Genetic diversity of[i] Rhizoctonia solani[/i] associated with potato tubers in France

Affiche, résuméThe plant pathogenic soil-borne fungus Rhizoctonia solani causes severe damages in crops all around the world. Tubers of potato are frequently affected by R. solani leading to the downgrading of the production. Generally the isolates involved in the sclerotia occurring at the surface of the tuber are assigned to the anastomosis group (AG) 3 but a more precise characterization of the diversity of this deleterious group is needed to set up appropriate control strategies. The diversity of 73 French isolates from the mains potato seed production areas and 31 isolates originating from 9 other countries was assessed according to 3 molecular approaches. Three phylogenetic trees were built up based on the sequences of the internal transcribed spacer (ITS) region and the gene tef-1α as well as the comparison of the total DNA fingerprints of each strain established by amplified fragment length polymorphism (AFLP). The determination of the AGs of R. solani based on the sequencing of the ITS region showed 3 different AGs among our collection (60 AG 3, 8 AG 2-1 and 5 AG 5). Grouping of the isolates belonging to the same AG was confirmed by the sequencing of the gene tef-1α used for the first time to study the genetic diversity of R. solani. About 42 % of the ITS sequences and 73 % of the gene tef-1α sequences contained polymorphic sites where several nucleotides are possible, suggesting that the cells of R. solani strains contain several copies of ITS and gene tef-1α within the same nucleus or between different nuclei. Phylogenetic trees showed a greater genetic diversity within AGs in tef-1α sequences than in ITS sequences. The AFLP analyses showed an even greater diversity among the strains demonstrating that the French strains of R. solani isolated from potatoes were not a clonal population. Moreover, there was no relationship between the geographical origins of the strains or the potato variety from which they were isolated and their genetic diversity. This important and under evaluated genetic diversity as the lack of population structure suggest important genetic mixings leading to a constant evolution within R. solani and could explain the difficulties to control it successfully

Moyens communs: ensemble des ressources biologiques (ERB)

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Ensemble de Ressources Biologiques dédiées à l'Agroécologie (INRA, Dijon). Mieux connaître, conserver et utiliser les ressources du sol.

National audienceLes spécificités de la problématique biodiversité dans le domaine agricole sont directement liées à l'ensemble des ressources génétiques, qu'elles soient microbiennes, végétales ou animales, et nécessitent la prise en compte de ces multiples composantes, leur fonctionnalité et leurs interactions pour en assurer la conservation et la valorisation. Gérer ces ressources biologiques consiste à les préserver in situ, mais aussi, à les inventorier, les caractériser et les évaluer, les conserver ex situ éventuellement, les régénérer et les diffuser ainsi que les connaissances afférentes. En collaboration avec le CRB Ferdinand Cabanne (http://www.crbferdinandcabanne.fr/) du CHU de Dijon qui dispose d'une expertise dans la gestion de ressources biologiques d'origine humaine, l'UMR Agroécologie de Dijon a pour objectif de regrouper les différentes collections d'organismes non humains existantes sur le campus de Dijon, dans leur fonctionnement et le service qu’elles doivent fournir, en un Ensemble de Ressources Biologiques pour les Organismes et les Microorganismes d’Intérêt Agronomique et Environnemental (http://www2.dijon.inra.fr/umrmse/) dédié à l'Agroécologie. Dans un premier temps, un accent particulier sera porté sur les ressources microbiologiques afin d'obtenir dès 2013 la certification AFAQ/AFNOR NF S 96-900 permettant la création d'un CRB pour ces microorganismes, pour entrainer ensuite dans cette démarche qualité l'ensemble des autres ressources biologiques

Detection of viable fungal spores contaminant on documents and rapid control of the effectiveness of an ethylene oxide disinfection using ATP assay

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Approches complémentaires de l'étude de la méthylation des cytosines de l'ADN. Application au génome de la truite : LuMA vs LC-UV vs ELISA

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MIAE : a collection dedicated to soil microbial diversity and environment (INRA, Dijon, France)

International audienceThe MIAE (Microorganisms of Interest for Agriculture and Environment) structure is holding over 15 300 soil-borne microbial strains belonging to 48 genera of fungi (Fusarium, Rhizoctonia, Trichoderma, Clonostachys, Alternaria…) as well as yeast (Saccharomyces), and oomycetes (Pythium, Phytophthora) and 13 genera of bacteria (Pseudomonas, Bradyrhizobium, Synorhizobium, Rhizobium…). These microorganisms have been isolated for over 30 years of scientific investigations related to soil functioning: -nitrogen cycle -fate of pesticides in the soil and underground water -plant-microorganisms loop in the rhizosphere -use of beneficial microorganisms to control development and infectious activities of plant pathogenic fungi -impact of agricultural practices on the ecology of soil-borne plant pathogenic fungi -bio-indicators of soil health. More than 100 strains a year are deposited at MIAE collection. So far, fungal and bacterial identification focused on cultural, chemotaxonomic and/or metabolic properties. At the present time a specific focus is being given to the molecular characterization and identification including the set up of appropriate molecular tools. Up to 2008, each microbial resource was preserved by the scientist involved in isolation, leading sometimes to orphan collections. The creation of a unique and common collection aiming at guaranteeing the preservation of these microbial resources and all the related data required a specific approach based on High Quality Standard. In that frame, the setting up of this collection and its management are performed to get in 2013 the certification ISO9001:2000. To achieve this, following items are under advancement: - preservation of microbial strains. Most of the strains are preserved at -80°C with glycerol in duplicate. Rhizoctonia and oomycota (Pythium, Phytophthora) are preserved on agar slants at room temperature. Long-term preservation protocols at 4°C are under evaluation. - exploitation and valorization of the collection, through a database. It will be used for the administration of the collection and the on-line catalogue - distribution of microbial strains to scientific community, for educational, research and industrial purposes, provided that Material Transfer Agreement (MTA) is being concluded - national/international showcase via a MIAE webpag