Differential Regulation of Genes Involved in Root Morphogenesis and Cell Wall Modification is Associated with Salinity Tolerance in Chickpea
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ABSTRACT:
PROVIDER: PRJNA432923 | ENA |
REPOSITORIES: ENA
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Project description: Not available
| S-EPMC5859185 | biostudies-literature
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: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 salinity stress in different chickpea genotypes. We generated about 600 million high-quality reads from 16 libraries (control and stress samples for two chickpea genotypes for salinity 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 | GSE70377 | GEO
Project description:In this study, we have identified small RNA during salinity stress response in chickpea. Small RNA library was prepared and sequencing was performed using Illumina platform. A total of 79 million reads were generated. These reads were mapped to the chickpea genome using Bowtie.
2023-02-15 | GSE204728 | GEO
Project description:Bisulphite sequencing of salinity sensitive and salinity tolerant chickpea genotypes during salinity stress response using Illumina platform has been performed. At least 195 million reads in bisulphite sequencing were generated in each sample. Methylated cytosines in each sample were identified for their genomic location and sequence context.
2023-02-15 | GSE204729 | GEO
Project description:In this study, we performed transcriptomic analysis salinity stress response in salinity sensitive and tolerant genotypes of chickpea using Illumina platform. A total of 87 million reads in RNA-sequencing data were generated in all the samples. Mapping of the reads to the Kabuli genome was performed using tophat (v2.1.1). Differentially expressed genes were identified using cufflilnks-cuffdiff (2.2.1) pipeline.
2023-02-15 | GSE204727 | GEO
Project description:ETTIN (ETT) encodes a member of the Auxin Response Factor (ARF) family of transcription factors. The gynoecia of strong ett mutants show a partial breakdown in abaxial-adaxial (internal -external) polarity, and a shift in tissue boundaries along the apico-basal axis of the gynoecium. This latter effect increases the size of the stigma, style and stipe in ett mutants at the expense of ovary tissue. Among the putative direct targets of ETT, we found several genes encoding either pectin methylesterases (PMEs) or their inhibitors. PMEs may function to increase the extensibility of the cell wall and thus contribute directly to cellular growth. The identification of genes encoding PMEs and related molecules as direct targets of ETT therefore suggests this factor to be situated near the end of a hierarchy of genetic regulation acting on growth through cell wall modification. Other putative direct targets of ETT encode two members of the Aux/IAA protein family, which have been found to negatively regulate ARFs as an inverse function of auxin concentration. ETT lacks the protein domains, present in most ARFs, that are necessary for negative regulation by Aux/IAA proteins and its own activity should not therefore be subject to regulation by auxin concentration. However, the regulation of two Aux/IAA proteins by ETT may represent an input of this protein into an auxin-regulated network involving other ARFs.
2021-03-05 | GSE14660 | GEO
Project description:In this study, we aim to present a global view of transcriptome dynamics during flower development in chickpea. We generated around 234 million high-quality reads for eight flower development stages (ranging from 16 to 40 million reads for each stage) and 91 million high-quality reads from three vegetative tissues using Illumina high-throughput sequencing GAII platform. Because of non-availability of reference genome sequence, we mapped the reads to chickpea transcriptome comprised of 34,760 transcripts for estimation of their transcriptional activity in different tissue samples. The transcriptome dynamics was studied by comparison of gene expression during flower development stages with vegetative tissues. We collected different tissue samples used in this study and total RNA isolated was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to 34760 chickpea transcripts and reads per kilobase per million (RPKM) was calculated for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using DESeq software. The genes preferentially expression during various stages of flower development as compared to vegetative stages and those with speciifc expression were identified.
2014-01-09 | E-GEOD-42679 | biostudies-arrayexpress
Project description:The total RNA were extracted from pooled tissues of leaves and flowers from several plants of chickpea (Cicer arietinum) using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Then small RNAs ranging in 18–30 nucleotides were size fractionated electrophoretically, isolated from the gel, ligated with the 5′ and 3′ RNA adapters. The ligated product was reverse transcribed and subsequently amplified using 10–12 PCR cycles. The purified PCR product was sequenced using Illumina Genome Analyzer II. The qualified reads were used to predict microRNAs and phased small interfering RNAs from chickpea. Identification of microRNAs and phased small inferfering RNAs in chickpea (Cicer arietinum) by analyzing small RNA sequencing profiles of leaves and flowers using Illumina GAII.
2015-05-08 | E-GEOD-62216 | biostudies-arrayexpress