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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)

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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.

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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.

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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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