Ontology highlight
ABSTRACT:
PROVIDER: PRJNA598805 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10824900_1.fastq.gz | Fastqsanger.gz | |||
| SRR10824900_2.fastq.gz | Fastqsanger.gz | |||
| SRR10824901_1.fastq.gz | Fastqsanger.gz | |||
| SRR10824901_2.fastq.gz | Fastqsanger.gz | |||
| SRR10824902_1.fastq.gz | Fastqsanger.gz |
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Project description:As no commercial array is available for sorghum microarray analysis, we designed an array based on the annotation of Sbi1.4 gene set and the available 209,835 sorghum ESTs from the NCBI EST database. The array will be used for investigating the expression divergence between grain and sweet sorghum lines under normal and sucrose treatments
2012-04-08 | GSE36689 | GEO
Project description:Bioenergy sorghum accumulates 75% of shoot biomass in stem internodes. Grass stem internodes are formed during vegetative growth and elongate in response to developmental and environmental signals. To identify genes and molecular mechanisms that modulate the extent of internode growth, we conducted microscopic and transcriptomic analysis of four successive sub-apical vegetative internodes representing different stages of internode development of the bioenergy sorghum genotype R.07020.
2017-08-17 | GSE98817 | GEO
Project description:As no commercial array is available for sorghum microarray analysis, we designed an array based on the annotation of Sbi1.4 gene set and the available 209,835 sorghum ESTs from the NCBI EST database. The array will be used for investigating the expression divergence between grain and sweet sorghum lines under normal and sucrose treatments The expression analysis was carried out using 14-day old whole seedlings from both grain and sweet sorghum lines. Three samples from sucrose treatment (0h, 2h and 6h) for each line were collected for the analysis . Two biological replicates were carried out for both control and sucrose treatments, resulting in a dataset of 12 microarrays.
2012-04-07 | E-GEOD-36689 | biostudies-arrayexpress
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:Sorghum bicolor is one of the most important cereal crops in the world, predominantly grown in sub‑Saharan Africa by smallholder farmers. Despite its outstanding resilience to abiotic stresses, approximately 20% of sorghum yield is annually lost on the African continent due to infestation with the parasitic weed Striga hermonthica. Existing Striga management strategies to decrease Striga infestation often show low efficiency and are not easily integrated into current agricultural practices. Microbial-based solutions may prove an effective, low-cost mode for reducing Striga parasitism in sub-Saharan Africa. Here, we demonstrate that the microbiome component of a field soil suppresses Striga infection of sorghum. Potential mechanisms underlying the soil microbiome’s influence on the host plant include root endodermal suberization and aerenchyma formation. Moreover, we observed a depletion of haustorium inducing factors, compounds essential for Striga to establish the host-parasite association, in root exudates collected from sorghum grown in the presence of the soil microbiome as compared to sterile conditions. We further identified individual microbial taxa associated with reduced Striga infection via changes in root cellular anatomy and differentiation as well as in exudate composition. Our study identifies a suite of traits that can be harnessed by individual microbial isolates or their consortia to induce Striga resistance. Combining microbes that elicit Striga resistance directly (affecting the parasite) via repression of haustorium formation with those that act indirectly (affecting the host), by reducing of Striga penetration through root tissue, can broaden the effectiveness of microbe-induced protection from Striga.
2022-10-31 | GSE216351 | GEO
Project description:Background: Sorghum bicolor is a remarkably drought tolerant cereal crop. Its natural biodiversity that enables this tolerance has developed in sub-Saharan Africa. The sequencing of the sorghum genome in 2009 has expedited research of this crop which has also been proposed as a model C4 cereal crop for genomics. In this study, the genetic response mechanisms involved in sorghums’ tolerance to progressive water deficit and moderate re-watering were investigated in three previously uncharacterized South African landraces (designated: LR5, LR6 and LR35) using cDNA microarrays comprising 35 899 transcript probes. Results: Across the three landraces, significant differential expression of 1 797 genes, including 264 genes with currently unknown functions, were altered in response to progressive water stress and re-watering. The modulated sorghum genes had homology to proteins involved in growth, regulation, and protection. Gene ontology analysis identified significant enrichment of 26 genes involved in the ‘response to abiotic stimulus’ GO category in LR6 during severe stress. The expression of USP responded to progressive water stress and moderate re-watering in LR6 and LR35. Moreover, our results indicate a putative role for β-alanine betaine biosynthesis in drought tolerance of sorghum. Conclusions: This study identified the drought responsive gene complement of three previously uncharacterized South African sorghum landraces. Each landrace is a distinct genotype and similar responses to water deficit and re-watering were not expected. Functional characterizations of some of the differentially expressed genes found in this study may be used as possible targets for marker-assisted breeding or transgenic initiatives for sorghum and, other closely related crop species.
2017-12-31 | GSE92487 | GEO
Project description:Whole Genome Sequencing of the soybean mini-core collection
| PRJDB7386 | ENA