Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray

BMC Genomics

Research Article

Jorge Duarte¹  Nathalie Rivière¹  Jeroen Wilmer²  Laurent Gutierrez³  Yves-Placide Assoumou Ndong⁴  Olivier van Wuytswinkel⁴  Emmanuelle Cariou⁵  Reynald Tavernier⁶  Xavier Guillot⁷  Brigitte Thomasset⁸  Brigitte Chabbert⁹  Godfrey Neutelings^1,10  Simon Hawkins^1,10  Stéphane Fenart^1,10  Anca Lucau^1,10 

[1] BIOGEMMA, Z.I. du Brezet, 8 rue des Frères Lumières, 63028, Clermont-Ferrand cedex 2, France;BIOGEMMA, domaine de Sandreau, Chemin de Panedautes, 31700, Mondonville, France;CRRBM, UFR des Sciences, UPJV, 33 rue Saint Leu, 80039, Amiens cedex, France;EA 3900-BioPI, UFR des Sciences, UPJV, 33 rue Saint Leu, 80039, Amiens cedex, France;Institut Technique de Lin, 27170, Ecardenville La Campagne, France;LINEA, 20 Avenue Saget, 60 210, Grandvilliers, France;Laboulet Semences, 80 270, Airaines, France;UMR CNRS 6022, GEC, Université de Technologie de Compiègne, BP 20529, 60205 Compiègne cedex, France;UMR- INRA, UMR614, URCA, FARE, 2 Esplanade R. Garros, CREA, BP 224, 51686, Reims, France;Université Lille Nord de France, Lille 1 UMR INRA 1281, SADV, F- 59650, Villeneuve d'Ascq cedex, France;

关键词: Secondary Cell Wall;    Stem Tissue;    Vegetative Stage;    Fibre Quality;    Fibre Flax;   

DOI  :  10.1186/1471-2164-11-592

 received in 2010-07-29, accepted in 2010-10-21,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundFlax (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.ResultsNine 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.ConclusionAll 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.

【 授权许可】

Unknown   
© Fenart et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.