Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray
Rattachement africain : fr, ca, br. Niveau de preuve : code pays fourni par la source.
Le résumé fourni par la source
Abstract Background Flax (Linum usitatissimum L.) has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars) and its cellulose-rich fibres (fibre-flax cultivars) used for high-value linen garments and composite materials. Despite the wide industrial use of flax-derived products, and our actual understanding of the regulation of both wood fibre production and oil biosynthesis more information must be acquired in both domains. Recent advances in genomics are now providing opportunities to improve our fundamental knowledge of these complex processes. In this paper we report the development and validation of a high-density oligo microarray platform dedicated to gene expression analyses in flax. Results Nine different RNA samples obtained from flax inner- and outer-stems, seeds, leaves and roots were used to generate a collection of 1,066,481 ESTs by massive parallel pyrosequencing. Sequences were assembled into 59,626 unigenes and 48,021 sequences were selected for oligo design and high-density microarray (Nimblegen 385K) fabrication with eight, non-overlapping 25-mers oligos per unigene. 18 independent experiments were used to evaluate the hybridization quality, precision, specificity and accuracy and all results confirmed the high technical quality of our microarray platform. Cross-validation of microarray data was carried out using quantitative qRT-PCR. Nine target genes were selected on the basis of microarray results and reflected the whole range of fold change (both up-regulated and down-regulated genes in different samples). A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates both in qRT-PCR and microarray results. Further experiments illustrated the capacity of our arrays to detect differential gene expression in a variety of flax tissues as well as between two contrasted flax varieties. Conclusion All results suggest that our high-density flax oligo-microarray platform can be used as a very sensitive tool for analyzing gene expression in a large variety of tissues as well as in different cultivars. Moreover, this highly reliable platform can also be used for the quantification of mRNA transcriptional profiling in different flax tissues.
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Laboratoire de Génétique & Evolution des Populations Végétales pays non établi dans la noticeStructure de recherche
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Stress Abiotiques et Différenciation des Végétaux Cultivés pays non établi dans la noticeStructure de recherche
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Biologie des Plantes et Innovation pays non établi dans la noticeStructure de recherche
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Biogemma (France) pays non établi dans la noticeEntreprise
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Institut Technique de l'Aviculture pays non établi dans la noticeStructure de recherche
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Fractionnation of AgroResources and Environment pays non établi dans la noticeStructure de recherche
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Semtech (Canada) pays non établi dans la noticeEntreprise
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Laboratório Interinstitucional de e-Astronomia pays non établi dans la noticeOrganisme public
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Enzyme and Cell Engineering - Molecular Recognition and Biocatalysis pays non établi dans la noticeStructure de recherche
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Génétique et évolution des populations végétales pays non établi dans la noticeInstitution
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Institut Technique du Lin pays non établi dans la noticeStructure de recherche
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Centre de ressources régionales en biologie moléculaire (CRRBM) pays non établi dans la noticeInstitution
Laboratoire de Génétique & Evolution des Populations Végétales, Stress Abiotiques et Différenciation des Végétaux Cultivés et Biologie des Plantes et Innovation, avec 9 autres affiliations.
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