B. Palloix and . Moury, Different mutations in the genomelinked protein VPg of Potato Virus Y confer virulence on the pvr2 3 resistance in pepper, Molecular Plant-Microbe Interactions, vol.19, pp.557-563, 2006.

M. Betancourt, A. Fereres, A. Fraile, and F. Garc, Estimation of the Effective Number of Founders That Initiate an Infection after Aphid Transmission of a Multipartite Plant Virus, Journal of Virology, vol.82, issue.24, pp.12416-12421, 2008.
DOI : 10.1128/JVI.01542-08

F. Van-den-bosch and C. A. Gilligan, Measures of Durability of Resistance, Phytopathology, vol.93, issue.5, pp.616-625, 2003.
DOI : 10.1094/PHYTO.2003.93.5.616

R. Bourget, L. Chaumont, and N. Sapoukhina, Timing of Pathogen Adaptation to a Multicomponent Treatment, PLoS ONE, vol.84, issue.8, p.71926, 2013.
DOI : 10.1371/journal.pone.0071926.s002

URL : https://hal.archives-ouvertes.fr/hal-01209936

L. Bousset and A. M. Ch-evre, Stable epidemic control in crops based on evolutionary principles: Adjusting the metapopulation concept to agro-ecosystems, Agriculture, Ecosystems & Environment, vol.165, pp.118-129, 2013.
DOI : 10.1016/j.agee.2012.12.005

URL : https://hal.archives-ouvertes.fr/hal-01208640

J. K. Brown and A. Tellier, Plant-Parasite Coevolution: Bridging the Gap between Genetics and Ecology, Annual Review of Phytopathology, vol.49, issue.1, pp.345-367, 2011.
DOI : 10.1146/annurev-phyto-072910-095301

P. Carrasco, F. De-la-iglesia, and S. F. Elena, Distribution of Fitness and Virulence Effects Caused by Single-Nucleotide Substitutions in Tobacco Etch Virus, Journal of Virology, vol.81, issue.23, pp.12979-12984, 2007.
DOI : 10.1128/JVI.00524-07

P. Daszak, A. A. Cunningham, and A. D. Hyatt, Emerging Infectious Diseases of Wildlife-- Threats to Biodiversity and Human Health, Science, vol.287, issue.5452, pp.443-449, 2000.
DOI : 10.1126/science.287.5452.443

B. Dybiec, A. Kleczkowski, and C. A. Gilligan, Controlling disease spread on networks with incomplete knowledge, Physical Review E, vol.130, issue.6, p.66145, 2004.
DOI : 10.1016/S0378-4371(99)00042-4

F. Fabre, E. Rousseau, L. Mailleret, and B. Moury, Durable strategies to deploy plant resistance in agricultural landscapes, New Phytologist, vol.77, issue.4, pp.1064-1075, 2012.
DOI : 10.1094/PHYTO.2003.93.5.616

URL : https://hal.archives-ouvertes.fr/hal-01000305

F. Fabre, J. Montarry, J. Coville, R. Senoussi, V. Simon et al., Modelling the Evolutionary Dynamics of Viruses within Their Hosts: A Case Study Using High-Throughput Sequencing, PLoS Pathogens, vol.23, issue.4, p.1002654, 2012.
DOI : 10.1371/journal.ppat.1002654.s005

URL : https://hal.archives-ouvertes.fr/hal-01208592

J. A. Filipe, R. C. Cobb, R. K. Meentemeyer, C. A. Lee, Y. S. Valachovic et al., Landscape Epidemiology and Control of Pathogens with Cryptic and Long-Distance Dispersal: Sudden Oak Death in Northern Californian Forests, PLoS Computational Biology, vol.363, issue.1, p.1002328, 2012.
DOI : 10.1371/journal.pcbi.1002328.s001

H. H. Flor, Current Status of the Gene-For-Gene Concept, Annual Review of Phytopathology, vol.9, issue.1, pp.275-296, 1971.
DOI : 10.1146/annurev.py.09.090171.001423

A. Fraile, I. Pag-an, G. Anastasio, E. , and F. , Rapid Genetic Diversification and High Fitness Penalties Associated with Pathogenicity Evolution in a Plant Virus, Molecular Biology and Evolution, vol.28, issue.4, pp.1425-1437
DOI : 10.1093/molbev/msq327

F. Garc-ia-arenal and B. A. Mcdonald, An Analysis of the Durability of Resistance to Plant Viruses, Phytopathology, vol.93, issue.8, pp.941-952, 2003.
DOI : 10.1094/PHYTO.2003.93.8.941

K. A. Garrett, L. N. U~-niga, E. Roncal, G. A. Forbes, C. C. Mundt et al., Intraspecific functional diversity in hosts and its effect on disease risk across a climatic gradient, Ecological Applications, vol.64, issue.7, pp.1868-1883, 2009.
DOI : 10.1094/PHYTO.1998.88.8.754

C. A. Gilligan, Sustainable agriculture and plant diseases: an epidemiological perspective, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.406, issue.6797, pp.741-759, 2008.
DOI : 10.1038/35021046

URL : http://rstb.royalsocietypublishing.org/content/royptb/363/1492/741.full.pdf

C. A. Gilligan, J. E. Truscott, and A. J. Stacey, Impact of scale on the effectiveness of disease control strategies for epidemics with cryptic infection in a dynamical landscape: an example for a crop disease, Journal of The Royal Society Interface, vol.49, issue.4, pp.925-934, 2007.
DOI : 10.1046/j.1365-3059.2000.00483.x

S. Guti-errez, Y. Michalakis, and S. Blanc, Virus population bottlenecks during within-host progression and host-to-host transmission, Current Opinion in Virology, vol.2, issue.5, pp.546-555, 2012.
DOI : 10.1016/j.coviro.2012.08.001

M. R. Hajimorad, R. H. Wen, A. L. Eggenberger, J. H. Hill, and M. A. Maroof, Experimental Adaptation of an RNA Virus Mimics Natural Evolution, Journal of Virology, vol.85, issue.6, pp.2557-2564, 2011.
DOI : 10.1128/JVI.01935-10

B. D. Harrison, Virus variation in relation to resistance-breaking in plants, Euphytica, vol.124, issue.2, pp.181-192, 2002.
DOI : 10.1023/A:1015630516425

B. Janzac, J. Montarry, A. Palloix, O. Navaud, and B. Moury, Resistance of Pepper and a High Competitiveness Cost in Susceptible Cultivar, Molecular Plant-Microbe Interactions, vol.23, issue.6, pp.823-830, 2010.
DOI : 10.1094/MPMI-23-6-0823

C. E. Jenner, X. Wang, F. Pronz, and J. A. Walsh, A fitness cost for Turnip mosaic virus to overcome host resistance, Virus Research, vol.86, issue.1-2, pp.1-6, 2002.
DOI : 10.1016/S0168-1702(02)00031-X

B. C. Kang, I. Yeam, and M. M. Jahn, Genetics of Plant Virus Resistance, Annual Review of Phytopathology, vol.43, issue.1, pp.581-621, 2005.
DOI : 10.1146/annurev.phyto.43.011205.141140

S. Kiyosawa, Breakdown of blast resistance in relation to general strategies of resistance gene deployment to prolong effectiveness of resistance in plants, Plant Disease Epidemiology, vol.2, pp.251-283, 1989.

R. C. Lewontin, A general method for investigating the equilibrium of gene frequency in a population, Genetics, vol.43, pp.419-434, 1958.

L. Iacono, G. , F. Van-den, C. A. Bosch, and . Gilligan, Durable Resistance to Crop Pathogens: An Epidemiological Framework to Predict Risk under Uncertainty, PLoS Computational Biology, vol.104, issue.1, p.1002870, 2013.
DOI : 10.1371/journal.pcbi.1002870.s003

L. Mailleret and V. Lemesle, A note on semi-discrete modelling in the life sciences, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.4, issue.10, pp.4779-4799, 2009.
DOI : 10.1016/S1468-1218(02)00084-6

G. S. Mani, Evolution of Resistance with Sequential Application of Insecticides in Time and Space, Proceedings of the Royal Society of London. Series B, pp.245-276, 1989.
DOI : 10.1098/rspb.1989.0080

R. G. Masterton, Antibiotic heterogeneity, International Journal of Antimicrobial Agents, vol.36, pp.15-18, 2010.
DOI : 10.1016/S0924-8579(10)70005-4

R. K. Meentemeyer, S. E. Haas, and T. , Landscape Epidemiology of Emerging Infectious Diseases in Natural and Human-Altered Ecosystems, Annual Review of Phytopathology, vol.50, issue.1, pp.379-402, 2012.
DOI : 10.1146/annurev-phyto-081211-172938

N. Mideo, S. Alizon, and T. Day, Linking within- and between-host dynamics in the evolutionary epidemiology of infectious diseases, Trends in Ecology & Evolution, vol.23, issue.9, pp.511-517, 2008.
DOI : 10.1016/j.tree.2008.05.009

URL : https://hal.archives-ouvertes.fr/hal-01567939

B. Moury, F. Fabre, and R. Senoussi, Estimation of the number of virus particles transmitted by an insect vector, Proceedings of the National Academy of Sciences, vol.51, issue.2, pp.17891-17896, 2007.
DOI : 10.1016/0042-6822(85)90322-8

B. Moury, A. Fereres, F. Garc-ia-arenal, and H. Lecoq, Sustainable management of plant resistance to viruses, Recent Advances in Plant Virology, pp.219-236, 2011.

C. C. Mundt, Durable resistance: A key to sustainable management of pathogens and pests, Infection, Genetics and Evolution, vol.27, pp.446-455, 2014.
DOI : 10.1016/j.meegid.2014.01.011

C. C. Mundt and L. S. Brophy, Influence of Number of Host Genotype Units on the Effectiveness of Host Mixtures for Disease Control: A Modeling Approach, Phytopathology, vol.78, issue.8, pp.1087-1094, 1988.
DOI : 10.1094/Phyto-78-1087

A. Ohtsuki and A. Sasaki, Epidemiology and disease-control under gene-for-gene plant???pathogen interaction, Journal of Theoretical Biology, vol.238, issue.4, pp.780-794, 2006.
DOI : 10.1016/j.jtbi.2005.06.030

URL : http://pure.iiasa.ac.at/7774/1/IR-05-068.pdf

R. S. Ostfeld and F. Keesing, Effects of Host Diversity on Infectious Disease, Annual Review of Ecology, Evolution, and Systematics, vol.43, issue.1, pp.157-182, 2012.
DOI : 10.1146/annurev-ecolsys-102710-145022

J. Papa?-ix, H. Goyeau, P. Du-cheyron, H. Monod, and C. Lannou, Influence of cultivated landscape composition on variety resistance: an assessment based on wheat leaf rust epidemics, New Phytologist, vol.406, issue.4, pp.1095-1107, 2011.
DOI : 10.1038/35021046

J. Papa?-ix, O. David, C. Lannou, and H. Monod, Dynamics of Adaptation in Spatially Heterogeneous Metapopulations, PLoS ONE, vol.267, issue.2, p.54697, 2013.
DOI : 10.1371/journal.pone.0054697.s010

J. Papa?-ix, S. Touzeau, H. Monod, and C. Lannou, Can epidemic control be achieved by altering landscape connectivity in agricultural systems?, Ecological Modelling, vol.284, pp.35-47, 2014.
DOI : 10.1016/j.ecolmodel.2014.04.014

A. W. Park, S. Gubbins, and C. A. Gilligan, Invasion and persistence of plant parasites in a spatially structured host population, Oikos, vol.94, issue.1, pp.162-174, 2001.
DOI : 10.1034/j.1600-0706.2001.10489.x

S. Parnell, T. R. Gottwald, F. Van-den, C. A. Bosch, and . Gilligan, Optimal Strategies for the Eradication of Asiatic Citrus Canker in Heterogeneous Host Landscapes, Phytopathology, vol.99, issue.12, pp.1370-1376, 2009.
DOI : 10.1094/PHYTO-99-12-1370

S. Parnell, T. R. Gottwald, C. A. Gilligan, N. J. Cunniffe, F. Van-den et al., The Effect of Landscape Pattern on the Optimal Eradication Zone of an Invading Epidemic, Phytopathology, vol.100, issue.7, pp.638-644, 2010.
DOI : 10.1094/PHYTO-100-7-0638

M. Plantegenest, C. L. May, and F. Fabre, Landscape epidemiology of plant diseases, Journal of The Royal Society Interface, vol.406, issue.6797, pp.963-972, 2007.
DOI : 10.1038/35021046

A. Power and C. E. Mitchell, Pathogen Spillover in Disease Epidemics, The American Naturalist, vol.164, issue.S5, pp.79-89, 2004.
DOI : 10.1086/424610

L. A. Real and R. Biek, Spatial dynamics and genetics of infectious diseases on heterogeneous landscapes, Journal of The Royal Society Interface, vol.32, issue.4, pp.935-948, 2007.
DOI : 10.1146/annurev.py.32.090194.002443

N. Sapoukhina, C. E. Durel, and B. L. Cam, Spatial deployment of gene-for-gene resistance governs evolution and spread of pathogen populations, Theoretical Ecology, vol.406, issue.4, pp.229-238, 2009.
DOI : 10.1007/s12080-009-0045-5

P. Skelsey, W. A. Rossing, G. J. Kessel, and W. Van-der-werf, at the Landscape Level: How Do Spatial Scale and Weather Modulate the Consequences of Spatial Heterogeneity in Host Resistance?, Phytopathology, vol.100, issue.11, pp.1146-1161, 2010.
DOI : 10.1094/PHYTO-06-09-0148

. Fabre, Durable resistance in agricultural landscape

P. Skelsey, K. A. With, and K. A. Garrett, Pest and Disease Management: Why We Shouldn't Go against the Grain, PLoS ONE, vol.7, issue.9, p.75892, 2013.
DOI : 10.1371/journal.pone.0075892.g004

L. L. Sullivan, B. L. Johnson, L. A. Brudvig, and N. M. Haddad, Can dispersal mode predict corridor effects on plant parasites?, Ecology, vol.92, issue.8, pp.1559-1564, 2011.
DOI : 10.1890/04-0913

URL : http://onlinelibrary.wiley.com/doi/10.1890/10-1116.1/pdf

P. D. Taylor, L. Fahrig, K. Henein, and K. G. Merriam, Connectivity Is a Vital Element of Landscape Structure, Oikos, vol.68, issue.3, pp.571-573, 1993.
DOI : 10.2307/3544927

D. Tilman, Global environmental impacts of agricultural expansion: The need for sustainable and efficient practices, Proceedings of the National Academy of Sciences, vol.58, issue.2, pp.5995-6000, 1999.
DOI : 10.2136/sssaj1994.03615995005800020040x

C. Torres-barcelo, J. A. Daros, and S. F. Elena, Compensatory Molecular Evolution of HC-Pro, an RNA-Silencing Suppressor from a Plant RNA Virus, Molecular Biology and Evolution, vol.27, issue.3, pp.543-551, 2010.
DOI : 10.1093/molbev/msp272

M. S. Wolfe, The Current Status and Prospects of Multiline Cultivars and Variety Mixtures for Disease Resistance, Annual Review of Phytopathology, vol.23, issue.1, pp.251-273, 1985.
DOI : 10.1146/annurev.py.23.090185.001343

J. Zhan, P. H. Thrall, J. Papa?-ix, L. Xie, and J. J. Burdon, Playing on a Pathogen's Weakness: Using Evolution to Guide Sustainable Plant Disease Control Strategies, Annual Review of Phytopathology, vol.53, issue.1, pp.19-43, 2015.
DOI : 10.1146/annurev-phyto-080614-120040

URL : https://hal.archives-ouvertes.fr/hal-01536434

Y. Y. Zhu, H. R. Chen, J. H. Fan, Y. Y. Wang, Y. Li et al., Genetic diversity and disease control in rice, Nature, vol.406, issue.6797, pp.718-722, 2000.
DOI : 10.1038/35021046