Transcription profiling of two highly salt-tolerant wheat lines, their parental lines, and a salt-sensitive line in salt stress and control growth conditions
Ontology highlight
ABSTRACT:
ORGANISM(S): Triticum aestivum
SUBMITTER: Ivan Mott
PROVIDER: E-MEXP-971 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Transcriptional variation, also called expression level polymorphism (ELP), contributes to intra-specific phenotypic variation in many organisms. Differentially expressed transcripts are typically enriched for stress-related genes, suggesting that differences in response to the environment are a particularly common point of divergence among gentoypes. Analysis of ELPs also has been suggested as a way to assess unintended consequences of transgene introduction; however, it is important that interpretation of transcriptional changes be performed within the context of potential fitness effects. In these studies we sought to examine differential gene expression in response to salinity for two widely used Arabidopsis thaliana ecotypes, Wassilewskija (Ws) and Columbia (Col), and a single gene mutation (glabrous, gl1-1) in the Col background (Col(gl)), in relation to genetic, phenotypic, and fitness differences. Growth analyses were performed with seedlings germinated on culture media and growth chamber-grown plants carried through the full life cycle. Transcriptome analyses were performed with salt treated and control growth-chamber grown plants six days post initiation of salt stress. Ws plants had the least salt injury and highest dry matter accumulation and seed production in salt stressed conditions. ELPs among genoytypes and in response to 100 mM NaCl were enriched for genes associated with response to stress, including stress-associated transcription factors, heat shock and redox metabolism genes, and R genes. Application of salt resulted in many more transcripts up- or down-regulated in Col and Ws than in Col(gl). Many of the transcripts influenced by salt in Col were already altered in gl1-1 plants in the absence of salt, although Col(gl) plants did not show any detectable signs of stress, or effects on fecundity in the absence of salt treatment. The majority of salt-induced transcriptional changes that occurred in Ws also occurred in Col, suggesting common salt stress responses in these two ecotypes. Many more genes were affected by salt in Col than Ws, however, possibly reflecting the greater salt injury observed for Col. There was minimal overlap between the transcripts that differed for Ws and Col prior to salt treatment and those that were subsequently affected by salt stress. Thus, many genes conferring comparative salt stress tolerance in Ws likely differ from those whose expression levels are modified in response to salt stress. These studies demonstrate transcriptional variation among Arabidopsis genotypes in response to salt stress. Greater transcriptome differences did not necessarily correspond with greater genetic difference or phenotypic differences in morphology, fecundity, and resistance to salt stress. These results suggest that depending on circumstance, transcriptional changes can reflect response to injury, facilitate adaptive expression of fitness-associated traits, or allow for phenotypic buffering to minimize the impact of genetic changes. Three Arabidopsis genotypes were grown in the growth chamber in the absence and presence of salt stress. Plants from 20 days after sowing (6 days after salt treatment) were used for RNA extraction and hybridization on Affymetrix microarrays. There were two biological replicates for each genotype and salt treatment combination.
2011-08-15 | E-GEOD-16765 | biostudies-arrayexpress
Project description:Salt stress is one of the major abiotic stresses affecting the yield of ginseng (Panax ginseng C. A. Meyer). The objective of this study was to identify proteins of ginseng, which is responsive in salt stress. In this direction, ginseng plants of different growth stages (3, 4 and 5 years), were grown in the hydroponic conditions and exposed to 5 ds/m salt concentration. The secreted proteins, collected from the water, at 0, 24, 72 and 120 hours after exposure were used for the proteome analysis using shotgun approaches. Through the shotgun proteomics, a total of 155 and 88 secreted proteins were identified by searching in two RNA-sequencing (RNA-seq) database, respectively.
2022-11-17 | PXD010322 | Pride
Project description:Wild halophytic tomato has long been considered as an ideal gene donor for improving salt tolerance in tomato cultivars. Here, a wild tomato genotype, Solanum pimpinellifolium M-bM-^@M-^XPI365967M-bM-^@M-^Y is significantly more salt-tolerant than a cultivar, Solanum lycopersicom M-bM-^@M-^XmoneymakerM-bM-^@M-^Y. Affymetrix Tomato Genome Arrays was used to compare the transcriptome change of PI365967 and Moneymaker by salt treatment.After treatment with 200 mM NaCl for 5 h, PI365967 showed relatively fewer responsive genes compared to Moneymaker. Salt Overly Sensitive (SOS) pathway was found to be more active in PI365967 than in Moneymaker, coinciding with relatively less accumulation of Na+ in shoots of PI365967. A gene encoding salicylic acid-binding protein 2 (SABP2) was induced by salinity only in PI365967, suggesting a possible role of salicylic acid signaling in salt response of PI365967. The fact that two genes encoding lactoylglutathione lyase were salt-inducible only in PI365967, together with much higher basal expression of several glutathione S-transferase genes, suggested a more effective detoxification system in PI365967. Key words: salt tolerance, transcriptomic profiling, wild tomato, ion homeostasis, SABP2. In one treatment, 9 six-leaf-old plants of one tomato genotype (PI365967 or Moneymaker) were divided into three biological replicates and treated hydroponically under sterile condition with (or without) 200 mM NaCl for 5 h. RNA isolated from pooled three individual plants was used in hybridization to one chip, resulting in 12 chips in total.
2010-05-31 | E-GEOD-16401 | 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:Populus x canescens was inoculated with Paxillus involutus and grown in a climate chamber for 13 weeks. Afterwards, plants were salt stressed for 18 additional days with 150 mM NaCl in the nutrient solution. This resulted in 4 different treatments: no mycorrhiza<br>control (NC), mycorrhiza/control (MC), no mycorrhiza/salt (NS), mycorrhiza/salt (MS).
2009-09-16 | E-MEXP-1874 | biostudies-arrayexpress
Project description:Two tissues (root and shoot) of a salt tolerant (Khalas) and a salt sensitive (Nabut Saif) variety of date palm (Phoenix dactylifera) were salt treated and compared to control conditions by RNAseq.
2023-12-31 | E-MTAB-11001 | biostudies-arrayexpress
Project description:Two Near Isogenic soybean (Glycine max) lines were grown in hydroponic conditions with either 50uM ferric nitrate or 100uM ferric nitrate. After 10 days, half the plants were harvested (total root tissue). At 12 days after planting, iron was added to plants grown in low iron conditions bringing them up to sufficient iron growth conditions. Root tissue was harvested for the remaining plants at 14 days after planting. Gene expression analysis from root tissue of two Near Isogenic Lines (NILs), Clark (PI548553) and IsoClark (PI547430), grown in iron stress or iron stress recovered conditions. A total of 24 samples from four growth conditions, three biological replicates per treatment
2010-09-06 | E-GEOD-22227 | biostudies-arrayexpress
Project description:The aim of this study was to investigate ecotypic adaptation in Holcus lanatus in plants selected from two widely contrasting habitats, acid bog (pH 3.5) or limestone quarry spoil (pH 7.5), using a transcriptome based analysis approach including sequence analysis of root associated Glomeromycota. Differential gene expression in root and shoot of naturally occurring H. lanatus ecotypes, selected from either habitat and grown in a full factorial reciprocal soil transplant experiment were investigated and ecotype specific SNPs identified.
2018-03-15 | E-MTAB-4014 | biostudies-arrayexpress
Project description:The global emergence of soil salinization poses a serious challenge to many countries and regions. γ-Aminobutyric acid (GABA) is involved in systemic regulation of plant adaptation to salt stress, but the underling molecular and metabolic mechanism still remains largely unknown. The elevated endogenous GABA level by exogenous application of GABA could significantly improve salt tolerance in creeping bentgrass with the enhancement of antioxidant capacity, photosynthetic characteristics, osmotic adjustment (OA), and water use efficiency. GABA strongly upregulated transcript levels of AsPPa2, AsATPaB2, AsNHX2/4/6, and AsSOS1/20 in roots involved in enhanced capacity of Na+ compartmentalization and mitigation of Na+ toxicity in cytosol. Significant downregulation of AsHKT1/4 expression could be induced by GABA in leaves in relation to maintenance of significantly lower Na+ accumulation and higher K+/Na+ ratio. GABA-depressed aquaporins (AQPs) expression and accumulation induced declines in stomatal conductance and transpiration, thereby reducing water loss in leaves during salt stress. For metabolic regulation, GABA primarily enhanced sugars and amino acids accumulation and metabolism largely contributing to improved salt tolerance through maintaining OA and metabolic homeostasis. Other major pathways could be responsible for GABA-induced salt tolerance including increases in antioxidant defense, heat shock proteins, dehydrins, and myo-inositol accumulation in leaves. Integrative analyses of molecular, protein, metabolic, and physiological changes reveal systemic function of GABA on regulating ions, water, and metabolic homeostasis in non-halophytic creeping bentgrass under salt stress.
2020-01-13 | PXD015066 | Pride
Project description:Transcriptome analysis of roots and shoots from control, mildly, moderately and severely stressed, and re-watered conditions of Medicago plants.
2014-06-19 | E-MTAB-2681 | biostudies-arrayexpress