Montpellier Scientific Community



Biology and genetics of plant/pathogen interactions (BGPI)

Director: Philippe Rott
Research area
The JRU Biology and genetics of plant/pathogen interactions (BGPI) aims at improving the knowledge of the biology of plant pathogen populations and the mechanisms of plant/pathogen interactions with a view to improving the control of plant diseases caused by bacteria, fungi and viruses, using a systematic approach of integrative biology from the molecule to the population level.
Staff profile
Research Org.
Researchers
Professors
Research Eng.
Techn. & Admin. Staff
PhD
Mtp SupAgro, Cirad, INRA
 35 3 2 31 12
Research teams
Group 1: Detection, variability and expression of endogenous and exogenous Badnavirus
Badnavirus, belonging to the family Caulimoviridae, is an emerging viral genus on tropical crops. Four badnaviruses are particularly studied in our research topics, the cacao swollen shoot virus (CSSV), the sugar cane bacilliform virus (SCBV), the dioscorea bacilliform virus (DBV) and the banana streak virus (BSV). We study different questions related to the origin of the important molecular variability occurring in badnaviruses: the origin of the epidemics -exogenous versus endogenous origin-, the role and evolution of EPRVs and the mechanisms of their regulation.

Group 2: Caulimoviridae & Geminiviridae: Transmission & Evolution (CaGeTE)
The research group CaGeTE is interested in the impact of the mechanisms of host-to-host vector-transmission of viruses by vectors on the evolution of viral populations. We develop a multi-disciplinary approach (structural biology and biochemistry of interacting viral and vector proteins, cell biology of the host-virus relationship, and viral population genetics as well as experimental evolution). We use plant DNA viruses as biological models, in the families Caulimoviridae (Cauliflower mosaic virus, CaMV) and Geminiviridae (Tomato yellow leaf curl virus,TYLCV). Our research is based on the idea that specific mechanisms of virus-vector interactions might have been selected, not simply because they are securing efficient dispersal of the virus, but also because they optimize various traits of viral population genetics and evolution.

Group 3: Genomics and molecular analysis of pathogenicity of plant pathogenic bacteria
The objectives of our team are to analyze the genetic diversity of plant pathogenic bacteria and the molecular mechanisms that confer pathogenicity toward plants, with the aim of developing new control methods. Very few data are available to-date regarding the mechanisms that confer the capacity of these pathogens to colonize the host xylem. Our current goal is to identify and to study the function of bacterial pathogenicity genes involved in these mechanisms using the model Xanthomonas albilineans, a xylem-invading bacterium that attacks sugarcane.

Group 4: Rice-pathogens' interactions
Using the model interaction between rice and its major pathogen, the fungus Magnaporthe oryzae, a broad range of different forms of resistance (non-host, complete and partial resistance) are under study. Plant genes involved at different steps (pathogen perception, signal transduction and defense reactions) are identified and analyzed molecularly. Susceptibility is studied from both the pathogen side (identification of effector proteins contributing to fungal pathogenicity) and the plant side (biological functions required for hosting the pathogen). M. oryzae population diversity and adaptation to the host are characterized to integrate the evolution of the pathogen into breeding strategies for disease resistance.

Group 5: Biology and evolution of plant pathogenic fungi
The team aims at identifying the factors that contribute to the emergence and adaptation of fungal pathogens in response to fungicides and plant resistance use using two complementary approaches. A modelling approach is developed to study the evolution of pathogen life histories in agronomical landscapes and subsequent potential consequences of such evolution on emergence risks, resistance to fungicide and plant resistance breaking. Population genetics and quantitative genetics approaches are conducted on several biological models to study the adaptive potential of pathogen populations by (i) estimating parameters related to evolutionary factors, such as recombination, gene flow and selection, and (ii) determining the genetic support of adaptive traits. Combining both theoretical and empirical approaches will allow improving our evaluation of emergence risks and the elaboration of rational management strategies of fungicide and plant resistance use. The main biological models studied by the team are the fungi Magnaporthe oryzae and Mycosphaerella fijiensis that are pathogenic on rice and banana, respectively.

Group 6: Plant Epidemiology and vector transmission (EPI2V)
Researches on plant diseases transmitted by insects are conducted with the objective of understanding the dynamics of a pathosystem at temporal and spatial scales and to propose disease control strategies. Two stone-fruit trees diseases are used as biological models: the Sharka disease caused by the aphid-transmitted Plum pox virus and the European stone fruit yellows caused by ‘Candidatus Phytoplasma prunorum' transmitted by one species of Psyllidae. Complementary approaches are considered in the study of pathosystem dynamics: spatio-temporal analysis (at plant, field and regional level) of infected trees, modelling, molecular epidemiology, and insect biology.

Group 6: Plant Epidemiology and vector transmission (EPI2V)
Researches on plant diseases transmitted by insects are conducted with the objective of understanding the dynamics of a pathosystem at several temporal and spatial scales and to propose disease control strategies. Two stone-fruit trees diseases are used as biological models: the Sharka disease caused by the aphid-transmitted Plum pox virus and the European stone fruit yellows caused by ‘Candidatus Phytoplasma prunorum' transmitted by two sibling species of Psyllidae. Complementary approaches are considered in the study of pathosystem dynamics: spatio-temporal analysis (at plant, field and regional level) of infected trees, modelling, molecular epidemiology, and insect biology.

Group 7: Plant virus biodiversity and plant quarantine
The team aims at yielding large volumes of novel information regarding the viral biodiversity associated with threatened ecosystems, and the impact upon those biodiversities (and by extension the natural ecosystems) of human mediated disturbances. Studies of second generation metagenomics that link genome sequences to the plant hosts are currently conducted in two hot spots of biodiversity (South Africa/Western Cape and France/Camargue). The success of such a geo-metagenomics approach hinges on a sampling design that will enable us to address specific scientific questions such as: how do ecosystems respond to perturbation?, how widespread is gene flow between virus taxa infecting different host species?, etc. Besides these scientific activities, the team is developing quarantine services which include different processes such as disease indexing (sugarcane, banana, yam) and variety cleaning in transit centres (sugarcane, yam). Most of the applied diagnosis tests are aimed at detecting plant viruses and a few bacteria (including phytoplasmas) using a wide range of techniques. We also plan to develop in a near future improved plant virus diagnostic approaches, in particular using NGS-based plant viral metagenomics that could be used for routine indexing of quarantine plants.
Platforms and other tools
  • Greenhouse containment level 2: 400m2
  • Growth chambers containment level 3: 5x15 m2
  • Electron microscope
Most important international partnerships
- CARBAP and IRAD, Cameroon
- CNRA,Côte d'Ivoire
- CRIG, Ghana
- CSIC, Madrid and Barcelona, Spain
- ENA Meknes, laboratory of virology, Morocco
- PPT Lodi, Italy - PRI, Wageningen, The Netherlands
- Technical University of Berlin, Germany
- University of Basel, Switzerland
- University of Cape Town, South Africa
- University of Florida, Department of plant pathology, USA
- University of Glasgow, Institute of Biodiversity Animal Health and Comparative Medicine, UK
- University of Wisconsin-Madison, Department of plant pathology, USA
- Yunnan Academy of Agricultural Sciences, China
Facts and figures
Publications in international ranking journals
2009: 21
2008: 40
2007: 27
2006: 21
2005: 21
Representative publications
1. Ballini E., Morel J.B., Droc G., Price A.H., Courtois B., Nottéghem J.L., Tharreau D. (2008). A genome-wide meta-analysis of rice blast resistance genes and quantitative trait loci provides new insights into partial and complete resistance Molecular Plant-Microbe Interactions, 21(7):859-868.
2. Gayral P., Blondin L., Guidolin O., Carreel F., Hippolyte I., Perrier X., Iskra-Caruana M.-L. (2010). Evolution of endogenous sequences of Banana streak virus: what can we learn from banana (Musa sp.) evolution? Journal of Virology, 84(14):7346-7359.
3. Gutierrez S., Yvon M., Thebaud G., Monsion B., Michalakis Y., Blanc S. (2010). Dynamics of the multiplicity of cellular infection in a plant virus. PLoS Pathogens, 6.9e1001113.
4. Halkett F., Coste D., Rivas Platero G.G., Zapater M.F., Abadie C., Carlier J. (2010). Genetic discontinuities and disequilibria in recently established populations of the plant pathogenic fungus Mycosphaerella fijiensis. Molecular Ecology, 19:3909-3923.
5. Iskra-Caruana M.-L., Baurens F.-C., Gayral P., Chabannes M. (2010). A four-partner plant-virus interaction: Enemies can also come from within. Molecular Plant Microbe Interactions, 23(11):1394-1402.
6. Marguerettaz M., Pieretti I., Gayral P., Puig J., Brin C., Cociancich S., Poussier S., Rott P., Royer M., 2011. Genomic and evolutionary features of the SPI-1 type III secretion system that is present in Xanthomonas albilineans but not essential for xylem colonization and symptom development of sugarcane leaf scald. Molecular Plant-Microbe Interactions, 24(2):246-259.
7. Martinière A., Gargani D, Uzest M., Lautredou N., Blanc S., Drucker M. (2009) A role for plant microtubules in the formation of transmission-specific inclusion bodies of Cauliflower mosaic virus. Plant Journal, 58:135-146.
8. Pieretti I., Royer M., Barbe V., Carrere S., Koebnik R., Cociancich S., Couloux A., Darrasse A., Gouzy J., Jacques M.-A., Lauber E., Manceau C., Mangenot S., Poussier S., Segurens B., Szurek B., Verdier V., Arlat M., Rott P., 2009. The complete genome of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae. BMC Genomics, 10:616.
9. Ravigné V., Dieckmann U.,Olivieri I. 2009. Live where you thrive: Joint evolution of habitat choice and local adaptation facilitates specialization and promotes diversity. The American Naturalist, 174:141-169.
10. Rieux, A., Halkett, F., De Lapeyre De Bellaire, L., Zapater, M.-F., Rousset, F., Ravigné, V., Carlier J. (2011). Inferences on pathogenic fungus population structure from microsatellite data: an original landscape genetics approach reveals traces of historical events. Molecular Ecology, 20(8):1661-1674.
11. Thebaud G., Chadoeuf J., Morelli M.J., McCauley J.W., Haydon D.T. (2010). The relationship between mutation frequency and replication strategy in positive-sense single-stranded RNA viruses. Proceedings of the Royal Society B-Biological Sciences, 277:809-817.
12. Thébaud G., Yvon M., Alary R., Sauvion N., Labonne G. (2009). Efficient transmission of 'Candidatus Phytoplasma prunorum' is delayed by eight months due to a long latency in its host-alternating vector. Phytopathology, 99:265-273.
13. Uzest M., Gargani D., Drucker M., Hebrard E., Garzo E., Candresse T., Fereres A., Blanc S. (2007). A protein key to plant virus transmission at the tip of the insect vector stylet. Proceedings National Academy of Sciences USA, 104:17959-17964.
14. Vergne E., Grand X., Ballini E., Chalvon V., Saindrenan P., Tharreau D., Nottéghem J.L., Morel J.B. (2009). Preformed expression of defense is a hallmark of partial resistance to rice blast fungal pathogen Magnaporthe oryzae. BMC Plant Biology, 10:206.
15. Vuillaume F., Thébaud G., Urbino C., Forfert N., Granier M., Froissart R., Blanc S., Peterschmitt M. (2011). Distribution of the phenotypic effects of random homologous recombination between two virus species. PLoS Pathogens (in press).
Total annual budget
(in Euros) 2006 2007 2008
Total annual budget 3 844 000 1 548 000 4 170 000
External contracts: 807 000 969 000 1 211 000
ANR 130 000 266 000 406 000
EU 345 000 74 000 119 000
Private sector 77 000 113 000 198 000
Others 253 000 515 000