Dataset Information

Analysis of gene expression in response to water deficit of chickpea (Cicer arietinum L.) varieties differing in drought tolerance.

ABSTRACT: BACKGROUND: Chickpea (C. arietinum L.) ranks third in food legume crop production in the world. However, drought poses a serious threat to chickpea production, and development of drought-resistant varieties is a necessity. Unfortunately, cultivated chickpea has a high morphological but narrow genetic diversity, and understanding the genetic processes of this plant is hindered by the fact that the chickpea genome has not yet been sequenced and its EST resources are limited. In this study, two chickpea varieties having contrasting levels of drought-tolerance were analyzed for differences in transcript profiling during drought stress treatment by withdrawal of irrigation at different time points. Transcript profiles of ESTs derived from subtractive cDNA libraries constructed with RNA from whole seedlings of both varieties were analyzed at different stages of stress treatment. RESULTS: A series of comparisons of transcript abundance between two varieties at different time points were made. 319 unique ESTs available from different libraries were categorized into eleven clusters according to their comparative expression profiles. Expression analysis revealed that 70% of the ESTs were more than two fold abundant in the tolerant cultivar at any point of the stress treatment of which expression of 33% ESTs were more than two fold high even under the control condition. 53 ESTs that displayed very high fold relative expression in the tolerant variety were screened for further analysis. These ESTs were clustered in four groups according to their expression patterns. CONCLUSIONS: Annotation of the highly expressed ESTs in the tolerant cultivar predicted that most of them encoded proteins involved in cellular organization, protein metabolism, signal transduction, and transcription. Results from this study may help in targeting useful genes for improving drought tolerance in chickpea.

SUBMITTER: Jain D

PROVIDER: S-EPMC2831037 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Analysis of gene expression in response to water deficit of chickpea (Cicer arietinum L.) varieties differing in drought tolerance.

Jain Deepti D Chattopadhyay Debasis D

BMC plant biology 20100209

<h4>Background</h4>Chickpea (C. arietinum L.) ranks third in food legume crop production in the world. However, drought poses a serious threat to chickpea production, and development of drought-resistant varieties is a necessity. Unfortunately, cultivated chickpea has a high morphological but narrow genetic diversity, and understanding the genetic processes of this plant is hindered by the fact that the chickpea genome has not yet been sequenced and its EST resources are limited. In this study, ...[more]

PMID: 20144227

Similar Datasets

Project description:BackgroundChickpea (Cicer arietinum L.) is the second most widely grown pulse and drought (limiting water) is one of the major constraints leading to about 40-50% yield losses annually. Dehydration responsive element binding proteins (DREBs) are important plant transcription factors that regulate the expression of many stress-inducible genes and play a critical role in improving the abiotic stress tolerance. Transgenic chickpea lines harbouring transcription factor, Dehydration Responsive Element-Binding protein 1A from Arabidopsis thaliana (AtDREB1a gene) driven by stress inducible promoter rd29a were developed, with the intent of enhancing drought tolerance in chickpea. Performance of the progenies of one transgenic event and control were assessed based on key physiological traits imparting drought tolerance such as plant water relation characteristics, chlorophyll retention, photosynthesis, membrane stability and water use efficiency under water stressed conditions.ResultsFour transgenic chickpea lines harbouring stress inducible AtDREB1a were generated with transformation efficiency of 0.1%. The integration, transmission and regulated expression were confirmed by Polymerase Chain Reaction (PCR), Southern Blot hybridization and Reverse Transcriptase polymerase chain reaction (RT-PCR), respectively. Transgenic chickpea lines exhibited higher relative water content, longer chlorophyll retention capacity and higher osmotic adjustment under severe drought stress (stress level 4), as compared to control. The enhanced drought tolerance in transgenic chickpea lines were also manifested by undeterred photosynthesis involving enhanced quantum yield of PSII, electron transport rate at saturated irradiance levels and maintaining higher relative water content in leaves under relatively severe soil water deficit. Further, lower values of carbon isotope discrimination in some transgenic chickpea lines indicated higher water use efficiency. Transgenic chickpea lines exhibiting better OA resulted in higher seed yield, with progressive increase in water stress, as compared to control.ConclusionsBased on precise phenotyping, involving non-invasive chlorophyll fluorescence imaging, carbon isotope discrimination, osmotic adjustment, higher chlorophyll retention and membrane stability index, it can be concluded that AtDREB1a transgenic chickpea lines were better adapted to water deficit by modifying important physiological traits. The selected transgenic chickpea event would be a valuable resource that can be used in pre-breeding or directly in varietal development programs for enhanced drought tolerance under parched conditions.

Project description:Elucidation of the genetic basis of drought tolerance is vital for genomics-assisted breeding of drought tolerant crop varieties. Here, we used genotyping-by-sequencing (GBS) to identify single nucleotide polymorphisms (SNPs) in recombinant inbred lines (RILs) derived from a cross between a drought tolerant chickpea variety, Pusa 362 and a drought sensitive variety, SBD 377. The GBS identified a total of 35,502 SNPs and subsequent filtering of these resulted in 3237 high-quality SNPs included in the eight linkage groups. Fifty-one percent of these SNPs were located in the genic regions distributed throughout the genome. The high density linkage map has total map length of 1069 cm with an average marker interval of 0.33 cm. The linkage map was used to identify 9 robust and consistent QTLs for four drought related traits viz. membrane stability index, relative water content, seed weight and yield under drought, with percent variance explained within the range of 6.29%-90.68% and LOD scores of 2.64 to 6.38, which were located on five of the eight linkage groups. A genomic region on LG 7 harbors quantitative trait loci (QTLs) explaining > 90% phenotypic variance for membrane stability index, and > 10% PVE for yield. This study also provides the first report of major QTLs for physiological traits such as membrane stability index and relative water content for drought stress in chickpea. A total of 369 putative candidate genes were identified in the 6.6 Mb genomic region spanning these QTLs. In-silico expression profiling based on the available transcriptome data revealed that 326 of these genes were differentially expressed under drought stress. KEGG analysis resulted in reduction of candidate genes from 369 to 99, revealing enrichment in various signaling pathways. Haplotype analysis confirmed 5 QTLs among the initially identified 9 QTLs. Two QTLs, qRWC1.1 and qYLD7.1, were chosen based on high SNP density. Candidate gene-based analysis revealed distinct haplotypes in qYLD7.1 associated with significant phenotypic differences, potentially linked to pathways for secondary metabolite biosynthesis. These identified candidate genes bolster defenses through flavonoids and phenylalanine-derived compounds, aiding UV protection, pathogen resistance, and plant structure.The study provides novel genomic regions and candidate genes which can be utilized in genomics-assisted breeding of superior drought tolerant chickpea cultivars.

Project description:Chickpea is the second most important legume crop largely grown under semi-arid tropics where terminal drought is one of the major constraints for its productivity. A trait-based selection had been considered more beneficial in drought tolerance breeding to overcome the environmental influence on drought yields. Large number of traits had been suggested in literature, with less indication on their importance and priority, for use in such breeding programs resulting in poor utilization of critical traits in drought tolerance breeding. To identify the most critical traits that contribute to grain yield under drought, 12 chickpea genotypes, with well-defined drought response, were field evaluated by sampling at regular intervals during the cropping period. Large range of variation was observed for shoot biomass productivity, specific leaf area (SLA) and leaf area index (LAI) at different days after sowings (DAS), canopy temperature depression (CTD) at mid-reproductive stages, growth duration and both morphological and analytical yield components. Grain yield under drought was closely associated with the rate of partitioning (p), crop growth rate (C), CTD, phenology, LAI at mid-pod fill stage, pod number m-2 at maturity, shoot biomass at reproductive growth stages and SLA at physiological maturity. The shoot trait(s) were prioritized based on their significance and contribution to drought tolerance. The trait(s) that conferred tolerance varied across genotypes. The order of traits/plant functions identified as important and critical for the drought tolerance were p, C, CTD, growth duration and other related traits. Relatively less important traits were LAI, SLA at the mid reproductive stage and pod number per unit area at maturity. The traits Dr, seeds pod-1 and 100-seed weight were found to be least important. Breeding for the best combination of p and C with the right phenology was proposed to be the best selection strategy to enhance terminal drought tolerance in chickpea.

Dataset Information

Analysis of gene expression in response to water deficit of chickpea (Cicer arietinum L.) varieties differing in drought tolerance.

Publications

Analysis of gene expression in response to water deficit of chickpea (Cicer arietinum L.) varieties differing in drought tolerance.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets