D. A. St-clair, Quantitative disease resistance and quantitative resistance loci in breeding, Annu Rev Phytopathol, vol.48, issue.1, pp.247-68, 2010.

C. C. Mundt, C. Cowger, and K. A. Garrett, Relevance of integrated disease management to resistance durability, Euphytica, vol.124, issue.2, pp.245-52, 2002.

C. C. Mundt, Durable resistance: a key to sustainable management of pathogens and pests, Infect Genet Evol, vol.27, pp.446-55, 2014.

, Crop production information: Apricots

, Accessed, 2018.

L. Gardan, J. P. Prunier, J. Luisetti, and J. J. Bezelgues, Responsabilité de divers Pseudomonas dans le dépérissement bactérien de l'abricotier en France. Revue de Zoologie Agricole et de Pathologie Végétale, vol.4, pp.112-132, 1973.

J. E. Crosse, Bacterial diseases of stone-fruit trees in Britain: IX. Bacteriosis of apricot, Trans Br Mycol Soc, vol.36, issue.1, pp.38-45, 1953.

O. Berge, C. L. Monteil, C. Bartoli, C. Chandeysson, C. Guilbaud et al., A user's guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex, PLoS One, vol.9, issue.9, p.105547, 2014.

M. Scortichini, Epidemiology and predisposing factors of some major bacterial diseases of stone and nut fruit trees species, J Plant Pathol, vol.92, issue.1, pp.73-81, 2010.

J. R. Lamichhane, L. Varvaro, L. Parisi, J. M. Audergon, and C. E. Morris, Disease and frost damage of woody plants caused by Pseudomonas syringae: seeing the forest for the trees, Adv Agron, vol.126, pp.235-95, 2014.

M. M. Kennelly, F. M. Cazorla, A. De-vicente, C. Ramos, and G. W. Sundin, Pseudomonas syringae diseases of fruit trees: progress toward understanding and control, Plant Dis, vol.91, issue.1, pp.4-17, 2007.

A. Vigouroux, Ingress and spread of Pseudomonas in stems of peach and apricot promoted by frost-related water-soaking of tissues, Plant Dis, vol.73, issue.10, pp.854-859, 1989.

Z. Klement, D. S. Rozsnyay, E. Báló, M. Pánczél, and G. Prileszky, The effect of cold on development of bacterial canker in apricot trees infected with Pseudomonas syringae pv. syringae, Physiol Plant Pathol, vol.24, issue.2, pp.237-283, 1984.

J. M. Young, Orchard management and bacterial diseases of stone fruit, N Z J Exp Agric, vol.15, issue.2, pp.257-66, 1987.

J. P. Prunier and O. Bordjiba, Effect of frost on bacterial necrosis of apricot buds, Acta Hortic, vol.293, pp.495-502, 1991.

J. P. Prunier, J. M. Audergon, and J. Cotta, Etude de la sensibilité variétale de l'abricotier au chancre bacterien, Programme de recherche Agrimed: Deuxièmes rencontres sur l'abricotier: 1993. Avignon: Office des publications officielles des communautés européennes, pp.111-113, 1993.

L. Brun, F. Warlop, V. Mercier, J. Broquaire, G. Clauzel et al., Quelle sélection fruitière pour une production durable, à faible niveau d'intrants ? Méthodologie pour un réseau de sélection variétale décentralisée, Innovations Agronomiques, vol.15, pp.105-120, 2011.

C. Garrett, Screening Prunus rootstocks for resistance to bacterial canker, caused by Pseudomonas morsprunorum, J Hortic Sci, vol.54, issue.3, pp.189-93, 1979.

J. Mgbechi-ezeri, L. Porter, K. B. Johnson, and N. Oraguzie, Assessment of sweet cherry (Prunus avium L.) genotypes for response to bacterial canker disease, Euphytica, vol.213, issue.7, p.145, 2017.

K. E. Bedford, P. L. Sholberg, and F. Kappel, Use of a detached leaf bioassay for screening sweet cherry cultivars for bacterial canker resistance, XXVI International Horticultural Congress: Genetics and Breeding of Tree Fruits and Nuts: 2003. Leuven: International Society for Horticultural Science

B. Li, M. T. Hulin, P. Brain, J. W. Mansfield, R. W. Jackson et al., Rapid, automated detection of stem canker symptoms in woody perennials using artificial neural network analysis, Plant Methods, vol.11, p.57, 2015.

J. W. Davey, P. A. Hohenlohe, P. D. Etter, J. Q. Boone, J. M. Catchen et al., Genome-wide genetic marker discovery and genotyping using nextgeneration sequencing, Nat Rev Genet, vol.12, issue.7, pp.499-510, 2011.

C. Zhu, M. Gore, E. S. Buckler, and J. Yu, Status and prospects of association mapping in plants, Plant Genome J, vol.1, issue.1, p.5, 2008.

M. A. Khan and S. S. Korban, Association mapping in forest trees and fruit crops, J Exp Bot, vol.63, issue.11, pp.4045-60, 2012.

T. Ogura and W. Busch, From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development, Curr Opin Plant Biol, vol.23, pp.98-108, 2015.

M. Nordborg and D. Weigel, Next-generation genetics in plants, Nature, vol.456, issue.7223, pp.720-723, 2008.

P. K. Ingvarsson and N. R. Street, Association genetics of complex traits in plants, New Phytol, vol.189, issue.4, pp.909-931, 2011.

X. Huang and B. Han, Natural variations and genome-wide association studies in crop plants, Annu Rev Plant Biol, vol.65, issue.1, pp.531-51, 2014.

C. Font-i-forcada, N. Oraguzie, S. Reyes-chin-wo, and M. T. Espiau, Socias i Company R, Fernández i Martí A. Identification of genetic loci associated with quality traits in almond via association mapping, PLoS One, vol.10, issue.6, p.127656, 2015.

K. Cao, Z. K. Zhou, Q. Wang, J. Guo, P. Zhao et al., Genome-wide association study of 12 agronomic traits in peach, Nat Commun, vol.7, p.13246, 2016.

S. Mariette, F. Wong-jun-tai, G. Roch, A. Barre, A. Chague et al., Genome-wide association links candidate genes to resistance to plum pox virus in apricot (Prunus armeniaca), New Phytol, vol.209, issue.2, pp.773-84, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01198840

K. Arumuganathan and E. D. Earle, Nuclear DNA content of some important plant species, Plant Mol Biol Report, vol.9, issue.3, pp.208-226, 1991.

K. M. Folta and S. E. Gardiner, Genomics-based opportunities in apricot, Genetics and Genomics of Rosaceae, pp.315-350, 2009.

D. Zaurov, T. Molnar, S. Eisenman, T. M. Ford, R. Mavlyanova et al., Genetic resources of apricots (Prunus armeniaca L.) in Central Asia, HortScience, vol.48, issue.6, pp.681-91, 2013.

K. U. Yilmaz and K. Gurcan, Genetic Diversity in Plants Mahmut Caliskan, pp.249-70, 2012.

H. Bourguiba, J. Audergon, L. Krichen, N. Trifi-farah, A. Mamouni et al., Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin, BMC Plant Biol, vol.12, p.49, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01191293

E. Rikkerink, N. C. Oraguzie, and S. E. Gardiner, Prospects of association mapping in perennial horticultural crops, Association Mapping in Plants, pp.249-69, 2007.

C. Bartoli, S. Carrere, J. R. Lamichhane, L. Varvaro, and C. E. Morris, Whole-genome sequencing of 10 Pseudomonas syringae strains representing different host range spectra, Genome Announc, vol.3, issue.2, pp.379-394, 2015.

E. O. King, M. K. Ward, and D. E. Raney, Two simple media for the demonstration of pyocyanin and fluorescin, J Lab Clin Med, vol.44, issue.2, pp.301-308, 1954.

T. Cao, R. J. Sayler, T. M. Dejong, B. C. Kirkpatrick, R. M. Bostock et al., Influence of stem diameter, water content, and freezing-thawing on bacterial canker development in excised stems of dormant stone fruit, Phytopathology, vol.89, issue.10, pp.962-968, 1999.

A. R. Gilmour, R. Thompson, and B. R. Cullis, Average information REML: an efficient algorithm for variance parameter estimation in linear mixed models, Biometrics, vol.51, issue.4, pp.1440-50, 1995.

I. Verde, A. G. Abbott, S. Scalabrin, S. Jung, S. Shu et al., The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution, Nat Genet, vol.45, issue.5, pp.487-94, 2013.

S. Y. Kim, K. E. Lohmueller, A. Albrechtsen, Y. Li, T. Korneliussen et al., Estimation of allele frequency and association mapping using next-generation sequencing data, BMC Bioinformatics, vol.12, issue.1, p.231, 2011.

Y. S. Aulchenko, S. Ripke, A. Isaacs, and C. M. Van-duijn, GenABEL: an R library for genome-wide association analysis, Bioinformatics, vol.23, issue.10, pp.1294-1300, 2007.

D. H. Alexander, J. Novembre, and K. Lange, Fast model-based estimation of ancestry in unrelated individuals, Genome Res, vol.19, issue.9, pp.1655-64, 2009.

H. M. Kang, J. H. Sul, S. K. Service, N. A. Zaitlen, S. Kong et al., Variance component model to account for sample structure in genome-wide association studies, Nat Genet, vol.42, issue.4, pp.348-57, 2010.

B. Mangin, A. Siberchicot, S. Nicolas, A. Doligez, P. This et al., Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness, Heredity, vol.108, pp.285-91, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01267769

E. M. Heifetz, J. E. Fulton, N. O'sullivan, H. Zhao, J. Dekkers et al., Extent and consistency across generations of linkage disequilibrium in commercial layer chicken breeding populations, Genetics, vol.171, issue.3, pp.1173-81, 2005.

S. D. Turner, qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots: biorXiv, 2014.

F. Bonnafous, G. Fievet, N. Blanchet, M. Boniface, S. Carrère et al., Comparison of GWAS models to identify non-additive genetic control of flowering time in sunflower hybrids, Theor Appl Genet, vol.131, issue.2, pp.319-351, 2018.

V. Segura, B. J. Vilhjálmsson, A. Platt, A. Korte, Ü. Seren et al., An efficient multi-locus mixed model approach for genome-wide association studies in structured populations, Nat Genet, vol.44, issue.7, pp.825-855, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01267792

X. Zhou and M. Stephens, Efficient multivariate linear mixed model algorithms for genome-wide association studies, Nat Methods, vol.11, issue.4, pp.407-416, 2014.

J. Chen and Z. Chen, Extended bayesian information criteria for model selection with large model spaces, Biometrika, vol.95, issue.3, pp.759-71, 2008.

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J R Stat Soc Ser B Methodol, vol.57, issue.1, pp.289-300, 1995.

A. Luna, K. K. Nicodemus, and . Snp, plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package, Bioinformatics, vol.23, issue.6, pp.774-780, 2007.

Y. Choi and A. P. Chan, PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels, Bioinformatics, vol.31, issue.16, pp.2745-2752, 2015.

W. Muir, W. E. Nyquist, and S. Xu, Alternative partitioning of the genotype-byenvironment interaction, Theor Appl Genet, vol.84, issue.1-2, pp.193-200, 1992.

V. V. Kapitonov and J. Jurka, Harbinger transposons and an ancient HARBI1 gene derived from a transposase, DNA Cell Biol, vol.23, issue.5, pp.311-335, 2004.

A. Musacchio, T. Gibson, P. Rice, J. Thompson, and M. Saraste, The PH domain: a common piece in the structural patchwork of signalling proteins, Trends Biochem Sci, vol.18, issue.9, pp.343-351, 1993.

T. Quesada, V. Gopal, W. P. Cumbie, A. J. Eckert, J. L. Wegrzyn et al., Association mapping of quantitative disease resistance in a natural population of loblolly pine, Pinus taeda L.). Genetics, vol.186, issue.2, pp.677-86, 2010.

M. Foulongne, T. Pascal, F. Pfeiffer, and J. Kervella, QTLs for powdery mildew resistance in peach × Prunus davidiana crosses: consistency across generations and environments, Mol Breed, vol.12, issue.1, pp.33-50, 2003.

F. Calenge and C. E. Durel, Both stable and unstable QTLs for resistance to powdery mildew are detected in apple after four years of field assessments, Mol Breed, vol.17, issue.4, pp.329-368, 2006.

V. Segura, C. Durel, and E. Costes, Dissecting apple tree architecture into genetic, ontogenetic and environmental effects: QTL mapping, Tree Genet Genomes, vol.5, issue.1, pp.165-79, 2009.

A. Allard, M. Bink, S. Martinez, J. Kelner, J. Legave et al., Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population, J Exp Bot, vol.67, issue.9, pp.2875-88, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01298403

B. Brachi, G. P. Morris, and J. O. Borevitz, Genome-wide association studies in plants: the missing heritability is in the field, Genome Biol, vol.12, p.232, 2011.

P. Arús and S. Gardiner, Genomics for improvement of Rosaceae temperate tree fruit, Genomics-Assisted Crop Improvement, vol.2, pp.357-97, 2007.

W. Zhang, A. Collins, J. Gibson, W. J. Tapper, S. Hunt et al., Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps, Proc Natl Acad Sci U S A, vol.101, issue.52, pp.18075-80, 2004.

C. Duan, X. Wang, S. Xie, L. Pan, D. Miki et al., A pair of transposon-derived proteins function in a histone acetyltransferase complex for active DNA demethylation, Cell Res, vol.27, issue.2, pp.226-266, 2016.

M. J. Rebecchi, S. Scarlata, W. Van-leeuwen, L. Ökrész, L. Bögre et al., Pleckstrin homology domains: a common fold with diverse functions, Annu Rev Biophys Biomol Struct, vol.27, issue.1, pp.378-84, 1998.

C. B. Dieck, W. F. Boss, and I. Y. Perera, A role for phosphoinositides in regulating plant nuclear functions, Front Plant Sci, vol.3, p.50, 2012.

J. Figueiredo, S. Silva, M. Figueiredo, and A. , Subtilisin-like proteases in plant defence: the past, the present and beyond, Mol Plant Pathol, vol.19, issue.4, pp.1017-1045, 2018.

L. Jordá, A. Coego, V. Conejero, and P. Vera, A genomic cluster containing four differentially regulated subtilisin-like processing protease genes is in tomato plants, J Biol Chem, vol.274, issue.4, pp.2360-2365, 1999.

Y. Zhao, R. Thilmony, C. L. Bender, A. Schaller, S. Y. He et al., Virulence systems of Pseudomonas syringae pv. tomato promote bacterial speck disease in tomato by targeting the jasmonate signaling pathway, Plant J, vol.36, issue.4, pp.485-99, 2003.

C. Zhao, B. J. Johnson, B. Kositsup, and E. P. Beers, Exploiting secondary growth in Arabidopsis. Construction of xylem and bark cDNA libraries and cloning of three xylem endopeptidases, Plant Physiol, vol.123, issue.3, pp.1185-96, 2000.

B. Gunesekera, J. Torabinejad, J. Robinson, and G. E. Gillaspy, Inositol polyphosphate 5-phosphatases 1 and 2 are required for regulating seedling growth, Plant Physiol, vol.143, issue.3, pp.1408-1425, 2007.

M. De-torres-zabala, T. W. Bennett, M. H. Lafforgue, G. Mansfield, J. W. et al., Pseudomonas syringae pv. tomato hijacks the Arabidopsis abscisic acid signalling pathway to cause disease, EMBO J, vol.26, issue.5, pp.1434-1477, 2007.

L. Lievens, J. Pollier, A. Goossens, R. Beyaert, and J. Staal, Abscisic acid as pathogen effector and immune regulator, Front Plant Sci, vol.8, p.587, 2017.

V. G. Checker, H. R. Kushwaha, P. Kumari, and S. Yadav, Role of phytohormones in plant defense: signaling and cross talk, Molecular Aspects of Plant-Pathogen Interaction, pp.159-84, 2018.

H. Cui, C. Wang, T. Qin, F. Xu, Y. Tang et al., Promoter variants of Xa23 alleles affect bacterial blight resistance and evolutionary pattern, PLoS One, vol.12, issue.10, p.185925, 2017.

L. Shi, J. Weng, C. Liu, X. Song, H. Miao et al., Identification of promoter motifs regulating ZmeIF4E expression level involved in maize rough dwarf disease resistance in maize

, Mol Gen Genomics, vol.288, issue.3, pp.89-99, 2013.

E. Albert, V. Segura, J. Gricourt, J. Bonnefoi, L. Derivot et al., Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits, J Exp Bot, vol.67, issue.22, pp.6413-6443, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01403394

V. Jaiswal, V. Gahlaut, P. K. Meher, R. R. Mir, J. P. Jaiswal et al., Genome wide single locus single trait, multi-locus and multi-trait association mapping for some important agronomic traits in common wheat (T. aestivum L.), Plos One, vol.11, issue.7, p.159343, 2016.

J. J. Yang, L. K. Williams, and A. Buu, Identifying pleiotropic genes in genome-wide association studies for multivariate phenotypes with mixed measurement scales, PLoS One, vol.12, issue.1, p.169893, 2017.

T. Meuwissen, B. J. Hayes, and M. E. Goddard, Prediction of total genetic value using genome-wide dense marker maps, Genetics, vol.157, issue.4, pp.1819-1848, 2001.

J. Crossa, P. Pérez-rodríguez, J. Cuevas, O. Montesinos-lópez, D. Jarquín et al., Genomic selection in plant breeding: methods, models, and perspectives, Trends Plant Sci, vol.22, issue.11, pp.961-75, 2017.

H. F. Utz, A. E. Melchinger, and C. C. Schön, Bias and sampling error of the estimated proportion of genotypic variance explained by quantitative trait loci determined from experimental data in maize using cross validation and validation with independent samples, Genetics, vol.154, issue.4, pp.1839-1888, 2000.

D. Pierro, E. A. Gianfranceschi, L. , D. Guardo, M. Koehorst-van-putten et al., A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species, Hortic Res, vol.3, p.16057, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02516636

N. Billotte, M. F. Jourjon, N. Marseillac, A. Berger, A. Flori et al., QTL detection by multi-parent linkage mapping in oil palm, Elaeis guineensis Jacq.). Theor Appl Genet, vol.120, issue.8, pp.1673-87, 2010.

S. Tisné, V. Pomiès, V. Riou, I. Syahputra, B. Cochard et al., Identification of ganoderma disease resistance loci using natural field infection of an oil palm multiparental population, G3, vol.7, issue.6, pp.1683-92, 2017.

D. A. Skelly, P. M. Magwene, and E. A. Stone, Sporadic, global linkage disequilibrium between unlinked segregating sites, Genetics, vol.202, issue.2, pp.427-464, 2016.

B. Brachi, C. G. Meyer, R. Villoutreix, A. Platt, T. C. Morton et al., Coselected genes determine adaptive variation in herbivore resistance throughout the native range of Arabidopsis thaliana, Proc Natl Acad Sci, vol.112, issue.13, pp.4032-4039, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01134027

M. Pilet-nayel, B. Moury, V. Caffier, J. Montarry, M. Kerlan et al., Quantitative resistance to plant pathogens in pyramiding strategies for durable crop protection, Front Plant Sci, vol.8, p.1838, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01905321

F. Calenge, A. Faure, M. Goerre, C. Gebhardt, W. E. Van-de-weg et al., Quantitative trait loci (QTL) analysis reveals both broad-spectrum and isolate-specific QTL for scab resistance in an apple progeny challenged with eight isolates of Venturia inaequalis, Phytopathology, vol.94, issue.4, pp.370-379, 2004.

E. Dirlewanger, E. Graziano, T. Joobeur, F. Garriga-caldere, P. Cosson et al., Comparative mapping and marker-assisted selection in Rosaceae fruit crops, Proc Natl Acad Sci, vol.101, issue.26, pp.9891-9897, 2004.