Chantreau M.,University of Lille Nord de France |
Chantreau M.,French National Institute for Agricultural Research |
Grec S.,University of Lille Nord de France |
Grec S.,French National Institute for Agricultural Research |
And 18 more authors.
BMC Plant Biology | Year: 2013
Background: Flax (Linum usitatissimum L.) is an economically important fiber and oil crop that has been grown for thousands of years. The genome has been recently sequenced and transcriptomics are providing information on candidate genes potentially related to agronomically-important traits. In order to accelerate functional characterization of these genes we have generated a flax EMS mutant population that can be used as a TILLinG (Targeting Induced Local Lesions in Genomes) platform for forward and reverse genetics. Results: A population of 4,894 M2 mutant seed families was generated using 3 different EMS concentrations (0.3%, 0.6% and 0.75%) and used to produce M2 plants for subsequent phenotyping and DNA extraction. 10,839 viable M2 plants (4,033 families) were obtained and 1,552 families (38.5%) showed a visual developmental phenotype (stem size and diameter, plant architecture, flower-related). The majority of these families showed more than one phenotype. Mutant phenotype data are organised in a database and can be accessed and searched at UTILLdb (http://urgv.evry.inra.fr/UTILLdb). Preliminary screens were also performed for atypical fiber and seed phenotypes. Genomic DNA was extracted from 3,515 M2 families and eight-fold pooled for subsequent mutant detection by ENDO1 nuclease mis-match cleavage. In order to validate the collection for reverse genetics, DNA pools were screened for two genes coding enzymes of the lignin biosynthesis pathway: Coumarate-3-Hydroxylase (C3H) and Cinnamyl Alcohol Dehydrogenase (CAD). We identified 79 and 76 mutations in the C3H and CAD genes, respectively. The average mutation rate was calculated as 1/41 Kb giving rise to approximately 9,000 mutations per genome. Thirty-five out of the 52 flax cad mutant families containing missense or codon stop mutations showed the typical orange-brown xylem phenotype observed in CAD down-regulated/mutant plants in other species. Conclusions: We have developed a flax mutant population that can be used as an efficient forward and reverse genetics tool. The collection has an extremely high mutation rate that enables the detection of large numbers of independant mutant families by screening a comparatively low number of M2 families. The population will prove to be a valuable resource for both fundamental research and the identification of agronomically-important genes for crop improvement in flax. © 2013 Chantreau et al.; licensee BioMed Central Ltd.
Fenart S.,University of Lille Nord de France |
Ndong Y.A.,EA 3900 BioPI |
Duarte J.,Biogemma |
Riviere N.,Biogemma |
And 11 more authors.
BMC Genomics | Year: 2010
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. © 2010 Fenart et al; licensee BioMed Central Ltd.
Fontaine J.-X.,EA 3900 BioPI |
Fontaine J.-X.,Universite Ibn Tofail |
Molinie R.,EA 3900 BioPI |
Terce-Laforgue T.,French National Institute for Agricultural Research |
And 4 more authors.
Comptes Rendus Chimie | Year: 2010
It is now well established that the GS/GOGAT cycle is the major route for ammonium assimilation in higher plants. However, it has often been argued that other enzymes, such as glutamate dehydrogenase, have the capacity to assimilate ammonium, leading to the hypothesis that alternative ammonium assimilatory pathways could operate under particular physiological conditions. The GDH enzyme is encoded by two distinct genes, GDH1 and GDH2. A third gene, GDH3, potentially encoding GDH has recently been identified by in silico studies performed on Arabidopsis thaliana. In order to precise its function, the metabolic profile of gdh3 knock out mutants were compared to wild type plants using the 1H-NMR technique. 1H-NMR spectra coupled with principal component analysis and partial least square-discriminant analysis were applied to identify changes of the metabolic profiles. These experiments were performed on roots, leaves and stems. In the gdh3 mutant, metabolic variations were observed for carboxylic acids, amino acids and carbohydrates content. © 2009 Académie des sciences.