plants

Project description:250 adult T. urticae females from the London strain (grown on acyanogenic P. vulgaris cv. Prelude bean plants) were transferred to cyanogenic P. lunatus cv. 8078 bean plants. Thirty-five generations after the host transfer, total RNA was extracted from mites growing on both bean species (London and London-CYANO strain) and used in in a genome-wide gene expression microarray (Sureprint G3 microarray, Agilent) experiment to assess significantly differentially expressed genes (FC ≥ 2 and FDR-corrected p-value < 0.05) between mites grown on P. vulgaris (cv. Prelude) bean plants (London strain) and mites grown for 35 generations on P. lunatus (cv. 8078) bean plants (London-CYANO strain).

2014-04-30 | GSE50162 | GEO

Phaseolus vulgaris domestication metabolomics

Project description:Metabolomics of wild and domesticated varieties of common bean (Phaseolus vulgaris)

2022-05-13 | MSV000089468 | MassIVE