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We have developed applied research programs in order to describe the aetiology of bacterial diseases emerging in France and to develop reliable tools for rapid diagnostic and detection. These tools have been used for clarifying the epidemiology of the diseases and to provide recommendation to control the diseases in the field. These research programs have been conducted in collaboration with technical institutes and seed companies. Nine bacterial diseases and non-pathogenic strains of Xanthomonas have been studied in the frame of partenarial research projects.
1 - Vertical oozing canker of walnut
This disease was observed first in orchards and nurseries in the two main areas of walnut production, in France in late 90’s and since spreaded widely. We have identified the causal agent as singular genetic lineage within Xanthomonas arboricola pv. juglandis that is the causal agent of bacterial blight of walnut that causes early fruit fall (Hajri et al., accepted in Plant Pathology). This project served as a springboard for more academic researches on the phylogeny X. arboricola (MLSA) and population genetic within the X. arboricola species (VNTR analysis and Type III effectors repertoire analysis (Post-doc A. Hajri). This project led us to set up and participate in the management of the COST 873 action entitlte “Bacterial diseases of stone fruits and nuts”. We organized the first meeting that launched the Action in Angers (2007), participated in several scientific meetings and organized in Angers a training worhshop with courses and practical work in Angers where we demonstrated the technique that we set up for the  specific detection of X. a. pv. juglandis in plant samples to a panel of 12 students from various European countries.
2 - Four bacterial diseases in the frame of BASELE program
BASELE is a program funded by the Fonds Unique Interministériel (FUI). It has been conducted in collaboration with two seed companies (Vilmorin and Clause vegetable seeds), the National federation of seed growers (FNAMS) and the technical services of vegetable producers of Loire valley.
-    Bacterial blight of radish. We have identified and characterized the causal agent of the disease as being Pseudomonas syringae pv. maculicola. The phylogeny of the genomospecies III of P. syringae where is assigned P. s. pv. maculicola was established and the genetic structure of population occurring in France has been describe using microsattelite analyses. We have shown that the bacterium is seedborne and that epiphytic populations occur on weed around contaminated field. Epidemiological analyses are undertaken using VNTR markers to assess the role of weed and seed in the contamination of radish cultures.
-    Bacterial spot of lamb lettuce. A rapid pathogenicity test was set up in order to allow the selection of resistant ecotypes within the wild Vallerianella populations (ACL4, ACL20). The selection and the screening are performed by Clause vegetable seeds.
-    Bacterial blight of leek. The epidemiology of the disease caused by P. s. pv. porri as been studied at the different steps in the leek production : seed, nurseries and leek production.
-    Slippery skin disease of Shallotte. The causal agent of this disease that spread within the production areas in Fance (Loire valley an Brittany) was identified as Burkholderia gladioli subp. alliicola. We have shown the role of mother bulbs in he spread of the disease. This disease is a serious threat for the production of traditional Shallotte in Loire Valley.
-    Specific molecular reagents were designed and detection techniques were set up for all bacteria responsible for these diseases. A declaration of invention was deposited for tools and the procedure of detection of P. s. pv. porri.
This project has been conducted with the participation of two engineers in CDD S. Gironde and P. Portier and then E. Charbit financed by this project.
3 – Bacterial blight of squash.
A bacterial blight has been observed on squash in Rhône valley and later in Chili. We have identified the causal agent as a new pathovar of Pseudomonas syringae (proposed as pv. peponis). A pathogenicity test was set up and the host range of this bacterium was determined within Cucurbitae. A molecular reagent was designed and a detection technique was set up. They were protected by the patent n° FR 09 54734.
This project has been conducted with the participation of B. Briand (AI-CDD) paid by Clause Vegetable seeds.
4 – The crown gall on grapevine.
The crown gall of grapevine is widespread in France. However, the occurrence of gall on plants make the exportation of plants difficult even impossible to certain countries. Viniflhor, then FranceAgriMer, ask for a survey of bacterial strains that occur in France and for a reliable procedure to check the mother plants and cuttings of primary plants. Agrobacterium populations present in France including A. vitis, A. tumefaciens and Rhizobium rhizogenes were charcterized by phenotypic and molecular methods. ENTAV (french institut for vine and wine) was provided with a protocol including new molecular reagents in order to set up a process to supply A. vitis free plants.
This project was conducted with the participation of P. Portier (IR-CDD) paid by FranceAgriMer.
5- The bacterial blight of carrots.
French carrot seed production suffers from 2003 of bacterial blight contaminations decreasing carrot seed quality. No epidemiological parameters for this emerging disease and no control method were available for French seed production. The aim of this project was to determine the main inoculum sources for field crops and evaluated some control method to limit bacterial blight incidence in carrot seed production.
This project was financed from 2003 to 2007 b CER Pays de Loire and since 2008 by FNAMS.
6- The bacterial canker of tomato.
The subspecies Clavibacter michiganensis subsp. michiganensis causes bacterial wilt and canker of tomato (Solanum lycopersicum, formerly Lycopersicon esculentum), an economically important disease causing yield losses worldwide. This quarantine disease is actually one of the most prevalent disease in tomato greenhouse production suspected to originate in undetected plantlet contaminations.
The aim of the project “Clavitom’ funded by French Ministry of Agriculture (Contrat de branche 2009-2011) is to provide new reliable detection methods and to define nuisibility thresholds for bacterial contamination of tomato seed lots that can be managed in current conditions for tomato production.