Stress responsive gene expression in rice cultivars
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ABSTRACT:
ORGANISM(S): Oryza sativa
SUBMITTER: Mukesh Jain
PROVIDER: E-GEOD-60287 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2015-12-31 | E-GEOD-60288 | biostudies-arrayexpress
Project description:In this study, we aim to present a global view of transcriptome dynamics during various abiotic stresses in chickpea. We generated about 252 million high-quality reads from eight libraries (control, desiccation, salinity and cold stress samples for roots and shoots) using Illumina high-throughput sequencing GAII platform. We mapped the reads to the desi 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. We collected different tissue samples (root and shoot tissues of 10-day-old seedlings subjected to control (kept in water), desiccation (transferred on folds of tissue paper), salinity (transferred to beaker containing 150 mM NaCl solution) and cold (kept in water at 4 M-BM-1 1M-BM-0C) stress for 5 h. Total RNA isolated from these tissue samples 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 annotated chickpea genome using TopHat and fragments per exon kilobase per million (FPKM) was calculated using Cufflinks software for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using Cuffdiff software. The differentially expressed genes during various abiotic stress conditions were identified.
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Project description:In this study, we sequenced small RNA content from three different rice cultivars employing Illumina technology. More than 15 million reads were generated using Illumina high-throughput sequencing platform. After pre-processing, distinct small RNA sequences were identified for each rice cultivars. We collected seedlings of different rice cultivars 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 pre-processed using modified perl script provided in the miRTools software. After quality control, the identical reads were collapsed into a unique read and read count for each sequence was recorded. All the filtered unique reads from each sample were mapped on the rice genome to find their location.
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Project description:In this study, we aim to present a global view of transcriptome dynamics in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. More than 50 million high quality reads were obtained for each tissue sample using Illumina platform. Reference-based assembly was performed for each rice cultivar. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample.
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Project description:In this study, we aim to generate genome-scale DNA methylation profiles at single-base resolution in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. Using high-throughput whole genome bisulfite Sequencing, we generated DNA methylation maps covering the vast majority of cytosines in the rice genome. More than 152 million high quality reads were obtained for each tissue sample using Illumina platform. We discovered extensive DNA methylation in rice cultivars, identified the context and level of methylation at each site.Numerous differentially methylated regions (DMRs) among different cultivars under control and stress conditions were identified and many of them were associated with differential gene expression. The high resolution methylome maps of different rice genotypes and differentially methylated regions will serve as reference for understanding the epigenetic regulation of stress responses in plants.
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2015-11-02 | E-GEOD-58603 | biostudies-arrayexpress
Project description:Oilseed mustard, Brassica juncea, exhibits high levels of genetic variability for salinity tolerance. To obtain the global view of transcriptome and investigate the molecular basis of salinity tolerance in a salt-tolerant variety CS52 of B. juncea, we performed transcriptome sequencing of control and salt-stressed seedlings. De novo assembly of 184 million high-quality paired-end reads yielded 42,327 unique transcripts longer than 300 bp with RPKM ≥1. When compared with non-redundant proteins, we could annotate 67% unigenes obtained in our study. Based on the mapping to expressed sequence tags (ESTs), 52.6% unigenes are novel compared to EST data available for B. juncea and constituent genomes. Differential expression analysis revealed altered expression of 1469 unigenes in response to salinity stress. Of these, 587, mainly associated with ROS detoxification, sulfur assimilation and calcium signaling pathways, are up regulated. Notable of these is RSA1 (SHORT ROOT IN SALT MEDIUM 1) INTERACTING TRANSCRIPTION FACTOR 1 (RITF1) homolog up regulated by >100 folds in response to stress. RITF1, encoding a bHLH transcription factor, is a positive regulator of SOS1 and several key genes involved in scavenging of salt stress-induced reactive oxygen species (ROS). Further, we performed comparative expression profiling of key genes implicated in ion homeostasis and sequestration (SOS1, SOS2, SOS3, ENH1, NHX1), calcium sensing pathway (RITF1) and ROS detoxification in contrasting cultivars, B. juncea and B. nigra, for salinity tolerance. The results revealed higher transcript accumulation of most of these genes in B. juncea var. CS52 compared to salt-sensitive cultivar even under normal growth conditions. Together, these findings reveal key pathways and signaling components that contribute to salinity tolerance in B. juncea var. CS52. We report transcriptome sequencing of two-weeks-old seedlings of B. juncea var. CS52 under normal growth conditions (CTRL) and in response to salinity stress (SS) using Illumina paired-end sequencing
2015-02-28 | E-GEOD-66389 | biostudies-arrayexpress
Project description:Rice has developed several morphological and physiological strategies to adapt to phosphate starvation stress. In order to elucidate the molecular bases of response due to phosphate stress particularly the transcriptional profile of genotypes with variation in tolerance to phosphate starvation, we analyzed the gene expression profiles of 3 japonica rice cultivars and an indica cultivar with different levels of tolerance to phosphate starvation using the RNA-Seq method. We constructed a total of 48 libraries corresponding to root and shoot of the 4 cultivars for control (0 d) and âP treatment (22 d) with three biological replicates for root and shoot samples in each cultivar. Approximately 254 million sequenced tags were mapped onto the reference rice genome sequence (IRGSP1.0) and an average of about 5,000 transcripts in each genotype were found to be responsive to Pi-starvation. Comparative analysis of the responsive transcripts revealed an overall similarity in the transcriptome signatures resulting from phosphate starvation as well as distinct differences that distinguish the degree of tolerance among the 4 cultivars. We elucidated a set of core responsive transcripts commonly expressed in both root and shoot with different levels of expression reflecting variation as well genotype specificity in tolerance to Pi-starvation. De novo assembly of unmapped reads generated a large set of sequence assemblies that represent potential new transcripts that may be involved in tolerance to phosphate deficiency. Characterization of 88 assemblies unaligned in the reference genome revealed several dozen transcripts which correspond to plant ESTs. This study provides an overview of the diversity in response to P-starvation stress that can be used to identify the major genes for improving Pi acquisition and utilization in rice and other cereal crops. Note: Samples in DRA were assigned the same sample accession. This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original DRA sample accessions.
2014-05-23 | E-MTAB-4465 | biostudies-arrayexpress
Project description:The approval of genetically modified (GM) crops is preceded by years of intensive research to demonstrate safety to humans and environment. We recently showed that in vitro culture stress is the major factor influencing proteomic differences of GM vs. non-GM plants. This made us question the number of generations needed to erase such memory. We also wondered about the relevance of alterations promoted by transgenesis as compared to environment-induced ones. Here we followed three rice lines (1-control- C, 1-transgenic- Ta and 1-negative segregant- NSb) throughout eight generations after transgenesis, and further analyzed their response to salinity stress on the F6 generation. Three pools of 10 whole fifteen days-old rice seedlings (Oryza sativa L. ssp. japonica cv. Nipponbare) were selected from each line at F4, F6 and F8 generations. Because salinity stress was imposed on half of the seedlings (C, Ta and NSb) in F6 generation, from this generation onwards we worked with six rice lines (C, Csalt, Ta, Tasalt, NSb, NSbsalt).
2016-08-03 | E-GEOD-85113 | biostudies-arrayexpress
Project description:Purpose: understanding the complex genetic control of heat tolerance can be reached using whole transcriptome sequencing (RNA-seq) that is currently the most powerful tool to identify genes differentially regulated. Heat responses differ greatly between sensitive and tolerant genotypes, mainly in terms of the amount of genes and pathways involved in the response and differences in the expression level of constitutive genes in many pathways. The present study aims to compare the molecular response of Brazilian flooded rice cultivars with variable sensitivity to heat stress at anthesis stage and to discuss the possible processes involved in heat tolerance. Methods: Panicle mRNA profiles of cultivars IRGA 428 (sensitive) and BR-IRGA 409 (tolerant) were generated by deep sequencing, in triplicate (each replicate is composed of two plants), under three days of heat stress and control condition at anthesis stage, using Illumina Hiseq 2500. The sequence reads from each sample that passed quality filters were mapped independently, generating contigs that were aligned with the reference genome sequences in rice (cv. MH63-indica). The transcripts were analyzed at the expression level with statistic test (EdgeR – Rstudio) to identify the significant changes in the expression level of the genes for each treatment condition and cultivar follow by identification of metabolic pathways (MapMan and Cytoscape) based on different programs. Results: Using an optimized data analysis workflow, we identified 16,871 transcripts in the rice spikelet of sensitive and tolerant cultivars with HISAT workflow. Using filtered and aligned reads, transcript levels were used to find differentially expressed genes (DEGs) at different thermal condition and cultivars. We identified 2,064 genes for BR-IRGA 409 and 1,078 genes for IRGA 428 that showed a significant change in expression in response to heat stress (LogFC ≥0.5 and adjusted p-value <0.001). When it was examined the multi-factor responsive genes, that is genes with an interaction between cultivar and heat stress (multi-factor analysis - cultivars vs control and high temperature), it was identified 65 DEGs in response to heat stress (LogFC ≥0.5 and adjusted p-value <0.001). Comparison of our data set with other RNA-seq studies shows a significant overlap in heat responsive genes (hypergeometric enrichment test). This core set of genes common among RNA-seq studies indicates that it may be associated with basal response to heat. In the present study, genes related to light reaction pathway were induced in the panicle of the cultivar IRGA 428, while these genes in cultivar BR-IRGA 409 were already expressed highly in control conditions. The basal level of these genes in BR-IRGA 409 was as high as the heat-induced level in the sensitive IRGA 428. Photosynthesis is known to occur in rice panicles, but little has been reported about the photosynthetic characteristics of such panicles. To cope with heat stress, plants have developed a sophisticated mechanism to repair photosystem damage. Therefore, in IRGA 428 the induction of these genes suggests the activation of a repair mechanism to reverse damage on the photosynthetic apparatus caused by the heat stress. The difference in basal levels of the photosynthetic genes may be a contributing factor to the differences in spikelet fertility between the cultivars under heat stress. Conclusion: This is the first study to evaluate the heat tolerance of Brazilian rice cultivars. In panicle tissue, most canonical heat responsive genes, such as HSF family, small HSP family and FKBP family, show a similar response in both Brazilian cultivars, despite the fact that these cultivars have not been specifically selected for heat tolerance. The response of photosynthetic genes to heat stress is a major difference between the cultivars BR-IRGA 409 and IRGA 428. This study indicates that the higher basal expression of photosynthetic genes in the panicle provides improved spikelet fertility under heat stress. This may provide potential markers that can be used to identify heat tolerant genotypes among rice breeding programs. This study emphasizes that the characterization of heat stress responses in individual cultivars provides insights into both the basic mechanisms of heat response and assists with understanding the complex phenomenon of responses to high temperature stress.
2018-08-29 | GSE119109 | GEO