Project description:Characterization of bacterial and fungal community dynamics by high-throughput sequencing (HTS) metabarcoding during flax dew-retting
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.
Project description:Performances of flax gene expression analyses were compared in two categories of Nimblegen microarrays (short 25-mers oligonucleotides and long 60-mers oligonucleotides) Results obtained in this study are described in Intra-platform comparison of flax (Linum usitatissimum L.) high-density Nimblegen DNA microarrays submitted to Journal of Computational Biology We compared two categories of flax target probes: short (25-mers) oligonucleotides and long (60-mers) oligonucleotides in identical conditions of target production, design, labelling, hybridization, image analyses, and data filtering. This comparison was realized with two different flax samples and each RNA sample was used for the two categories of arrays. Experiments were realized in order to discriminate specific gene expression profiles of two different flax tissues (outer and inner stem tissues).
Project description:Performances of flax gene expression analyses were compared in two categories of Nimblegen microarrays (short 25-mers oligonucleotides and long 60-mers oligonucleotides) Results obtained in this study are described in Intra-platform comparison of flax (Linum usitatissimum L.) high-density Nimblegen DNA microarrays submitted to Journal of Computational Biology
Project description:We used our previously described gene expression platform (Fenart et al., 2010) to assess gene expression along the stem of flax, both in inner and outer tissues. 32 chips study using total RNA from Internal and external part of Flax stem, sampled on whole stem or in different parts of the stem.
