Dynamics of gene expression during devepolement and expansion of vegetative stem internodes of bioenergy sorghum
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ABSTRACT:
ORGANISM(S): Sorghum bicolor
PROVIDER: GSE98817 | GEO | 2017/08/17
SECONDARY ACCESSION(S): PRJNA386306
REPOSITORIES: GEO
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Project description:Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum’s 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type specific gene regulatory networks (GRNs) revealed that unique TF families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with a stem developmental transcriptome dataset to identify the GRN that differentially activates the secondary cell wall (SCW) formation in stem xylem sclerenchyma and epidermal cells. The cell-type transcriptomic dataset provides a valuable source of information about the function of sorghum stem cell types and GRNs that will enable the engineering of bioenergy sorghum stems.
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Project description:Advances in alfalfa [Medicago sativa (L.) subsp. sativa] breeding, molecular genetics and genomics have been slow because this crop is an allogamous autotetraploid (2n = 4x = 32) with complex polysomic inheritance. Increasing cellulose and decreasing lignin in alfalfa stem cell walls would improve this crop as a cellulosic ethanol feedstock. We selected two alfalfa genotypes (252, 1283) that differ in cellulose and Klason lignin concentration in stem cell walls. Analysis of GeneChip expression data files of alfalfa stem internodes of genotypes 252 and 1283 at two growth stages (elongating, post-elongation) revealed 10,887 SFPs in 8,230 probe sets. Validation analysis by PCR-sequencing of a random sample of SFPs indicated a 12% false discovery rate. Functional classification and over-representation analysis showed that both genotypes were highly enriched in SFP-harboring cell wall genes. We mapped 5,833 of the 8,230 SFP-harboring genes onto putative orthologous loci on Medicago truncatula chromosomes. Clustering and over-representation of SFP-harboring genes within the same functional class (e.g. cell wall genes) was observed on some chromosomes. Prior to analysis of expression data for the two alfalfa genotypes, SFP probes were masked to reduce false positives and false negatives. The combination of SFP and gene expression analysis provide a list of candidate cell wall genes that can be used as molecular markers in a breeding program to improve alfalfa as a cellulosic feedstock. The results of this study will also be useful in advancing understanding of genome organization in alfalfa and for comparative genomics research with other legume species. SUBMITTER_CITATION: Mesfin Tesfaye, S.S. Yang, J.F. Lamb, H.J. Jung, D.A. Samac, J. Gronwald, C.P. Vance and K.A. VandenBosch (2009). Medicago truncatula as a model for dicot cell wall development. BioEnergy Research 2: 59-76 Experiment Overall Design: The alfalfa clonal lines 252 and 1283 were propagated from cuttings and grown in the greenhouse. The greenhouse experiments consisted of three replicates arranged in a randomized complete block design. There were eight plants of each clone, in individual pots, in each replicate. Plant material for analysis was composited within each replicate at harvest. Stem internode tissues were harvested at full bloom. Based on tissue pliability and coloration, the internode in transition from elongation to post-elongation cambial growth was identified. The internodes immediately above (elongating internodes) and below this transition internode (post-elongation internodes) were collected for RNA extraction.
2009-06-08 | E-GEOD-13602 | biostudies-arrayexpress
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.
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Project description:Sorghum (Sorghum bicolor) is one of the world's most important cereal crops. S. propinquum is a perennial wild relative of S. bicolor with well-developed rhizomes. Functional genomics analysis of S. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. In this study, we used a whole rice genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of S. propinquum with special emphasis on rhizome development. A total of 548 tissue-enriched genes were detected, including 31 and 114 unique genes that were predominantly expressed in the rhizome tips (RT) and internodes (RI), respectively. Further GO analysis indicated that the functions of these tissue-enriched genes corresponded to their characteristic biological processes. A few distinct cis-elements, including ABA-responsive RY repeat CATGCA, sugar-repressive TTATCC, and GA-responsive TAACAA, were found to be prevalent in RT-enriched genes, implying an important role in rhizome growth and development. Comprehensive comparative analysis of these rhizome-enriched genes and rhizome-specific genes previously identified in S. propinquum indicated that phytohormones, including ABA, GA, and SA, are key regulators of gene expression during rhizome development. Co-localization of rhizome-enriched genes with rhizome-related QTLs in rice and sorghum generated functional candidates for future cloning of genes associated with rhizome growth and development. In conclusion, a whole rice genome oligonucleotide microarray was used to profile gene expression across five tissues of the perennial wild sorghum S. propinquum. Expression patterns of the five tissues were consistent with the different functions of each organ, and RT- and RI-enriched genes revealed clues regarding molecular mechanisms of rhizome development. Plant hormones, including ABA, GA, and SA, function as key regulators of rhizome gene expression and development. To shed further light on the identities of rhizome-specific genes, rhizome-enriched candidates were identified using QTL co-localization and comparative analysis. In this study, the specific gene expression patterns across five tissues, including rhizome tip (RT, distal 1 cm of the young rhizome), rhizome internodes (RI), shoot tip (ST, distal 5 mm of the tiller after removing all leaves), shoot internodes (SI) and young leaf (YL) in Sorghum propinquum, especially in the rhizome, were characterized by using a rice genome array. Three independent biological replicates for each tissue from individual plants were performed. The reference was equivalent to a mix of the 5 tissues.
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Project description:We developed a commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) and generated this dataset to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast and mitochondrial genomes. Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e.g., microRNAs), and confirmed functional small RNAs in related species (corn and sugarcane) were also included in our array design.
2013-12-31 | GSE49879 | GEO
Project description:Dynamics of gene expression during devepolement and expansion of vegetative stem internodes of bioenergy sorghum
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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
Project description:We developed a commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) and generated this dataset to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast and mitochondrial genomes. Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e.g., microRNAs), and confirmed functional small RNAs in related species (corn and sugarcane) were also included in our array design. 78 samples were analyzed from four different tissue types (shoot, seedling, leaves and stem), two dissected stem tissues (pith and rind) and six diverse genotypes (PI455230, Atlas, PI152611, AR2400, R159, and Fremont)
2013-12-31 | E-GEOD-49879 | biostudies-arrayexpress