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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of maizde - downregulation of cinnamoyl-coenzyme A reductase in maize (affy_ccr_maize)

ABSTRACT: affy_ccr_maize - affy_ccr_maize - Cinnamoyl-CoA reductase (CCR) catalyzes a key step in monolignol biosynthesis. We show that downregulation of CCR in maize was associated with lower lignin content and a strong decrease in H units. Concomitantly, these cell wall modifications were associated with higher digestibility. On another hand, immunocytochemistry indicated a modification of lignification pattern and cellulose content. Transcript profiling was used as comprehensive phenotyping tools to investigate how CCR downregulation impacted metabolism and the biosynthesis of other cell wall polymers. -2 wild type and 2 CCR mutants were compared. Plants were grown in greenhouse condition and harvested at 7-8 leaf stages. Experiment Overall Design: 4 arrays - maize

ORGANISM(S): Zea mays

SUBMITTER: sandrine balzergue

PROVIDER: E-GEOD-11531 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Similar Datasets

Downregulation of cinnamoyl-coenzyme A reductase in maize (affy_ccr_maize)

Project description:affy_ccr_maize - affy_ccr_maize - Cinnamoyl-CoA reductase (CCR) catalyzes a key step in monolignol biosynthesis. We show that downregulation of CCR in maize was associated with lower lignin content and a strong decrease in H units. Concomitantly, these cell wall modifications were associated with higher digestibility. On another hand, immunocytochemistry indicated a modification of lignification pattern and cellulose content. Transcript profiling was used as comprehensive phenotyping tools to investigate how CCR downregulation impacted metabolism and the biosynthesis of other cell wall polymers. -2 wild type and 2 CCR mutants were compared. Plants were grown in greenhouse condition and harvested at 7-8 leaf stages. Keywords: gene knock in (transgenic)

2009-07-22 | GSE11531 | GEO

RNA-seq analysis of total RNA from inflorescence stems of Arabidopsis Col-0, ccr-1, fer-4 and ccr-1/fer-4

Project description:A. thaliana lines with reduced lignin content through down-regulation of the lignin biosynthesis enzymes cinnamoyl CoA reductase (CCR) exhibit extensive cell wall remodeling which results in the release of a mixture of pectic oligosaccharide elicitors of pathogenesis-related (PR) protein gene expression through the salicylic acid signaling pathway. Loss of function of FERONIA, a CrRLK1-like subfamily receptor-like kinase resulted in loss of PR-1, -2 and- 5 gene activation in stems of the ccr1/fer-4 double mutant.

2023-03-20 | GSE210734 | GEO

Comparative transcriptomes analysis at different developmental stages of seed embryo in maize by RNA-sequencing

Project description:we used two contrasting maize genotypes with differential oil accumulation percentage. High oil content (HOC) maize had 11% oil content while low oil content (LOC) maize had significantly lower oil content (5.4%). Transmission electron microscopy revealed a higher accumulation of oil bodies in the HOC maize embryo as compared to LOC maize. Comparative RNA-sequencing analysis at different developmental stages of seed embryo identified 739 genes that are constantly differentially expressed (DEGs) at all the six developmental stages from 15 days after pollination (DAP) to 40 DAP. KEGG enrichment analysis identified fatty acid metabolism and fatty acid biosynthesis as the most enriched biological pathways contributed by these DEGs. Notably, transcriptional changes are more intense at the early stages of embryo development as compared to later stages. In addition, pathways related to oil biosynthesis and their corresponding genes were more enriched at 30 DAP, which seems to be the key stage for oil accumulation. The study also identified 33 key DEGs involved in fatty acid and triacylglycerols biosynthesis, most of them were up-regulated in HOC, which may shape the differential oil contents in the two contrasting maize. Notably, we uncovered that both acyl-CoA-dependent and acyl-CoA-independent processes are essential for the high oil accumulation in maize embryo.

2019-08-20 | GSE136087 | GEO

Down-regulation of a gene encoding CCR affects... cell wall function in embryogenic cultures of Norway spruce

Project description:An attractive objective in the breeding of forest trees is to reduce the content of lignin or alter the lignin composition. However, for long-lived forest trees, such as conifers, it is time consuming and expensive to wait until mature wood is formed for estimating how different ligninfication genes affect cell wall differentiation. The aim of this work was to examine the possibility of detecting changes in global gene expression and of genes involved in lignin biosynthesis already in embryogenic cultures carrying the native Norway spruce cinnamoyl CoA reductase (CCR) gene in antisense orientation. Several genes, including genes regulating phenylalanine ammonia-lyase and peroxidase, regulating different pathways associated with lignin biosynthesis were affected but the transcript abundances of genes regulating lignin biosynthesis were not affected. Functional assignment defined by Gene Ontology terms, which provide functional classification for genes and gene products representing their corresponding biological process, cellular component and molecular function showed that transformation with asCCR affects a broad spectrum of functional categories, especially processes taking place in the cell wall. Furthermore, many changes in genes related to chromatin, DNA and chromosome take place. Keywords: transgenic Norway spruce, embryogenic culture

2006-12-27 | GSE6524 | GEO

Transcription profiling time series of Arabidopsis seedlings treated with the cellulose biosynthesis inhibitor isoxaben

Project description:We are interested in understanding how plants respond to cell wall stress. The stress is created through inhibition of cellulose biosynthesis. Isoxaben is a drug that inhibits cellulose biosynthesis in a dose dependent manner. We used a concentration of 600 nM isoxaben which should inhibit appr. 80% of cellulose biosynthesis. We performed a time course experiment where seedlings were treated for 36h with isoxaben and in parrallel untreated seedlings were grown. At 8 different timepoints treated and untreated samples were harvested.

2008-01-08 | E-MEXP-711 | biostudies-arrayexpress

Gibberellin-induced gene expression in maize mesocotyl under deep-sowing condition

Project description:In order to elucidate the molecular mechanism of gibberellin (GA)-induced mesocotyl elongation, gene expression profiling analyses were performed in a deep-sowing tolerant maize inbred line 3681-4. Gene expression studies combing Affymetrix GeneChip analysis and Real-time PCR were employed to determine the molecular mechanism underlying GA promotion of maize mesocotyl elongation. These studies showed that the GA receptor GID1, the transcriptional factor MYB, and the genes encoding DELLA protein DWRF8, kinases, Raf, LRR, RLCK, and involved in flavonoid biosynthesis, aminosugars metabolism, cell wall synthesis and modification, might play critical roles in maize mesocotyl elongation. In two independent experiments, we generate 10-day-old maize mesocotyl-specific gene expression profiles through comparing genome-wide expression patterns of GA3 treatment and UCZ (a GA biosynthesis inhibitor) treatment under 20 cm deep-sowing condition in darkness by using 17,555 Affymetrix maize whole genome array.

2009-03-07 | E-GEOD-15048 | biostudies-arrayexpress

Understanding the Diversity of Maize Cell Wall (affy_cellwall_maize)

Project description:affy_cellwall_maize - affy_cellwall_maize - Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription.-Comparison of internodes from 5 maize lines grown in field conditions 10 arrays - maize; organ comparison

2010-12-07 | E-GEOD-24624 | biostudies-arrayexpress

Gibberellin-induced gene expression in maize mesocotyl under deep-sowing condition

2009-03-07 | GSE15048 | GEO

affy_tj_maize-Understanding the Diversity of Maize Cell Wall

Project description:affy_en-tj_maize - affy_tj_maize - Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription, and eQTL.-Comparison of 2 maize lines : Cm484: good digestibility F98902: bad digestibility at the following development stage : 21 days after sowing -7 leaves- Keywords: genotype comparaison 4 arrays - maize

2011-06-01 | E-GEOD-18846 | biostudies-arrayexpress

affy_en_maize-Understanding the Diversity of Maize Cell Wall

Project description:affy_en-tj_maize - affy_en_maize - Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription, and eQTL.-Comparison of 2 maize lines : Cm484: good digestibility F98902: bad digestibility) , at the following developmental stade 2: male flowering Keywords: genotype comparaison 4 arrays - maize

2011-06-01 | E-GEOD-18857 | biostudies-arrayexpress

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