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Sorghum gene expression using Agilent custom 4x44K Microarray

ABSTRACT: 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

ORGANISM(S): Sorghum bicolor

PROVIDER: GSE36689 | GEO | 2012/04/08

SECONDARY ACCESSION(S): PRJNA153607

REPOSITORIES: GEO

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Sorghum gene expression using Agilent custom 4x44K Microarray

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

Identification of N6-methyladenosine (m6A) modification in sweet sorghum under salt stress

Project description:The N6-methyladenosine (m6A) modification is the most common internal post-transcriptional modification, with important regulatory effects on RNA export, splicing, stability，and translation. However, the effects of m6A modifications on the resistance of sweet sorghum to salt stress remain unclear. In this study, we mapped the m6A modifications in two sorghum inbred lines (salt-tolerant M-81E and salt-sensitive Roma) that differ regarding salt tolerance. Dynamic changes to m6A modifications in sweet sorghum were identified in response to salt stress. Our data suggest that the differences in the m6A modifications between salt-tolerant and salt-sensitive sweet sorghum might contribute to the diversity in salt tolerance.

2022-05-02 | GSE146936 | GEO

Identification of non-coding RNA in sweet sorghum under salt stress

Project description:Salt stress has become one of the main abiotic stress factors restricting agricultural production worldwide. Sweet sorghum is an important salt and drought tolerant feed and energy crop. Its salt tolerance mechanism has not been widely studied. With the development of transcriptome sequencing technology, it is possible to study the molecular mechanism of sweet sorghum salt tolerance. The purpose of this study was to further reveal the potential salt-tolerant molecular mechanisms of sweet sorghum through high-throughput sequencing analysis of the transcriptome. Finally, through high-throughput sequencing, we read approximately 54.4G of raw base and 53.7G of clean base in total, and used FastQC to assign a quality score (Q) to each base in the read using a similar phred algorithm, Analysis shows that the data is highly credible. We conclude that RNA-based transcriptome characterization will accelerate the study of genetics and molecular biology of sweet sorghum salt tolerance mechanisms and provide a framework for this.

2020-03-19 | GSE145748 | GEO

small RNAs sequencing in sweet sorghum under cadmium stress

Project description:Four small RNA libraries from two contrasting sweet sorghum genotypes were sequenced. In this study, One hundred and ninety-five conserved miRNAs belonging to 56 families and 25 putative novel miRNAs from 28 precursors were identified, among which 38 conserved and 24 novel miRNAs were differentially expressed under Cd stress and/or between H18 and L69. Two groups of them: miR169p/q-nov_23 and miR408 were further focused through the coexpression analysis and might be involved in Cd transport, cytoskeleton activity and cell wall construction by regulating their targets. This study presents new insights into the regulatory roles of miRNAs in Cd accumulation and tolerance in sweet sorghum and will help to develop high-Cd accumulation or high Cd-resistant germplasm of sweet sorghum through molecular breeding and/or genetic engineering approaches.

2023-10-12 | GSE145617 | GEO

Stem tranascriptome of sweet sorghum variety ICSA38

Project description:We report transcriptome profiling from three developing stages of middle internode in sweet sorghum. Samples were harvested at Booting, milky stages and physiological maturity.

2023-12-31 | GSE153690 | GEO

Stem transcriptome of sweet sorghum hybrid CSH22SS during development and in response to water limiting conditions.

Project description:We report transcriptome profiling from three developing stages of middle internode in Hybrid sweet sorghum. Samples were harvested at Booting, milky stages and physiological maturity.

2023-12-31 | GSE153418 | GEO

Phylogenomic Analysis of R2R3 MYB Transcription Factors in Sorghum and their Role in Conditioning Biofuel Syndrome

Project description:We report transcriptome profiling from three developing stages of middle internode in sweet sorghum. Sequencing of 6 libraries (two replicates from each stage) each stage yielded approximately 80 million reads.

2022-04-30 | GSE148558 | GEO

Sugar accumulation enhancement in sorghum stem is associated with reduced reproductive sink strength and increased phloem unloading activity

Project description:Sweet sorghum has emerged as a promising source of bioenergy mainly due to its high biomass and high soluble sugar yield in stems. Studies have shown that loss-of-function Dry locus alleles have been selected during sweet sorghum domestication, and decapitation can further boost sugar accumulation in sweet sorghum, indicating that the potential for improving sugar yields is yet to be fully realized. To maximize sugar accumulation, it is essential to gain a better understanding of the mechanism underlying the massive accumulation of soluble sugars in sweet sorghum stems in addition to the Dry locus. We performed a transcriptomic analysis upon decapitation of near-isogenic lines for mutant (d, juicy stems, and green leaf midrib) and functional (D, dry stems and white leaf midrib) alleles at the Dry locus. Our analysis revealed that decapitation suppressed photosynthesis in leaves, but accelerated starch metabolic processes in stems. SbbHLH093 negatively correlates with sugar levels supported by genotypes (DD vs. dd), treatments (control vs. decapitation), and developmental stage post anthesis (3d vs.10d). D locus gene SbNAC074A and other programmed cell death-related genes were downregulated by decapitation, while sugar transporter-encoding gene SbSWEET1A was induced. Both SbSWEET1A and Invertase 5 were detected in phloem companion cells by RNA in situ assay. Loss of the SbbHLH093 homolog, AtbHLH093, in Arabidopsis led to a sugar accumulation increase. This study provides new insights into sugar accumulation enhancement in bioenergy crops, which can be potentially achieved by reducing reproductive sink strength and enhancing phloem unloading.

2023-06-17 | GSE206420 | GEO

Whole-genome transcriptomic analysis in Sorghum bicolor variety CSV24SS

Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in sweet sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .

2023-12-31 | GSE155194 | GEO

Development of Vegetative Oil Sorghum: From Lab-to-Field

Project description:Biomass crops engineered to accumulate energy-dense triacylglycerols (TAG or “vegetable oils”) in their vegetative tissues have emerged as potential feedstocks to meet the growing demand for renewable diesel and sustainable aviation fuel (SAF). Unlike oil palm and oilseed crops, the current commercial sources of TAG, vegetative tissues, such as leaves and stems, only transiently accumulate TAG. In this report, we used grain (Texas430 or TX430) and sugar-accumulating “sweet” (Ramada) genotypes of sorghum, a high-yielding, environmentally resilient biomass crop, to accumulate TAG in leaves and stems. We initially tested several gene combinations for a “push-pull-protect" strategy. The top TAG-yielding constructs contained five oil transgenes for a sorghum Wrinkled1 transcription factor (“push”), a Cuphea viscosissima diacylglycerol acyltransferase (DGAT; "pull"), a modified sesame oleosin (“protect”) and two combinations of specialized Cuphea lysophosphatidic acid acyltransferases and medium-chain acyl-acyl carrier protein thioesterases. Though intended to generate oils with medium-chain fatty acids, engineered lines accumulated oleic acid-rich oil to amounts of up to 2.5% DW in leaves and 2.0% DW in stems in the greenhouse, 36-fold and 49-fold increases relative to wild-type plants, respectively. Under field conditions, the top-performing event accumulated TAG to amount of up to 5.5% DW in leaves and 3.5% DW in stems, 78-fold and 58-fold increases, respectively, relative to wild-type TX430. Transcriptomic and fluxomic analyses revealed potential bottlenecks for increased TAG accumulation. Overall, our studies highlight the utility of a lab-to-field pipeline coupled with systems biology studies to deliver high vegetative oil sorghum for SAF and renewable diesel production.

2024-07-31 | GSE272636 | GEO

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