Cicer arietinum
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PROVIDER: PRJNA111119 | ENA |
REPOSITORIES: ENA
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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: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
Project description:Transcriptional response to drought stress in chickpea
| PRJNA288321 | ENA
Project description:The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE
| PRJNA136463 | ENA
Project description:Gene expression profiling of chickpea responses to drought stress
| PRJNA105513 | ENA
Project description:Transcriptome for drought tolerance mechanism in chickpea
| PRJNA738320 | ENA
Project description:Chickpea Transcriptome Atlas II - Abiotic Stress
| PRJNA232700 | ENA
Project description:Transcriptome data of chickpea under heat stress
| PRJNA748749 | ENA
Project description:Chickpea (Cicer arietinum L.) seeds are valued for their nutritional scores and limited information on the molecular mechanisms of chickpea fertilization and seed development is available. In the current work, comparative transcriptome analysis was performed on two different stages of chickpea ovules (pre- and post-fertilization) to identify key regulatory transcripts. Two-staged transcriptome sequencing was generated and over 208 million reads were mapped to quantify transcript abundance during fertilization events. Mapping to the reference genome showed that the majority (92.88%) of high-quality illumina reads were aligned to the chickpea genome. Reference-guided genome and transcriptome assembly yielded a total of 28,783 genes. Of these, 3399 genes were differentially expressed after the fertilization event. These involve up-regulated genes including LOC101500970, LOC101506539 and down-regulated genes LOC101493897, LOC101491695 and so on. Transcription factor families including UDP-glucuronyltransferase, NAC transcription factor, heat shock transcription factor, and auxin-responsive transcription factor were also found to be activated after fertilization. Activation of these genes and transcription factors results in the accumulation of carbohydrates and proteins by enhancing their trafficking and biosynthesis. Total 17 differentially expressed genes, were randomly selected for qRT-PCR for validation of transcriptome analysis and showed statistically significant correlations with the transcriptome data. Our findings provide insights into the regulatory mechanisms underlying changes in fertilized chickpea ovules. This work may come closer to a comprehensive understanding of the mechanisms that initiate developmental events in chickpea seeds.
2022-11-06 | GSE217186 | GEO
Project description:Sequencing data of chickpea drought tolerance introgression lines
| PRJNA772517 | ENA