Small RNAs of sorghum in response to drought stress
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ABSTRACT:
ORGANISM(S): Sorghum bicolor
PROVIDER: GSE227308 | GEO | 2023/09/25
REPOSITORIES: GEO
Similar Datasets
Project description:The present study is expected to reveal regulatory network of small RNAs under drought in Sorghum (Sorghum bicolor (L.) Moench). Sorghum genotype drought tolerant (DT) and drought susceptible (DS) were grown at 28-32 degrees C day/night temperature with 12/12 h light/dark period in the phytotron glass house. The fully opened uppermost leaves from control and drought stressed seedlings were sampled and stored at -80 degrees C, and used for generation of a small RNA library. Total RNA was isolated from the leaves using the TRIzol reagent (Invitrogen, USA). Small RNA sequencing libraries were prepared using Illumina Truseq small RNA Library preparation kit following manufacturer's protocol and these libraries were sequenced on GAIIx platform (Illumina Inc., USA). Small RNA reads contaminated with poor-quality and adaptor sequences were trimmed by using the UEA sRNA workbench 2.4- Plant version sequence file pre-processing (http://srna-tools.cmp.uea.ac.uk/). Then, all unique reads were submitted to the UEA sRNA toolkit-Plant version miRCat pipeline (http://srna-tools.cmp.uea.ac.uk/) to predict novel miRNAs from high-throughput small RNA sequencing data.
2014-04-15 | E-MTAB-1630 | biostudies-arrayexpress
Project description:Two cultivars of sorghum were examined from a study performed at the Kearney Research Station in California; 1) a pre-flowering drought tolerant, post-flowering drought susceptible cultivar RTx430 and 2) a pre-flowering drought susceptible, post-flowering drought-tolerant cultivar BTx642. These data are the methanol/water metabolite fraction obtained from a Folsh extraction from Sorghum bicolor leaves and roots. The metabolites were derivatized and analyzed via GC-MS at PNNL. Analyses represent the metabolite profile collected at 2, 3, 4, 6, 8, 9, 10, 11, 13, 15, 17 weeks post soil emergence and under a perturbation of either well-watered (control), pre-flowering drought, or post-flowering drought.
2017-10-23 | MSV000081639 | MassIVE
Project description:Background: Drought stress is the major environmental stress that affects plant growth and productivity. It triggers in plants a wide range of responses detectable at different scales: molecular, biochemical and physiological levels. At the molecular level the response to drought stress results in the differential expression of several metabolic pathways. For this reason, explore the subtle differences existing in gene expression of drought sensitive and drought tolerant genotypes allows to identify drought-related genes that could be used for selection of drought tolerance traits. Genome-wide RNA-Seq technology was used to compare the drought response of two sorghum genotypes characterized by contrasting water use efficiency. Results: the physiological measurements carried out confirmed the drought sensitivity of IS20351 and the drought tolerance of IS22330 previously studied. The expression of drought-related genes was more abundant in the sensitive genotype IS20351 compared to the tolerant IS22330. The Gene Ontology enrichment highlighted a massive increase in transcript abundance in “response to stress” and “abiotic stimulus”, “oxidation-reduction reaction” in the sensitive genotype IS20351 under drought stress. “Antioxidant” and “secondary metabolism”, “photosynthesis and carbon fixation process”, “lipids” and “carbon metabolism” were the pathways most affected by drought in the sensitive genotype IS20351. The sensitive genotype IS20351 showed under well-watered conditions a lower constitutive expression level of “secondary metabolic process” (GO:0019748) and “glutathione transferase activity” (GO:000004364). Conclusions: RNA-Seq analysis revealed to be a very useful tool to explore differences between sensitive and tolerant sorghum genotypes. The transcriptomic results supported all the physiological measurements and were crucial to clarify the tolerance of the two genotypes studied. The connection between the differential gene expression and the physiological response to drought states unequivocally the drought tolerance of the genotype IS22330 and the strategy adopted to cope with drought stress.
2016-04-27 | GSE80699 | GEO
Project description:MicroRNAs (miRNAs) are part of gene regulatory networks that direct all most all biological processes in plants including their growth and development, as well as adaptation to biotic and abiotic stresses. Sorghum is largely grown for its grain production, but recently it also emerged a major feedstock for biofuel production. Interestingly, Sorghum is relatively drought tolerant crop and largely grown in semi-arid tropical and sub-tropical regions where the drought or high temperature or their combination co-occur in the field. Although miRNA profiles have been reported in Sorghum leaves exposed to drought, but thus far miRNAs in heat- or drought and heat-exposed conditions have not been reported. In this study, we report miRNA profiles in Sorghum leaves exposed to drought or heat or their combination. The bioinformatic analysis of small RNA libraries revealed the expression of approximately 30 conserved miRNA families represented by 81 individual miRNAs as well as 11 novel miRNA families in Sorghum leaves. Of these, 26 miRNAs were found to be differentially regulated in response to one or more of the stress treatments. Overall, the number of miRNAs regulated by heat was more than the drought. Furthermore, miRNA profiles revealed more similarities between heat and the combination of drought and heat stresses. We also have analyzed degradome profiles in control and drought-exposed plants to identify potential targets for the miRNAs. This study provides a frame work for better understanding of miRNA-guided gene regulations that vary between individual drought or heat or combination of drought and heat treatments.
2021-12-31 | GSE157523 | GEO
Project description:MicroRNAs (miRNAs) are part of gene regulatory networks that direct all most all biological processes in plants including their growth and development, as well as adaptation to biotic and abiotic stresses. Sorghum is largely grown for its grain production, but recently it also emerged a major feedstock for biofuel production. Interestingly, Sorghum is relatively drought tolerant crop and largely grown in semi-arid tropical and sub-tropical regions where the drought or high temperature or their combination co-occur in the field. Although miRNA profiles have been reported in Sorghum leaves exposed to drought, but thus far miRNAs in heat- or drought and heat-exposed conditions have not been reported. In this study, we report miRNA profiles in Sorghum leaves exposed to drought or heat or their combination. The bioinformatic analysis of small RNA libraries revealed the expression of approximately 30 conserved miRNA families represented by 81 individual miRNAs as well as 11 novel miRNA families in Sorghum leaves. Of these, 26 miRNAs were found to be differentially regulated in response to one or more of the stress treatments. Overall, the number of miRNAs regulated by heat was more than the drought. Furthermore, miRNA profiles revealed more similarities between heat and the combination of drought and heat stresses. We also have analyzed degradome profiles in control and drought-exposed plants to identify potential targets for the miRNAs. This study provides a frame work for better understanding of miRNA-guided gene regulations that vary between individual drought or heat or combination of drought and heat treatments.
2021-12-31 | GSE157521 | GEO
Project description:Larix kaempferi is important afforestation species in northeastern China and is one of the most drought-tolerant pine species.Larix kaempferi has a very complex genetic background and a large genome, and study on the molecular mechanisms of drought resistance is still lag behind. Four-month-old of L. kaempferi seedlings grown in the greenhouse into two groups, the drought treatment group was no watering for 14 d (D14), while normally watered seedlings were used as control group (CK). All plants harvested on the same day and at the same time for the upper part of seedling (circa 3 cm from the top), frozen in liquid nitrogen. We designed six samples (CK-1, CK-2, CK-3, D14-1, D14-2, and D14-3) in total for Illumina HiSeq.
2021-07-15 | GSE154534 | GEO
Project description:Sorghum is an important crop often subjected to simultaneous high temperatures and drought in the field. We examined the gene expression response to heat and drought stress both individually, and in combination, with the aim of identifying important stress tolerance mechanisms.
2014-06-20 | GSE48205 | GEO
Project description:Drought is a critical issue in modern agriculture, therefore there is a need to create crops with drought resilience. The complexity of plant responses to abiotic stresses, particularly in the field of brassinosteroid (BR) signaling, has been the subject of extensive research. In this study, we unveil compelling insights indicating that the BRASSINOSTEROID INSENSITIVE 1 (BRI1) receptor in Arabidopsis and Sorghum plays a critical role as a negative regulator of drought responses. Introducing untargeted mutation in the sorghum BRI1 receptor (SbBRI1) effectively enhances the plant ability to withstand osmotic and drought stress. Through DNA Affinity Purification sequencing (DAP-Seq) we show that the sorghum BRI1-EMS-SUPPRESSOR 1 (SbBES1) transcription factor, a downstream player of the BR signaling, binds to a conserved G-box binding motif, and it is responsible for regulating BR homeostasis, as its Arabidopsis ortholog AtBES1. We further characterized the drought tolerance of sorghum bri1 mutants and decipher SbBES1-mediated regulation of phenylpropanoid pathway. Our findings suggest that SbBRI1 signaling serves as a dual purpose: under normal conditions, it regulates lignin biosynthesis by SbBES1, but during drought conditions, BES1 becomes less active, allowing the activation of the flavonoid pathway. This adaptive shift improves the photosynthetic rate and photoprotection, reinforcing crop adaptation to drought.
2024-08-31 | GSE262062 | GEO
Project description:We analyzed lncRNAs from sorghum leaves under water control treatment using high-throughput sequencing technology and bioinformatic approaches to explore the genome-wide quantity of lncRNAs and their potential function in the regulation of drought responses.
2023-09-25 | GSE232788 | GEO
Project description:We report here the RNAseq data generated from a drought experiment using tomato leaves (Solanum lycopersicum), in which three timepoints and two treatments were collected. More specifically, RNAseq was generated from tomato plants prior to drought (T0), during a period of drought (T1) and after a period of recovery from drought (T2). At timepoints 1 and 2 (T1 & T2), a control set of plants that were continuously watered are also included. Furthermore, at each timepoint, each leaf was dissected into two parts, including the vein and intervein. The samples are therefore named as Tissue/Timepoint/Treatment, and include VT0W (vein, T0, watered), VT1W (vein, T1, watered), VT1D (vein, T1, drought), VT2D, VT2W and IVT0W (intervein, T0, Watered), IVT1D, IVT1W, IVT2D, IVT2W. Note that VT2D and IVT2D, while named "drought", were actually recovered from drought.
2020-10-31 | GSE156402 | GEO