Transcript profiling of six rice cultivars with different tolerance level under high night temperatures
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PROVIDER: PRJNA239369 | ENA |
REPOSITORIES: ENA
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Project description:Regulation of transcript expression in different tolerance classes of rice cultivars in response to high night temperatures (HNT) is investigated. The aim was to identify marker genes which are responsible for HNT tolerance. Addiditionally gene expression data are combined with GC-MS data analysis (primary metabolites) to identify global changes in response to HNT.
2016-12-01 | GSE55341 | GEO
Project description:Transcript and metabolite profiling were performed in leaf segments (sheath, base, middle, tip) of six rice cultivars with different sensitivity to high night temperatures (HNT). On the phenotypic level, leaves of HNT-sensitive rice cultivars showed clear stress symptoms by chlorosis and necrosis while almost no leaf phenotype different from the control was observed for the tolerant varieties. The aim of this study was to identify molecular key-player for HNT-sensitivity causing leaf senescence.
2021-09-27 | GSE179662 | GEO
Project description:Differentiation of the high night temperature response in leaf segments of rice cultivars with contrasting tolerance
| PRJNA744520 | ENA
Project description:Purpose: we conducted a six time-point transcriptomic analysis using two tobacco cultivars with contrasting cold responses, Taiyan8 tobacco (TT, cold susceptibility) and Yanyan97 tobacco (YT, cold resistance). Methods: mRNA profiles of Tobacco seedlings from CK and cold-treated plants were generated by deep sequencing, in triplicate, usingIllumina Hiseq4500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with methods: hisat2 (v2.0.5), SAMtools (v1.9). StringTie (v1.3.4d) and FeatureCounts (v1.6.4) Results: We found that both cultivars had common mechanisms to cope with cold stress, including common differentially expressed genes (DEGs), similar time-point-related differential expression profile of genes, and similar NtCBF gene co-expression modules, suggesting conservation of adaptation strategies for cold responses. Importantly, we found that YT experienced DEGs even under normal growth condition and had less DEGs in early stage of cold stress (0.5-2 h) when compared to TT, reflecting occurrence of genotype-dependent gene transcription. Moreover, a gene co-expression module (brown) with stress-related genes up-regulated in YT instead of TT at late stage (4-8 h), which might contribute to contrasting phenotypic changes during cold stress between TT and YT. Conclusions: our study provides valuable resources for transcriptomic studies of cold responses in plants. It also helps to identify key cold responsive genes for genetic manipulation for breeding of tobacco cultivars in the future.
2022-08-03 | GSE173352 | GEO
Project description:Temperature is a critical environmental factor governing plant growth and development. The difference between day temperature (DT) and night temperature (NT), abbreviated as DIF, influences plant architecture. Subjecting plants to artificial DIF treatments is an effective strategy in ornamental horticulture. For example, negative DIF (when DT – NT < 0) generally inhibits stem elongation, resulting in dwarf plants. However, the mechanisms underlying stem growth regulation by DIF remains to be completely elucidated. In this study, we aimed to analyze the growth, transcriptome, and phytohormone profiles of tomato (Solanum lycopersicum) seedlings grown under different DIF treatments. Under positive DIF (when DT – NT > 0), in contrast to the control temperature (25°C/20°C, DT/NT), high temperature (30°C/25°C) increased stem length and thickness, as well as the number of xylem vessels. Conversely, compared with the positive high temperature DIF treatment (30°C/25°C), under negative DIF treatment (25°C/30°C) stem elongation was inhibited, but stem thickness and the number of xylem vessels were not affected. The negative DIF treatment decreased the expression of gibberellin (GA)-, auxin-, and cell wall-related genes in the epicotyl, as well as the concentrations of GAs and indole-3-acetic acid (IAA). The expression of these genes and concentrations of these hormones increased under high temperature compared to those under the control temperature positive DIF. Our results suggest that stem length in tomato seedlings is controlled by changes in GA and IAA biosynthesis in response to varying day and night temperatures.
2020-11-18 | GSE131496 | GEO
Project description:A IR64 variety of rice was grown in a field plot at the International Rice Research Institute (IRRI) in the Philippines. The data gained from the experiment provides information of the daily transcriptional changes occur in panicle tissue during an important developmental period under control and warm night temperatures.
2019-08-15 | GSE135847 | GEO
Project description:Systems responses of mature leaves from 4 reference cultivars of a larger collection of European potato cultivars (Solanum tuberosum L.) are investigated by metabolome profiling and RNA-Sequencing. The chosen reference cultivars, Milva, Alegria, Desiree, and Saturna, vary in ascending order in regard to drought tolerance. Systems analyses are based on 3 independent field trials and 3 paralleled greenhouse trials. Robust responses across all cultivars and conditions to natural seasonal drought stress comprise proline, raffinose, galactinol, arabitol, arabinonic acid, chlorogenic acid, and 102 transcripts which consist to a high proportion of heat shock proteins and genes with signaling or regulatory functions, such as a homolog of abscisic acid receptor PYL4. Constitutive differences of the tolerant cultivars, Desiree and Saturna, compared to the sensitive cultivars include arbutin (hydroquinone-β-D-glucopyranoside), octopamine (p-hydroxyphenylethanolamine), ribitol and 248 differential transcripts. Many of these transcripts are disease related, receptor kinases, or regulatory genes, for example a homolog of the Arabidopsis FOUR LIPS MYB-regulator of stomatal cell proliferation. Functional enrichment analyses imply that heat stress is a major acclimation component of potato leaves to agronomical relevant drought stress. Enhanced leaf heat stress is a result of drought caused by loss of transpiration cooling. This effect and CO2-limitation are the main dilemmas of drought- or ABA-induced stomatal closure. Constitutive differences between tolerant and sensitive cultivars indicate partially synergistic interactions of drought and biotic stress responses. We suggest that drought tolerance of the potato reference cultivars may be caused by general resistance mechanisms which are part of previously selected pathogen tolerance.
2016-07-06 | GSE77826 | GEO
Project description:The sustainable production of perennial grasses in Northern Norway is at risk due to the ongoing climate change. The predicted increase in temperatures and variable weather patterns are further expected to create challenges for winter survival of timothy. Therefore, knowledge about the molecular mechanisms underlying freezing tolerance is crucial for developing robust cultivars. The current study is aimed at identifying genes involved in the freezing stress response of Timothy and studying gene expression differentiation due to field selection in contrasting environments. Four timothy cultivars, namely Engmo, Noreng, Grindstad and Snorri were field tested for three years at locations Tromsø and Vesterålen in Northern Norway. The surviving material from the field tests along with plants raised from the original seed lots were subjected to freezing tests. Following the tests, crown tissue was collected for RNA extraction. All samples from different treatment points were paired-end sequenced at 20 million reads/sample. LT50 values varied across cultivars and materials. Plant material from cold-acclimated (CA) samples was used as controls, while two pools for each cultivar were made of plant material from temperature points below the LT50, one with the higher temperatures termed Treatment 1 (T1) and one with the lower temperatures termed Treatment 2 (T2). Many genes coding for transcription factors and proteins which are known to play an important role in freezing tolerance like dehydrins, c-repeat binding factors, late embryogenesis abundant proteins are upregulated with decreasing temperatures. Moreover, genes associated with glycolysis/gluconeogenesis, TCA cycle, glutathione metabolism, proteasome, glyoxylate and dicarboxylate metabolism pathways and genes encoding heat shock proteins, autophagy-related, plasma membrane-associated proteins, sugar and amino acid transporters had elevated expression in field survivors compared to plants raised from the original material. These DEGs might be crucial for winter survival of timothy in a changing climate. Furthermore, differences in freezing stress response between northern and southern adapted cultivars, and surviving material from two field trial locations are discussed briefly
2023-11-24 | E-MTAB-13531 | biostudies-arrayexpress
Project description:Systems responses of mature leaves from 4 reference cultivars of a larger collection of European potato cultivars (Solanum tuberosum L.) are investigated by metabolome profiling and RNA-Sequencing. The chosen reference cultivars, Milva, Alegria, Desiree, and Saturna, vary in ascending order in regard to drought tolerance. Systems analyses are based on 3 independent field trials and 3 paralleled greenhouse trials. Robust responses across all cultivars and conditions to natural seasonal drought stress comprise proline, raffinose, galactinol, arabitol, arabinonic acid, chlorogenic acid, and 102 transcripts which consist to a high proportion of heat shock proteins and genes with signaling or regulatory functions, such as a homolog of abscisic acid receptor PYL4. Constitutive differences of the tolerant cultivars, Desiree and Saturna, compared to the sensitive cultivars include arbutin (hydroquinone-beta-D-glucopyranoside), octopamine (p-hydroxyphenylethanolamine), ribitol and 248 differential transcripts. Many of these transcripts are disease related, receptor kinases, or regulatory genes, for example a homolog of the Arabidopsis FOUR LIPS MYB-regulator of stomatal cell proliferation. Functional enrichment analyses imply that heat stress is a major acclimation component of potato leaves to agronomical relevant drought stress. Enhanced leaf heat stress is a result of drought caused by loss of transpiration cooling. This effect and CO2-limitation are the main dilemmas of drought- or ABA-induced stomatal closure. Constitutive differences between tolerant and sensitive cultivars indicate partially synergistic interactions of drought and biotic stress responses. We suggest that drought tolerance of the potato reference cultivars may be caused by general resistance mechanisms which are part of previously selected pathogen tolerance. Transcriptome profiling by RNA-sequencing of 48 leaf samples from 4 potato cultivars grown under control or drought stress conditions in 6 independent experiments
2016-07-06 | E-GEOD-77826 | biostudies-arrayexpress
Project description:Heat stress along with other abiotic stresses is one of the major factors affecting crop health and overall yield in a tropical country like India. Thus, there is an urgent need to understand the dynamics of heat responsiveness at the molecular as well as physiological level. Fortunately, India has a number of indigenous varieties that show tolerance to extremes in temperature during the scorching summer months. The cultivar Annapurna is a fast growing dwarf variety of rice that is heat tolerant while the most widely grown indica rice in South and Southeast Asia, IR64, is susceptible to high temperatures. These two cultivars present an excellent opportunity to study the differences in response to heat stress, and, thereby help in elucidating the genes involved in conferring tolerance to high temperature. The present study involves transcript profiling of the two cultivars, Annapurna (tolerant) and IR64 (susceptible) under both control and heat stressed conditions.
2021-07-26 | GSE41648 | GEO