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Open Access Research article

PT-Flax (phenotyping and TILLinG of flax): development of a flax (Linum usitatissimum L.) mutant population and TILLinG platform for forward and reverse genetics

Maxime Chantreau12, Sébastien Grec12, Laurent Gutierrez3, Marion Dalmais4, Christophe Pineau5, Hervé Demailly3, Christine Paysant-Leroux6, Reynald Tavernier5, Jean-Paul Trouvé6, Manash Chatterjee78, Xavier Guillot9, Véronique Brunaud4, Brigitte Chabbert1011, Olivier van Wuytswinkel12, Abdelhafid Bendahmane4, Brigitte Thomasset13 and Simon Hawkins12*

Author Affiliations

1 Université Lille Nord de France, Lille 1 UMR 1281, Villeneuve d'Ascq cedex F-59650, France

2 INRA UMR, 281 Stress Abiotiques et Différenciation des Végétaux Cultivés, Villeneuve d’Ascq F-59650, France

3 CRRBM, UFR des Sciences, UPJV, 33 rue Saint Leu, Amiens cedex 80039, France

4 URGV, Unité de Recherche en Génomique Végétale, Université d'Evry Val d'Essonne, INRA, 2 rue Gaston Crémieux CP 5708, Evry cedex 91057, France

5 LINEA, 20 Avenue Saget, Grandvilliers, 60 210, France

6 Terre de Lin, société cooperative agricole, Saint-Pierre-Le-Viger, 76 740, France

7 Bench Bio Pvt Ltd., c/o Jai Research Foundation, Vapi, Gujarat 396195, India

8 National University of Ireland Galway (NUIG), University Road, Galway, Ireland

9 Laboulet Semences, Airaines, 80 270, France

10 INRA, UMR614 Fractionnement des AgroRessources et Environnement, Reims F-51100, France

11 Université de Reims Champagne-Ardenne, UMR614 Fractionnement des AgroRessources et Environnement, Reims F-51100, France

12 EA 3900-BioPI, UFR des Sciences, UPJV, 33 rue Saint Leu, Amiens cedex 80039, France

13 CNRS-FRE 3580, GEC, Université de Technologie de Compiègne, CS 60319, Compiègnecedex 60203, France

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BMC Plant Biology 2013, 13:159  doi:10.1186/1471-2229-13-159

Published: 15 October 2013

Abstract

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 webcite). 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.

Keywords:
Flax; TILLinG; Mutants; Fiber; Lignin; Lignan; Oil; Fatty acids