Genome-wide transcriptional changes triggered by water deficit on a drought-tolerant common bean cultivar
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ABSTRACT:
PROVIDER: PRJNA508605 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8284480.fastq.gz | Fastqsanger.gz | |||
| SRR8284481.fastq.gz | Fastqsanger.gz |
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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:Identification of gene expression changes responding to water deficit in leaves of maize drought tolerant mutant line Chang7-2t.
2022-02-28 | E-MTAB-11331 | biostudies-arrayexpress
Project description:Background: Soil salinity is a major abiotic stress factor that limit agricultural productivity worldwide, and this problem is expected to grow in the future. Common bean (Phaseolus vulgaris L.) is an important protein source in developing countries is highly susceptible to salt stress. To understand the underlying mechanism of salt stress responses, transcriptomics, metabolomics, and ion content analysis were utilized for response comparison of salt-tolerant and salt-susceptible common bean genotypes in saline conditions. Results: Transcriptome analysis has revealed that the tolerant genotype had increased photosynthesis in saline conditions while the susceptible genotype acted in a contrasting way. The chlorophyll content measurements have backed up this result with increase in tolerant and decrease in susceptible genotype. Transcriptome also displayed a more active carbon and amino acid metabolism for the tolerant genotype as well. Analysis of primary metabolites with GC-MS demonstrated the boosted carbohydrate metabolism in the tolerant genotype with increased sugar content as well as better amino-acid metabolism with the accumulation of glutamate and asparagine and hinted a lowered photorespiration level for the tolerant one. Accumulation of lysine, valine, and isoleucine in the roots of the susceptible genotype suggested a halted stress response pathway. According to ion content comparison, the tolerant genotype managed to block accumulation of Na+ in the leaves while accumulating significantly less Na+ in the roots compared to susceptible genotype. K+ levels increased in the leaves of both genotype and the roots of the susceptible one but dropped in the roots of the tolerant genotype. Additionally, Zn+2 and Mn+2 levels were also dropped in the tolerant roots, while Mo+2 levels were significantly higher in all tissues in both control and saline conditions for tolerant genotype. Conclusion:The results of the presented study have demonstrated the differences in contrasting genotypes and thus provide valuable information on the pivotal molecular mechanisms underlying salt tolerance mainly in common bean, but for all crops.
2020-11-20 | GSE156113 | GEO
Project description:Drought is a major limiting constraint to faba bean production worldwide, including Tunisia. However, molecular mechanisms underlying faba bean responses to drought stress are not well understood. In this context, transcriptome analysis by RNA-seq was performed to investigate drought-related genes and construct a network of faba bean drought stress response and tolerance. De novo assembly of the transcriptome generated 26,728 differentially expressed genes (DEGs). Of these, 13,920 were up-regulated and 12,808 down-regulated in faba bean drought-stressed leaves. Moreover, a total of 10,800 simple sequence repeats (SSRs) and 2130 transcription factors involved in major metabolic pathways including abscisic acid (ABA)-dependent and -independent signaling pathway were identified. GO, KOG and KEGG enrichment analyses revealed that these DEGs were involved in several important processes including photosynthesis, flavonoid biosynthesis, response to stimulus and abiotic stress, reactive oxygen species (ROS) scavengers, signal transduction, biosynthesis of secondary metabolites and transporters, suggesting the involvement of these important pathways in faba bean response to water deficit. Various stress proteins such as late embryogenesis abundant proteins (LEA), dehydrins (DHNs) and heat shock proteins (HSPs) have been identified and their expression was robustly upregulated in drought-stressed leaves, indicating their key contribution to drought response and adaptation by conferring protection and providing stability to faba bean plant cellular processes under water deficit. The reliability of the RNA-seq results was confirmed by the analysis of 10 randomly selected genes using qRT-PCR. Taken together, these findings help advancing our knowledge and can guide breeding programs aimed at improving the tolerance of faba bean to drought stress.
2025-03-31 | GSE292422 | GEO
Project description:Drought is one of the most critical factors limiting legume crop productivity. Understanding the molecular mechanisms of drought tolerance in the common bean is required to improve the yields of this important crop under adverse conditions. In this work, RNA-seq analysis was performed to compare the transcriptome profiles of drought-stressed and well-irrigated plants of a previously characterized drought-tolerant common bean landrace. The analysis revealed responses related with the abscisic acid signaling, including downregulation of a phosphatase 2C (PP2C) and an abscisic acid-8' hydroxylase, and upregulation of several key transcription factors and genes involved in cell wall remodeling, synthesis of osmoprotectants, protection of photosynthetic apparatus, and downregulation of genes involved in cell expansion. The results also highlighted a significant proportion of differentially expressed genes related to phosphate starvation response. In addition, the moderate detrimental effects of drought in the biomass of these tolerant plants were abolished by the addition of phosphate, thus indicating that, besides the ABA-mediated response, acquisition of phosphate could be crucial for the drought tolerance of this common bean genotype. These results provided information about the mechanisms involved in drought response of common bean response that could be useful for enhancing the drought tolerance of this important crop legume.
| S-EPMC7238123 | biostudies-literature
Project description:Common bean viruses Metagenomic assembly
| PRJNA1226238 | ENA
Project description:Common bean (Phaseolus vulgaris L.) is a leguminous in high demand for human nutrition and a very important agricultural product. Production of common bean is constrained by environmental stresses such as drought. Although conventional plant selection has been used to increase production yield and stress tolerance, drought tolerance selection based on phenotype is complicated by associated physiological, anatomical, cellular, biochemical, and molecular changes. These changes are modulated by differential gene expression. A common method to identify genes associated with phenotypes of interest is the characterization of Single Nucleotide Polymorphims (SNPs) to link them to specific functions. In this work, we selected two drought-tolerant parental lines from Mesoamerica, Pinto Villa, and Pinto Saltillo. The parental lines were used to generate a population of 282 families (F3:5) and characterized by 169 SNPs. We associated the segregation of the molecular markers in our population with phenotypes including flowering time, physiological maturity, reproductive period, plant, seed and total biomass, reuse index, seed yield, weight of 100 seeds, and harvest index in three cultivation cycles. We observed 83 SNPs with significant association (p < 0.0003 after Bonferroni correction) with our quantified phenotypes. Phenotypes most associated were days to flowering and seed biomass with 58 and 44 associated SNPs, respectively. Thirty-seven out of the 83 SNPs were annotated to a gene with a potential function related to drought tolerance or relevant molecular/biochemical functions. Some SNPs such as SNP28 and SNP128 are related to starch biosynthesis, a common osmotic protector; and SNP18 is related to proline biosynthesis, another well-known osmotic protector.
| S-EPMC4508514 | biostudies-literature
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:Complete genome sequence of bean common mosaic virus from black bean in Vietnam
| PRJDB16961 | ENA