Drought tolerance mechanisms in chickpea studied through transcriptomic analysis
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ABSTRACT:
PROVIDER: PRJEB62862 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR11526165_1.fastq.gz | Fastqsanger.gz | |||
| ERR11526165_2.fastq.gz | Fastqsanger.gz | |||
| ERR11526166_1.fastq.gz | Fastqsanger.gz | |||
| ERR11526166_2.fastq.gz | Fastqsanger.gz | |||
| ERR11526167_1.fastq.gz | Fastqsanger.gz |
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Project description:In order to identify genes and pathways involved in drought tolerance, RNA was isolated from control and 15-days drought-stressed chickpea plants. Two chickpea genotypes, Desi PI598080 (“D”) and Kabuli Flip07 318C (“K”), respectively sensitive and tolerant to drought stresses were used. The 12 extracted RNAs (2 genotypes x 2 water regimes x 3 biological replicates) were sequenced, and the transcriptomic changes between the genotypes and water conditions were analysed. The genotype with higher drought sensitivity showed a generally higher change of gene transcripts than the genotype with less sensitivity, upregulating genes involved in photophosphorylation process (transferases, oxygen lyases and oxidoreductases), hormones (brassinosteroids, abscissic acid and gibberellin response), solute transporters, nutrient uptake and cell wall properties (cellulose synthases, hemicellulose synthases, poligalacturonases, pectate lyases). These results will be helpful for further studies aiming at identifying genes and molecular markers to develop chickpea cultivars resilient to water stress.
2023-09-03 | E-MTAB-13037 | biostudies-arrayexpress
Project description:In this study, we aim to present a global view of transcriptome dynamics during drought stress in different chickpea genotypes. We generated about 800 million high-quality reads from 14 libraries (control and stress samples for two chickpea genotypes for drought stress at two developmental stages) using Illumina high-throughput sequencing platform. We mapped the reads to the kabuli chickpea genome for estimation of their transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample for each genotype.
2016-07-08 | GSE70274 | GEO
Project description:In this study, to obtain a clear picture of drought mechanism involved in two distinctive chickpea genotype, the aim was to identify the DNA methylation patterns which potentially regulate drought tolerance/sensitivity of these selected genotypes. The leaf tissues from the shoot apical meristem from drought sensitive and drought tolerant genotypes were used for RRBS (Reduced representation bisulphite sequencing) under drought stress. The sequencing data was analysed using Bismark and methylkit to recall the methylation levels in control and samples for both genotypes and identify differentially methylated regions.
2021-12-01 | GSE129110 | GEO
Project description:Background Drought is the major constraint to increase yield in chickpea (Cicer arietinum). Improving drought tolerance is therefore of outmost importance for breeding. However, the complexity of the trait allowed only marginal progress. A solution to the current stagnation is expected from innovative molecular tools such as transcriptome analyses providing insight into stress-related gene activity and, combined with molecular markers and expression (e)QTL mapping, may accelerate knowledge-based breeding. SuperSAGE, an improved version of the serial analysis of gene expression (SAGE) technique, currently is the most advanced tool for transcriptome analysis. SuperSAGE generates genome-wide, high-quality transcription profiles from any eukaryote. The method produces 26bp long fragments (SuperTags26bp tags) from defined positions in cDNAs, providing sufficient sequence information to unambiguously characterize the mRNAs. Further, SuperSAGE Tags may be immediately used to produce so called SuperTag microarrays and probes for real-time-PCR thereby overcoming the lack of genomic tools in non-model organisms. Results We applied SuperSAGE to the analysis of gene expression in chickpea roots in response to drought. To this end, we sequenced 80,238 26bp SuperTtags representing 17,493 unique transcripts (UniTags) from drought-stressed and non-stressed control roots. A total of 7,532 (43%) UniTags were more than 2.7-fold differentially expressed , and 880 (5.0%) were regulated more than 8-fold upon stress. Their large size enabled the unambiguous annotation of 2,798 (16.3%) UniTags to genes or proteins in public data bases and thus to stress-response processes. We designed a microSuperTag array carrying 3,000 of these SuperTags26bp tags. The chip data confirmed the SuperSAGE results in 79 % of cases whereas RT-PCR confirmed the SuperSAGE data in all cases. Conclusions This study represents the most comprehensive analysis of the drought-response transcriptome of chickpea available to date. It demonstrates that - inter alias - signal transduction, transcription regulation, osmolyte accumulation, chromosome organization, and ROS scavenging undergo strong transcriptional remodelling in chickpea roots already 6h after drought stress. Certain transcript isoforms characterizing these processes are potential targets for breeding for drought tolerance. We demonstrate that these can be easily accessed by micro-arrays and RT-PCR assays readily produced downstream of SuperSAGE. Our study proves that SuperSAGE has a good potential is best suited for molecular breeding also in non-model crops.
2008-09-26 | GSE12812 | GEO
Project description:RNA sequencing of leaf tissues from two contrasting chickpea genotypes reveals mechanisms for drought tolerance
| PRJNA413294 | ENA
Project description:This study was aimed to deal with a comparative proteome analysis of the two chickpea genotypes with contrasting response to drought stress, ICC 4958 (drought-tolerant, DT) and ICC 1882 (drought-sensitive, DS). Proteins were extracted from the root tissues collected from the control and drought stressed plants of both the genotypes. NanoLC-MS/MS analysis of the protein sample was performed using EASY-nLC 1000 system for the separation and identification of peptides/proteins. This study provided a mechanistic insight of drought stress tolerance in chickpea.
2023-07-20 | PXD041434 | Pride
Project description:Chickpea (Cicer arietinum) is the third largest legume grown worldwide and are prone to drought and various pathogen infections. These stresses often occur concurrently in the field conditions. Previous studies in other plant species indicated that plant senses concurrently occurring stresses as new state of stress however, the molecular events in response to that is largely unknown. In the present study, we studied the transcriptome changes in chickpea plants exposed to combination of drought stress and a potential wilt pathogen, Ralstonia solanacearum by microarray analysis. Chickpea plants were exposed to short duration individual drought (SD-drought, soil field capacity, FC-35%), long duration individual drought (LD-drought, FC-30%), short duration individual pathogen stress (SD-pathogen = 2 days pathogen infection), long duration individual pathogen stress (LD-pathogen = 4 days of infection) and short duration and long duration combined stress, SD-combined = 2 days of pathogen infection with progressive drought (FC-40% to FC- 35%), LD combined = 4 days of pathogen infection with progressive drought (FC-35% to 30%).Transcriptome analysis for the leaf samples from above treatment were done by microarray analysis using Agilent ChickpeaGXP_8X60K chip. Result indicated presence of specific molecular events and also some common but tailored events in response to combined stress. Global transcriptional analysis in chickpea leaves exposed to individual and combined drought stress and Ralstonia solanacearum infection.
2017-06-13 | GSE89228 | GEO
Project description:Chickpea (Cicer arietinum L.) is an important pulse crop grown mainly in the arid and semi-arid regions. Due to its taxonomic proximity with the model legume Medicago truncatula and its ability to grow in arid soil, chickpea has its unique advantage to understand how plant responds to drought stress. This microarray was used for analyze the transcriptomic profiles of unigenes in leaf and root of chickpea seedling under drought stress, respectively. Microarray data showed that 4805 differentially expressed unigenes were either greater than 2 fold up- or less than 0.5 fold down-regulated in at least one of the 5 time points during drought stress. 2003 and 3488 unigenes were time-dependent differentially expressed in root and leaf, respectively. 110 pathways in two tissues were found to respond to drought stress. Compared to control, 88 and 52 unigenes were expressed only in drought-stressed root and leaf, respectively, while nine genes were expressed in both tissues. 2484 function-unknown unigenes were found to be remarkably regulated by drought stress. The expression profiles of these time-dependent differentially expressed unigenes were useful in furthering our knowledge of the drought tolerance mechanism of plant.
2024-11-30 | GSE25705 | GEO
Project description:In this study, the leaf tissue from shoots apical meristem stage of drought tolerant (ICC8261) and drought sensitive (ICC283) genotypes were analyzed using RNA sequencing to identify genes/pathways associated with drought tolerance/sensitivity in the both genotypes. It was observed that genes related to ethylene response, MYB-related protein, xyloglucan endotransglycosylase, alkane hydroxylase MAH-like, BON-1 associated, peroxidase 3, cysteine rich and transmembrane domain, vignain and mitochondrial uncoupling were specifically up-regulated in the tolerant genotype whereas, same genes were down-regulated in sensitive genotype.
2018-12-31 | GSE104609 | GEO
Project description:Drought is one of the major constraints for crop productivity across the globe. Chickpea (Cicer arietinum L.) is mainly cultivated in the arid and semi-arid tropical regions under rain-fed conditions and drought stress is one of the major constraints, which causes up to 50% yield losses annually. In this study, transcriptomics, proteomics and metabolomics datasets from root tissues of contrasting drought responsive chickpea genotypes, ICC 4958 (drought-tolerant), JG 11 (drought-tolerant); an introgression line, JG 11+ (drought-tolerant) and ICC 1882, (drought-sensitive) under control and stress conditions were generated. The integrated analysis of these multi-omics data revealed complex molecular mechanism underlying drought stress response in chickpea. Transcriptomics integrated with proteomics data identified enhancement of hub proteins encoding isoflavone 4’-O-methyltransferase (Ca_06356), UDP-D-glucose/UDP-D-Galactose 4-epimerase (Ca_15037) and delta-1-pyrroline-5-carboxylate synthesis (Ca_24241). These proteins highlighted the involvement of critical pathways such as antibiotic biosynthesis, galactose metabolism and isoflavonoid biosynthesis in activating drought stress response mechanism. Subsequently, integration of metabolomics data identified six key metabolites (fructose, galactose, glucose, myo-inositol, galactinol and raffinose) that showed enhanced correlation with galactose metabolism. Further, integration of root -omics data together with genomic dataset of the “QTL-hotspot” region harbouring several drought tolerance related traits revealed involvement of candidate genes encoding aldo keto reductase family oxidoreductase (Ca_04551) and leucine rich repeat extensin 2 (Ca_04564). These results from integrated multi-omics approach provided a comprehensive understanding and new insights into the drought stress response mechanism of chickpea.
2023-08-23 | PXD027033 | Pride