RNA sequencing of leaf tissues from two contrasting chickpea genotypes reveals mechanisms for drought tolerance
Ontology highlight
ABSTRACT:
ORGANISM(S): Cicer arietinum
PROVIDER: GSE104609 | GEO | 2018/12/31
REPOSITORIES: GEO
Similar Datasets
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: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:Background: Drought stress is the major environmental stress that affects plant growth and productivity. It triggers in plants a wide range of responses detectable at different scales: molecular, biochemical and physiological levels. At the molecular level the response to drought stress results in the differential expression of several metabolic pathways. For this reason, explore the subtle differences existing in gene expression of drought sensitive and drought tolerant genotypes allows to identify drought-related genes that could be used for selection of drought tolerance traits. Genome-wide RNA-Seq technology was used to compare the drought response of two sorghum genotypes characterized by contrasting water use efficiency. Results: the physiological measurements carried out confirmed the drought sensitivity of IS20351 and the drought tolerance of IS22330 previously studied. The expression of drought-related genes was more abundant in the sensitive genotype IS20351 compared to the tolerant IS22330. The Gene Ontology enrichment highlighted a massive increase in transcript abundance in “response to stress” and “abiotic stimulus”, “oxidation-reduction reaction” in the sensitive genotype IS20351 under drought stress. “Antioxidant” and “secondary metabolism”, “photosynthesis and carbon fixation process”, “lipids” and “carbon metabolism” were the pathways most affected by drought in the sensitive genotype IS20351. The sensitive genotype IS20351 showed under well-watered conditions a lower constitutive expression level of “secondary metabolic process” (GO:0019748) and “glutathione transferase activity” (GO:000004364). Conclusions: RNA-Seq analysis revealed to be a very useful tool to explore differences between sensitive and tolerant sorghum genotypes. The transcriptomic results supported all the physiological measurements and were crucial to clarify the tolerance of the two genotypes studied. The connection between the differential gene expression and the physiological response to drought states unequivocally the drought tolerance of the genotype IS22330 and the strategy adopted to cope with drought stress.
2016-04-27 | GSE80699 | GEO
Project description:To understand the drought responsive mechanisms and the harmful effects of stress, it is necessary to develop drought tolerant genotype. In this study, drought-sensitive and -tolerant fennel genotypes were selected. Using these materials, a gel-free/label-free proteomic technique was performed to identify responsive proteins in fennel leaf under drought stress
2017-09-11 | PXD006040 | Pride
Project description:In this study, the root tissues from the salt tolerant genotype (JG 11) and the salt sensitive genotype (ICCV 2) were analyzed using RNA sequencing to identify genes/pathways associated with salt tolerance/sensitivity in the both genotypes.
2018-04-03 | GSE110127 | GEO
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:Drought stress is a major problem around the world and although progress in understanding how vegetable crops and model plants adapt to drought have been made, there is still little information about how fruit crops deal with moderate drought stress. In this study, we investigated the response of two apple genotypes: a drought-sensitive genotype (M26) and a drought-tolerant genotype (MBB). Our results of the morphology, physiology and biochemistry under moderate drought stress, indicated that relative water content (RWC) and leaf area (LA) were not significant changes in two genotypes. However, it had larger leaf mass per area (LMA), and accumulated higher free proline (CFP), soluble sugars (CSS) and malonaldehyde (MDA) in the leaves. Thus, it appears that the MBB genotype could produce more osmosis-regulating substances. Phosphoproteomic was analyzed from leaves of both genotypes under moderate drought stress using the isobaric tags for relative and absolute quantification (iTRAQ) technology. A total of 595 unique phosphopeptides, 682 phosphorylated sites and 446 phosphoproteins were quantitatively analyzed in the two genotypes. Motif analyses of the phosphorylation sites showed that six motifs including [PxsP], [sP], [sD], [Rxxs], [sxP] and [sxs] were enriched. We identified 12 and 48 PLSC phosphoproteins in M26 and MBB, respectively. Among these, 9 PLSC phosphoproteins were common to both genotypes, perhaps indicating a partial overlaps of the mechanisms to moderate drought stress. Gene ontology analyses revealed that the PLSC phosphoproteins present a unique combination of metabolism, transcription, translation and protein processing, suggesting that the response in apple to moderate drought stress encompasses a new homeostasis of major cellular processes. The basic trend was an increase in protein abundance related to drought and organic substance upon moderate drought stress between two genotypes. These increases were higher in the drought-tolerant genotype (MBB) than in the drought-sensitive genotype (M26). The 23 differentially expressed mRNA encoding phosphoproteins were analysis by quantitative real-time PCR (qRT-PCR). Our study is the first to address the phosphoproteome of a major fruit crop, apple rootstocks, in response to moderate drought stress, and provide insights into the molecular regulation mechanisms of apple rootstock under moderate drought stress.
2016-11-08 | PXD005238 | Pride
Project description:‘Pulsechip’, a boutique cDNA microarray, generated from a set of chickpea (Cicer arietinum L.) unigenes, grasspea (Lathyrus sativus L.) ESTs and lentil (Lens culinaris Med.) resistance gene analogs, was employed to generate an expression profile of chickpea accessions tolerant and susceptible to drought stress. Two groups of a tolerant and susceptible accession were challenged with drought stress. The experiments were performed in three biological replications. The experiments were conducted in reference design where respective tissues from unstressed plants served as control. The leaf and flower/bud tissues were collected and used for hybridization to measure changes in RNA abundance of treatment vs. control. The tissues from five experimental replicate plants per biological replication were pooled together (leaf and flower tissues separate) before RNA extraction. This RNA was used to prepare cDNA targets for expression analysis using microarray. The microarray had six technical replicate spots per EST. The transcript level for each EST/cDNA was firstly calculated as the average intensity of the six technical replicates and then the average intensity of three biological replicates. Data analysis included LOWESS normalization (LOcally WEighted polynomial regreSSion) to adjust for differences in quantity of initial RNA, labeling and detection efficiencies. A dye swap in one biological replicate adjusted dye bias, if any. The Differentially Expressed (DE) ESTs were identified as those with a 95% confidence interval for mean fold change (FC) that extended beyond the two-fold cut-off and also passed the Students t test (P<0.05) and FDR correction. These cut-offs translate into induced ESTs having a log2 ratio > 1 and repressed ESTs a ratio of < -1. The analysis consisted of three fold comparison. Firstly, the ESTs that were differentially expressed between treatment and control plants of each accession were detected. Then the ESTs that were similarly expressed by tolerant and susceptible accessions were then eliminated by comparison. This included a two-way comparison, where tolerant and susceptible genotypes were compared within and between groups. Lastly, ESTs that were consensually differentially expressed between tolerant and susceptible accessions of the two batches were identified. The hypothesis was that if a putative gene was consistently expressed only in tolerant or susceptible genotype for a particular stress, it might be a candidate for tolerance/susceptibility for that stress. Globally, the level of 114 transcripts was affected in response to drought stress in all the genotypes and tissue types studied. The DE transcripts in response to drought stress coded for various functional and regulatory proteins, most of which were repressed. Protein and other solute transport was repressed in susceptible-1 flowers but induced in tolerant-2 flowers, as evidenced by the induction of a protein-transport facilitation protein (DY475074) in flowers of tolerant-2 and repression of a aquaporin-like membrane channel protein (DY396334) and DNA-J like protein involved in intracellular protein transport (DY475488) in flowers of susceptible-1. Two putative auxin-repressed proteins (DY396289, DY396359) were highly repressed in flowers and leaves of tolerant-2, whilst being induced in flowers and leaves of susceptible-1. Defence-related genes including pathogenesis-related proteins (DY396305 and DY396343), nematode-resistance protein (CV793603), Cf-9 gene cluster (DY396352) and disease resistance response proteins (DY396265 and DY396276) were repressed in flowers of tolerant and susceptible genotypes. A Pea (pi230) disease resistance response protein (DY396390) and a multi-resistance protein ABC transporter (CV793605) were induced in flowers of both tolerant genotypes. Some genes involved in energy metabolism (DY396279 and DY475316) were repressed in leaves and flowers of tolerant and susceptible genotypes. Additionally, some transcripts related to senescence, including auxin responsive protein IAA9 (DY396315), senescence-associated protein DIN 1 (DY396338), and dehydration stress-induced protein (DY396321) were repressed in leaves and flowers of the tolerant genotypes. Of the 114 DE transcripts expressed in drought tolerant and susceptible genotypes, only two were consistently expressed. These included a cytosolic fructose 1,6-bisphosphatase (DY475548) and a gene with unknown function, which were repressed in flowers of both susceptible genotypes. Keywords: Chickpea, Drought stress, Tolerant, Susceptible, cDNA microarray
2007-04-03 | GSE7416 | GEO
Project description:Genome-wide Transcriptional Analysis of Genes Associated with Drought Stress in Gossypium herbaceum root This experiment was designed to investigate the molecular mechanism associated with drought tolerance in root tissue of Gossypium herbaceum. The gene expression profiles of the root tissue using Affymetrix Cotton Genome Array were compared with drought tolerant and drought sensitive genotype of G.herbaceum under drought stress and watered condition. Many genes in various molecular function or biological processes were over- or under-represented between drought tolerant and sensitive genotype, suggesting various molecular mechanism and biochemical pathways are interlinked and tolerant genotype have developed multiple mechanisms as an adaptory behavior against drought stress.
2012-03-29 | GSE36249 | GEO
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