Ontology highlight
ABSTRACT:
PROVIDER: PRJNA631585 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11747777_1.fastq.gz | Fastqsanger.gz | |||
| SRR11747777_2.fastq.gz | Fastqsanger.gz | |||
| SRR11747778_1.fastq.gz | Fastqsanger.gz | |||
| SRR11747778_2.fastq.gz | Fastqsanger.gz | |||
| SRR11747779_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose:Identification of genes and miRNAs responsible for salt tolerance in upland cotton (Gossypium hirsutum L.) would help reveal the molecular mechanisms of salt tolerance. We performed physiological experiments and transcriptome sequencing (mRNA-seq and small RNA-seq) of cotton leaves under salt stress using Illumina sequencing technology. And quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods:We investigated two distinct salt stress phases—dehydration (4 h) and ionic stress (osmotic restoration; 24 h)—that were identified by physiological changes of 14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive, during a 72-h NaCl exposure. A comparative transcriptomics approach was used to monitor gene and miRNA differential expression at two time points (4 and 24 h) in leaves of the two cotton genotypes under salinity conditions. Results:During a 24-h salt exposure, 819 transcription factor unigenes were differentially expressed in both genotypes, with 129 unigenes specifically expressed in the salt-tolerant genotype. Under salt stress, 108 conserved miRNAs from known families were differentially expressed at two time points in the salt-tolerant genotype. Conclusions:Our comprehensive transcriptome analysis has provided new insights into salt-stress response of upland cotton. The results should contribute to the development of genetically modified cotton with salt tolerance.
2017-06-18 | GSE58655 | GEO
Project description:A comparative transcriptomics approach was used as a tool to unravel gene regulatory networks underlying salinity response in olive trees by simulating as much as possible olive growing conditions in the field. Specifically, we investigated the genotype-dependent differences in the transcriptome response of two olive cultivars, a salt tolerant and a salt sensitive. A 135 day long comparative salinity experiment was conducted using one year old trees exposed to NaCl stress for 90 days followed by 45 days of post-stress period. Total RNA was extracted from the root samples after 15, 45 and 90 days of NaCl-treated and un-treated olive trees as well as after 15 and 45 days of post-treatment period and used for microarray hybridizations using a loop design. Hierarchical clustering of differentially expressed transcripts revealed two major, distinct clusters for each cultivar. Despite the limited number of probe set, transcriptional regulatory networks were constructed for the salt-tolerant and salt-sensitive cultivar. The comparison of the salt responsive transcriptional regulatory networks in olive with those reported for Arabidopsis suggests that a tree species might respond in a similar to Arabidopsis way at the transcriptome level under salinity stress.
2012-11-20 | GSE36197 | GEO
Project description:Analysis of root gene expression of salt-tolerant genotypes FL478, Pokkali and IR63731, and salt-sensitive genotype IR29 under control and salinity-stressed conditions during vegetative growth. Results provide insight into the genetic basis of salt tolerance in indica rice. Keywords: stress response
2009-07-16 | GSE14403 | GEO
Project description:Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress. This study reports the development of salt tolerant introgressed lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol QTL, and the salt-sensitive japonica elite cultivar PL12. Although the introgression of the Saltol QTL has been widely used to improve salinity tolerance, the molecular basis underlying the salinity tolerance conferred by Saltol remains poorly understood. Equally, the impact of introgressions from a Saltol donor parent on the global transcriptome of ILs is largely unknown. Here, genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASP) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL line (IL22). A total of 1,595 genes were identified in indica regions in IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes potentially contributing to salt stress tolerance were identified in indica segments of IL22. Comparative transcript profiling also revealed important transcriptional reprograming in IL22 plants both under non-stress and salt-stress conditions, indicating an impact on the transcriptome of the japonica background by the indica introgressed genes and vice versa. Interactions among indica and japonica genes would provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines.
2021-12-20 | GSE167342 | GEO
Project description:A comparative transcriptomics approach was used as a tool to unravel gene regulatory networks underlying salinity response in olive trees by simulating as much as possible olive growing conditions in the field. Specifically, we investigated the genotype-dependent differences in the transcriptome response of two olive cultivars, a salt tolerant and a salt sensitive. A 135 day long comparative salinity experiment was conducted using one year old trees exposed to NaCl stress for 90 days followed by 45 days of post-stress period. Total RNA was extracted from the root samples after 15, 45 and 90 days of NaCl-treated and un-treated olive trees as well as after 15 and 45 days of post-treatment period and used for microarray hybridizations using a loop design. Hierarchical clustering of differentially expressed transcripts revealed two major, distinct clusters for each cultivar. Despite the limited number of probe set, transcriptional regulatory networks were constructed for the salt-tolerant and salt-sensitive cultivar. The comparison of the salt responsive transcriptional regulatory networks in olive with those reported for Arabidopsis suggests that a tree species might respond in a similar to Arabidopsis way at the transcriptome level under salinity stress. Five experimental time-points were analyzed: 15days stress, 45days stress, 90days stress, 15days post-stress and 45days post-stress. In each timepoint treated and untreated (control) samples were obtained. Dye swap hybridizations and 4 biological replicates were performed for each treatment/timepoint in a loop design experimental setup. Each sample included three spot replicates.
2012-11-20 | E-GEOD-36197 | biostudies-arrayexpress
Project description:With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive Western Canadian alfalfa population grown under hydroponic saline conditions. All three populations accumulated two-fold higher sodium in roots than shoots as a function of increased electrical conductivity. At least 50% of differentially expressed genes (p < 0.05) were down-regulated in the salt-sensitive population growing under high salinity, while remaining unchanged in the saline-tolerant populations. In particular, most reduction in transcript levels in the salt-sensitive population were observed in genes specifying cell wall structural components, lipids, secondary metabolism, auxin and ethylene hormones, development, transport, signalling, heat shock, proteolysis, pathogenesis-response, abiotic stress, RNA processing, and protein metabolism. Transcript diversity for transcription factors, protein modification, and protein degradation genes was also more strongly affected in salt-tolerant CW064027 than in salt-tolerant Bridgeview and salt-sensitive Rangelander, while both saline-tolerant populations showed more substantial up-regulation in redox-related genes and B-ZIP transcripts. The report highlights the first use of bulked genotypes as replicated samples to compare the transcriptomes of obligate out-cross breeding populations in alfalfa. Three lines of Alfalfa (salt-tolerant CW064027, salt-tolerant Bridgeview, salt-sensitive Rangelander) were grown on 3 different concentrations of salt. For each cultivar-salt condition, 3 biological replicates were collected for a total of 27 samples.
2016-07-26 | E-GEOD-84825 | biostudies-arrayexpress
Project description:Expression Data of Rice Crown and Growing Point Tissue Under Salt Stress imposed during the Panicle Initiation Stage Experiment Overall Design: Rice Genotypes a sensitive japonica, m103, tolerant japonica agami, sensitive indica ir29 and tolerant indica ir63731 were used for expression anlaysis using the tissue from crown and growing point under control and salt stressed conditions at the sensitive early reproductive stage (panicel initiation).
2008-11-05 | E-GEOD-4438 | biostudies-arrayexpress
Project description:Soil salinity is a major environmental stress that restricts crop growth and yield. Here, crucial proteins and biological pathways were investigated under salt-stress and recovery conditions in Tritipyrum “Y1805” to explore its salt-tolerance mechanism. In total, 44 and 102 differentially expressed proteins (DEPs) were identified in “Y1805” under salt-stress and recovery conditions, respectively. A proteome-transcriptome-associated analysis revealed that the expression patterns of 13 and 25 DEPs were the same under salt-stress and recovery conditions, respectively. “Response to stimulus”, “antioxidant activity”, “carbohydrate metabolism”, “amino acid metabolism”, “signal transduction”, “transport and catabolism” and “biosynthesis of other secondary metabolites” were present under both conditions in “Y1805”. In addition, “energy metabolism” and “lipid metabolism” were recovery-specific pathways, while “antioxidant activity”, and “molecular function regulator” under salt-stress conditions, and “virion” and “virion part” during recovery, were “Y1805”-specific compared with the salt-sensitive wheat “Chinese Spring”. “Y1805” contained 83 specific DEPs related to salt-stress responses. The strong salt tolerance of “Y1805” could be attributed to the strengthened cell walls, reactive oxygen species scavenging, osmoregulation, phytohormone regulation, transient growth arrest, enhanced respiration, ammonium detoxification, transcriptional regulation and error information processing. These data will facilitate an understanding of the molecular mechanisms of salt tolerance and aid in the breeding of salt-tolerant wheat.
2021-12-08 | PXD026671 | Pride
Project description:To detect salt-tolerance-related miRNAs, comparative analysis of miRNA expression profiles was performed between the salt-tolerant and -sensitive cotton cultivars in control and salt-stressed conditions (treated with 300 mM NaCl for 24 h) using microRNA microarray
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