Sugarcane genes associated with sucrose content relate to drought and cell wall metabolism
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ABSTRACT:
PROVIDER: PRJNA112191 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE4968: Sugarcane transcriptome - ABA treatment GSE4971: Sugarcane transcriptome - Drought response GSE14730: Expression profile in internodes 1, 5 and 9 from high and low brix plants for sucrose content GSE14731: Expression profile between internodes 1 and 9 from high and low brix plants for sucrose content Refer to individual Series
2010-06-30 | E-GEOD-14732 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2009-02-12 | GSE14732 | GEO
Project description:Background: Sugarcane is an important sugar and energy crop largely used for bioethanol production in the world. The development of sugarcane cultivars with high sucrose content and yield is one of the biggest challenges of breeding programs nowadays. To identify genes networks that underlie sucrose content and yield, we used a custom designed oligonucleotide array with 21,901 different probes to study the transcriptome from breeding populations of sugarcane contrasting to sucrose content and genotypes contrasting to photosynthesis rate. Results: Physiological and biochemical data reveals that the transcriptome profiles described here showed a close relationship between sucrose content and stem development. A total of 2135 genes were differentially expressed in at least one experimental hybridization. We identified genes related to carbohydrate metabolism, cell wall metabolism and signal transduction. The same oligoarrays was used to detect transcription in both sense and antisense orientation. The enriched functional category from antisense expressed genes reveals light harvesting and circadian clock as the two top categories that can be related to photosynthesis and yield in sugarcane. Conclusions: Knowledge on the mechanisms underlying carbon partitioning and its relationship with sucrose accumulation in sugarcane stems would help defines routes to increase yield. Our findings showed for instance that sucrose accumulation and yield in sugarcane may be regulated by hormone signaling pathways, light harvesting and circadian clock genes. Analysis of the expression data and gene category enrichment provided an insight into signaling pathways and transcriptional control contrasting in high brix and low brix plants as well as differing photosynthesis rates and yield.
2016-12-31 | GSE44389 | GEO
Project description:Sugarcane is an important crop in tropical regions of the world, producing a very large biomass and accumulating large amounts of sucrose in the stem. In this study, we present the first report of transcript profiling using the GeneChip Sugarcane Genome Array. We have identified transcripts that are differentially expressed in the sugarcane stem during development by expression profiling using the array and total RNA derived from three disparate stem tissues (meristem, internodes 1-3; internode 8; internode 20) from four replicates of the sugarcane variety Q117 grown in the field. We have identified 119 transcripts that were highly differentially expressed with stem development and have characterised members of the cellulose synthase (CesA) and cellulose synthase-like (Csl) gene families which displayed coordinated expression during stem development. In addition, we determined that many other transcripts involved in cell wall metabolism and lignification were also co-expressed with members of the CesA and Csl gene families, offering additional insights into the dynamics of primary and secondary cell wall synthesis in the developing sugarcane stem. Keywords: stem development profile
2006-11-19 | GSE5021 | GEO
Project description:Sugarcane accumulates high concentrations of sucrose in the mature stalk, with numerous physiological processes in maturing stalk tissue both directly and indirectly involved. A considerable portion of carbohydrate metabolism is also devoted to cell wall synthesis and fibre production. Previously, we have identified differentially expressed transcripts correlated with sucrose accumulation and fibre production in various internodes of the sugarcane stalk. In this study, we have examined tissue-specific expression patterns to further explore gene pathways responsible for sucrose accumulation and fibre synthesis. We performed large-scale expression profiling of storage parenchyma, vascular bundles and rind dissected from a maturing stalk internode from field-grown commercial sugarcane harvested at 11 months of age. We identified 10 cellulose synthase subunit genes in sugarcane and examined significant differences in the expression of their corresponding transcripts and those of several sugar transporters between the different tissues. These were further correlated with differential expression patterns for transcripts of specific COBRA-like proteins and other proteins with acknowledged roles in cell wall metabolism. We found that the sugar transporters ShPST2a, ShPST2b and ShSUT4 were significantly up-regulated in storage parenchyma while ShSUT1 was up-regulated in vascular bundles. Two co-ordinately expressed groups of cell wall related transcripts were also identified. One group which is associated with primary cell wall synthesis (ShCesA1, ShCesA7, ShCesA9 and Shbk2l3) was up-regulated in parenchyma. The other group which is associated with secondary cell wall synthesis (ShCesA10, ShCesA11, ShCesA12 and Shbk-2) was up-regulated in rind. We also report an unexpected paucity in differential expression of cell wall-related genes in vascular bundles. Our results indicate that there is spatial separation for elevated expression of these important targets in both sucrose accumulation and cell wall synthesis, allowing for increased clarity in our understanding of sucrose transport and fibre synthesis in sugarcane.
2015-10-13 | GSE67897 | GEO
Project description:Sugarcane established industrial crop providing sugar, ethanol and biomass-derived electricity around the world. Cane sugar content is an important, breeding target, but its improvement remains very slow in many breeding programmes. Biotechnology strategies to improve sucrose accumulation made little progress at crop level, mainly due to the limited understanding of its regulation. MiRNAs regulate many metabolic processes in plants. However, their roles and target genes associated with sugarcane sucrose accumulation remains unknown. Here, we conducted high-throughput sequencing of transcriptome, small RNAs and degradome of leaves and stem of two sugarcane genotypes with contrasting sucrose content from the early to late stages of sucrose accumulation stages, which provided more insights into miRNA-associated gene regulation during sucrose accumulation. Transcriptome analysis identified 18,722 differentially expressed genes (DEGs) between both genotypes during sucrose accumulation. The major DEGs identified were involved in starch and sucrose metabolism, and photosynthesis etc. miRNA sequencing identified 563 known and 281 novel miRNAs from both genotypes during sucrose accumulation. Of these, 311 miRNAs were differentially expressed.752 targets of 368 miRNAs (609 targets for 260 known miRNAs and 168 targets for 108 novel miRNAs) were identified by degradom sequencing.Several known and novel miRNAs and their target genes associated with sugar metabolism, sugar transport and sucrose storage were identified in this study.This new insight into the complex network of sucrose accumulation in sugarcane will help identify candidate targets for sucrose improvement in sugarcane through molecular means.
2021-12-30 | GSE188303 | GEO
Project description:Transcripts libraries were prepared from three sugarcane genotypes with high-sugar (HS), medium-sugar (MS) or low-sugar (LS) content that were treated with ethylene or H2O. The libraries were sequenced with the Illumina paired-end HiSeq platform.Transcriptomic analyses have identified about 160,000 unigenes of which 86000 annotated genes were classified into functional groups associated with carbohydrate metabolism, signaling, localization, transport, hydrolysis, growth, catalytic activity, membrane and storage, suggesting the structural and functional specification, including sucrose accumulation, occurring in maturing internodes. About 25,000 genes were differentially expressed between all genotypes and treatments combined. Genotype had a dominant effect on differential gene expression than ethylene treatment. Sucrose and starch metabolism genes were more responsive to ethylene treatment in low-sugar genotype. Ethylene caused differential gene expression of many stress-related transcription factors, carbohydrate metabolism, hormone metabolism and epigenetic modification. Ethylene-induced expression of ethylene-responsive transcription factors, cytosolic acid- and cell wall-bound invertases, and ATPase was more pronounced in low- than in high-sugar genotype, suggesting an ethylene-stimulated sink activity and consequent increased sucrose accumulation in low-sugar genotype.
2019-05-07 | GSE130757 | GEO
Project description:Sucrose is the major product of photosynthesis in many higher plants. It is transported from the source tissue through the phloem to various sink tissues to support plant growth, development and reproduction. Knowledge of the signal transduction pathways involved in carbohydrate metabolism is limited. Genes involved in the regulation of sucrose synthesis and accumulation could be used as tools in the development of genetically manipulated plants with higher sucrose content or aid in breeding programs as molecular markers. Using the SUCEST (Sugarcane EST) database information and a microarray approach, the expression profiles of 1920 sugarcane (Saccharum spp.) genes encoding signal transduction elements, transcription factors and stress-related proteins were analyzed. In order to assess their involvement in sucrose metabolism, the expression profiles of individuals from a sugarcane population segregated for sugar content were compared. From a population of 500 F1 individuals, the seven with the highest and the seven with the lowest sugar contents were selected, pooled and profiled using cDNA microarrays. Twenty-four genes were identified as differentially expressed. Five of them were more expressed in the plants with the highest sugar contents and 19 in the plants with the lowest sugar contents. RNA-blot hybridization was used to validate the expression profiles obtained for individuals in each group. These genes were shown to have differential expression throughout the growing season and in the different tissues. Our data supports the view that sugar levels modulate a complex signal transduction network that seems to involve responses related to stress. Keywords: Segregated population
2006-02-14 | GSE4233 | GEO
Project description:The rate of improvement of sugar content in sugarcane remains low for decades worldwide. Our previous transcriptome studies provided an atlas of sucrose accumulation-related gene expression but little is known about proteins involved. Here this knowledge gap is addressed by a proteomic analysis of experimentally altered sucrose accumulation in sugarcane. Analysis of stem proteomes of ripener ethephon-treated high- and low-sugar genotypes had identified 2983 proteins of which 139 were significantly differentially expressed (DEPs). These DEPs were found to be involved in sugar metabolism-related processes with 25 of them may have a regulatory role in sucrose accumulation. The key proteins identified include UDP-glucose 6-dehydrogenase associated with amino sugar and nucleotide sugar metabolism; those involved in carbon fixation; and fructokinase, β-D-glucosidase and α-glucan phosphorylase involved in starch and sucrose metabolism. Distinct genotype- and ethephon-dependent DEP expression was evident providing new insights on one of the most intractable sugarcane traits to breeding.
2022-08-12 | PXD024569 | Pride
Project description:By characterizing the cell wall proteomes of different sugarcane organs (leaves and stems) at two developmental stages (young vs mature/apical vs basal), it was possible to address unique characteristics in each of them. Four-month-old leaves showed a higher proportion of oxido-reductases and proteins related to lipid metabolism (LM), besides a lower proportion of proteins acting on polysaccharides, in comparison to four-month-old internodes. It was possible to note that sugarcane leaves and young stems have the highest LM rate than all species, which was assumed to be linked to cuticle formation. The data generated enriched the number of cell wall proteins (CWPs) identified in sugarcane, reaching 277. To our knowledge, sugarcane has now the second higher coverage of monocot CWP in plants
2018-01-05 | PXD007893 | Pride