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Transcriptomics modifications in inner stem tissues of the flax lignified bast fiber mutant1 (lbf1)

ABSTRACT: Comparison of whole genome transcriptomics between stem inner tissues from flax lignified bast fiber mutant1 (lbf1) and wild-type

ORGANISM(S): Linum usitatissimum

PROVIDER: GSE61309 | GEO | 2014/09/11

SECONDARY ACCESSION(S): PRJNA260724

REPOSITORIES: GEO

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Transcriptomics modifications in outer stem tissues of the flax lignified bast fiber mutant1 (lbf1)

Project description:Comparison of whole genome transcriptomics between stem outer tissues from flax lignified bast fiber mutant1 (lbf1) and wild-type

2014-09-11 | GSE61310 | GEO

Transcriptomics modifications in inner/outer stem tissues of the flax lignified bast fiber mutant1 (lbf1)

Project description:Transcriptomics modifications in inner/outer stem tissues of the flax lignified bast fiber mutant1 (lbf1)

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Transcription profiling of flax stems and leaves from 4 week old flax plants to identify transcripts enriched in stem and phloem bast fibres

Project description:Stems and leaves from 4 week old flax plants were hybridized to an array of cDNAs from the outer (i.e. phloem enriched) layer of stems of the same age to identify transcripts enriched in stem (and phloem bast fibres).

2007-05-01 | E-MEXP-989 | biostudies-arrayexpress

Linum usitatissimum

Project description:Transcriptomics modifications in inner stem tissues of the flax lignified bast fiber mutant1 (lbf1)

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Transcriptomics modifications in inner/outer stem tissues of the flax lignified bast fiber mutant1 (lbf1)

Project description:This SuperSeries is composed of the SubSeries listed below.

2014-09-11 | GSE61311 | GEO

Identification of new potential molecular actors related to fiber quality in flax through Omics

Project description:One of the biggest challenges to a more widespread utilization of natural fibers from flax and other fiber plants is to obtain a better understanding of the different factors underlying the observed variability in fiber quality. To do this, we measured fiber morphometric parameters from seven different flax varieties (4 spring fiber, 2 winter fiber and 1 winter oil) and undertook Partial Least-Squares Discriminant Analysis (sPLS-DA) of transcriptomic data obtained from the same varieties in an attempt to identify high-information molecular markers. The calculation of Pearson correlation coefficients identified 5 putative gene-markers strongly correlated with morphometric features. Proteomic analysis on the two varieties showing the most discriminant and significant differences regarding to morphometrics identified an additional 4 protein-markers. The majority of the obtained markers are involved in lipid metabolism and the senescence process. Further comparative analysis of the obtained expression data with fiber mechanical measurements (strength, maximum force, area) obtained after field-retting for all 7 varieties allowed us to identify 4 highly-correlated putative molecular markers for the mechanical parameters. Three genes, connected directly or indirectly to cell wall metabolism (Expansin-related protein 3 precursor, beta-glucosidase and ascorbate peroxidase), and one gene coding an enzyme that catalyzes the oxidative decarboxylation of L-malate (NADP-malic enzyme 3). Based on our results, we hypothesize that a reduced number of RNA and protein functional markers can be used to more accurately monitor and/or predict fiber yield and quality properties in different flax varieties, thereby contributing to an Agriculture 4.0 for this economically-important species.

2023-07-18 | PXD039389 | Pride

Transcription profiling of flax (Linum usitatissimum) developmental series

Project description:Three 2cm segments were excised from different parts (TOP, MID, BOT) along the vertical axis of a 4 week old (25cm) stem of flax (L. usitatissimum) were compared using a cDNA amplicon array. Each segment represented a different developmental stage, especially in relation to bast fibre differentiation (i.e. TOP= elongation, MID=transition, BOT= thickening). Only the cDNAs that showed the highest differential expression were sequenced.

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gene expression analysis in different tissues of Flax (Linum usitatissimum L.)

Project description:We developped a new oligo microarray platform to analyse flax transcriptome. Here, we validated this microarray on several tissues of flax, at different developmental stages. 30 chips study using total RNA from 9 different tissue samples of Flax (Leaf sample at green capsule stage, stem inner tissue at vegetavie stage, stem outter tissue at vegetative stage, stem inner tissue at green capsule stage, stem outter tissue at green capsule stage, roots, embryos of 10, 20 and 40 days after flowering) for an overall survey of microarry accuracy and total RNA from 6 stem tissue at green capsule stage (3 of the cultivar 'Belinka' and 3 of the cultivar 'Drakkar') for an analysis of biological replicates reproducibility.

2010-06-15 | E-GEOD-21868 | biostudies-arrayexpress

Linum usitatissimum

Project description:Transcriptomics modifications in outer stem tissues of the flax lignified bast fiber mutant1 (lbf1)

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Whole transcriptome profiling of bast fibers of ramie

Project description:Ramie fibers extracted from the stem barks have been utilized for thousands years in China, and its biosynthetic mechanism is poorly understood. Here, we have characterized and compared the expression profiling of the barks from the top and middle part of stem where the secondary cellular walls (SCWs) of fiber cell have not initiated growth and was thickening, respectively; resulting in 4,520 differential expression (DE) protein-coding transcripts (PCTs), 1,287 DE long noncoding RNAs (lncRNAs), 88 DE miRNAs and 78 DE circular RNAs (circRNAs). Among the 4,520 DE PCTs, 75 were identified to be the homolog of the Arabidopsis SCW-biosynthetic genes. Overexpression of whole_GLEAN_10014861 (a homolog of SND1) in Arabidopsis caused a significant up-regulation in the expression of AtMYB46 and AtMYB83 that are two key regulators for SCW biosynthesis, thus conferring more fiber cells, along with a remarkable thickening in the SCWs of these cells. Bioinformatic prediction revealed 14 of the 75 homolog targeted by 16 noncoding RNAs (including 8 miRNAs and 8 lncRNAs), and two involved in the competing endogenous RNAs networks, indicating a complex regulatory network for the SCW biosynthesis of bast fiber in ramie. This study provides important insights into the bast fiber biosynthesis of ramie.

2019-05-02 | GSE130587 | GEO

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