E. Baron, J. Richirt, R. Villoutreix, L. Amsellem, and F. Roux, The genetics of intra-and interspecific competitive response and effect in a local population of an annual plant species, Funct Ecol, vol.29, pp.1361-1370, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01134029

M. Bartelheimer, C. Schmid, J. Storf, K. Hell, and S. Bauer, Interspecific competition in Arabidopsis thaliana: a knowledge gap is starting to close, Prog Bot, vol.76, pp.303-319, 2015.

M. M. Barthet and K. W. Hilu, Expression of matK: functional and evolutionary implications, Am J Bot, vol.94, pp.1402-1412, 2007.

C. Bartoli and F. Roux, Genome-Wide Association studies in plant pathosystems: toward an ecological genomics approach, Front Plant Sci, vol.8, p.763, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01606059

C. Bartoli, L. Frachon, M. Barret, M. Rigal, C. Zanchetta et al., In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana, ISME J, vol.12, pp.2024-2038, 2018.

R. A. Bay, N. Rose, R. Barrett, L. Bernatchez, C. K. Ghalambor et al., Predicting Responses to Contemporary Environmental Change Using Evolutionary Response Architectures, Am Nat, vol.189, pp.463-473, 2017.

J. Bergelson and F. Roux, Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana, Nature Rev. Genet, vol.11, pp.867-879, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00563568

B. Brachi, R. Villoutreix, N. Faure, N. Hautekeete, Y. Piquot et al., Investigation of the geographical scale of adaptive phenological variation and its underlying genetics in Arabidopsis thaliana, Mol Ecol, vol.22, pp.4222-4240, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00860399

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. Nat. Acad. Sci. U.S.A, vol.112, pp.4032-4037, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01134027

L. M. Carrascal, I. Galvá, and O. Gordo, Partial least squares regression as an alternative to current regression methods used in ecology, Oikos, vol.118, pp.681-690, 2009.

F. Chen, B. Li, J. Demone, J. B. Charron, X. Shi et al., Photoereceptor partner FHY1 has an independent role in gene modulation and plant development under far-red light, Proc Natl Acad Sci, vol.111, pp.11888-11893, 2014.

G. O. Consortium, The gene ontology project in 2008, Nucleic Acids Res, vol.36, 2008.

S. De-mita, A. C. Thuillet, L. Gay, N. Ahmadi, S. Manel et al., Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations, Mol. Ecol, vol.22, pp.1383-1399, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01268008

U. Dubiella, H. Seybold, G. Durian, E. Komander, R. Lassig et al., Calcium-dependent protein kinase/NADPH oxidase activation circuit is required for rapid defense signal propagation, Proc. Nat. Acad. Sci. U.S.A, vol.110, pp.8744-8749, 2013.

A. Dubuis, S. Giovanettina, L. Pellissier, J. Pottier, P. Vittoz et al., Improving the prediction of plant species distribution and community composition by adding edaphic to topo-climatic variables, J Veg Science, vol.24, pp.593-606, 2013.

R. C. Edgar, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, vol.26, pp.2460-2461, 2010.

R. C. Edgar, UPARSE: highly accurate OTU sequences from microbial amplicon reads, Nat Methods, vol.10, pp.996-998, 2013.

C. T. Ellison, F. Vandenbussche, D. Van-der-straeten, and S. L. Harmer, XAP5 CIRCADIAN TIMEKEEPER regulates ethylene responses in aerial tissues of Arabidopsis, Plant Physiol, vol.155, pp.988-999, 2011.

M. Fan, M. Y. Bai, J. G. Kim, T. Wang, E. Oh et al., The bHLH transcription factor HBI1 mediates the trade-off between growth and pathogen-associated molecular pattern-triggered immunity in Arabidopsis, Plant Cell, vol.26, pp.828-841, 2014.

Á. Ferrero-serrano and S. M. Assmann, Phenotypic and genome-wide association with the local environment of Arabidopsis, Nat. Ecol. Evol, vol.3, pp.274-285, 2019.

L. Frachon, C. Libourel, R. Villoutreix, S. Carrère, C. Glorieux et al., Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time, Nat Ecol Evol, vol.1, pp.1551-1561, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01723277

L. Frachon, C. Bartoli, S. Carrère, O. Bouchez, A. Chaubet et al., A genomic map of climate adaptation in Arabidopsis thaliana at a micro-geographic scale, Front Plant Sci, vol.9, p.967, 2018.

M. Gao, X. Wang, D. Wang, F. Xu, X. Ding et al., Regulation of cell death and innate immunity by two receptor-like kinases in Arabidopsis, Cell Host Microbe, vol.6, pp.34-44, 2009.

M. Gautier, Genome-wide scan for adaptive divergence and association with populationspecific covariates, Genetics, vol.201, pp.555-1579, 2015.

S. E. Gilman, M. C. Urban, J. Tewksbury, G. W. Gilchrist, and R. D. Holt, A framework for community interactions under climate change, Trends Ecol Evol, vol.25, pp.325-331, 2010.

W. A. Gould and M. D. Walker, Plant communities and landscape diversity along a Canadian Arctic river, J Veg Science, vol.10, pp.537-548, 1999.

T. Günther and G. Coop, Robust identification of local adaptation from allele frequencies, Genetics, vol.195, pp.205-220, 2013.

L. G?mez-g?mez and T. Boller, FLS2: An LRR Receptor-like Kinase Involved in the Perception of the Bacterial Elicitor Flagellin in Arabidopsis, Mol. Cell, vol.5, pp.1003-1011, 2000.

A. M. Hancock, B. Brachi, N. Faure, M. W. Horton, L. B. Jarymowycz et al., Adaptation to climate across the Arabidopsis thaliana genome, Science, vol.334, pp.83-86, 2011.

N. Hautekéete, L. Frachon, C. Luczak, B. Toussaint, W. Van-landuyt et al., Habitat type shapes long-term plant biodiversity budgets in two densely populated regions in north-western Europe. Diversity Distrib. 21:631-642. relative importance of intraspecific and interspecific plant competition in a changing climate, AoB Plants, vol.10, p.39, 2015.

M. W. Horton, N. Bodenhausen, K. Beilsmith, D. Meng, B. D. Muegge et al., Genome-wide association study of Arabidopsis thaliana leaf microbial community, Nat. Comm, vol.5, p.5320, 2014.

J. R. Lasky, D. Marais, D. L. Mckay, J. K. Richards, J. H. Juenger et al., Characterizing genomic variation of Arabidopsis thaliana: the roles of geographt and climate, Mol. Ecol, vol.21, pp.5512-5529, 2012.

J. R. Lasky, H. D. Upadhyaya, P. Ramu, S. Deshpande, C. T. Hash et al., Genomeenvironment associations in sorghum landraces predict adaptive traits, Sci. Adv, vol.1, p.1400218, 2015.

L. Cao, K. A. Rossouw, D. Robert-granié, C. Besse, and P. , A sparse PLS for variable selection when integrating Omics Data, Stat. Appl. Genet. Mol. Biol, vol.7, p.35, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00300204

L. Cao, K. A. Meugnier, E. Mclachlan, and G. , Integrative mixture of experts to combine clinical factors and gene markers, Bioinformatics, vol.26, pp.1192-1198, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01982016

L. Corre and V. , Variation at two flowering time genes within and among populations of Arabidopsis thaliana: comparison with markers and traits, Mol. Ecol, vol.14, pp.4181-4192, 2005.

W. M. Leu, X. L. Cao, T. J. Wilson, D. P. Snustad, and N. H. Chua, Phytochrome A and phytochrome B mediate the hypocotyl-specific downregulation of TUB1 by light in arabidopsis, Plant Cell, vol.7, pp.2187-2196, 1995.

J. Li, J. Wen, K. A. Lease, J. T. Doke, F. E. Tax et al., BAK1, an Arabidopsis LRR receptor-like protein kinase, interacts with BRI1 and modulates brassinosteroid signaling, Cell, vol.110, pp.213-222, 2002.

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., of competitive response of Arabidopsis thaliana is highly flexible between monospecific and plurispecific neighborhoods, Bioinformatics, vol.25, pp.2078-2079, 2009.

I. Litrico and C. Violle, Diversity in plant breeding: a new conceptual framework, Trends Plant Sci, vol.20, pp.604-613, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01214153

J. Lorek, T. Griebel, A. M. Jones, H. Kuhn, and R. Panstruga, The role of Arabidopsis heterotrimeric G-protein subunits in MLO2 function and MAMP-triggered immunity, Mol. Plant Microbe Interact, vol.26, pp.991-1003, 2013.

A. E. Kelly and M. L. Gloulden, Rapid shifts in plant distribution with recent climate change, Proc. Nat. Acad. Sci. U.S.A, vol.105, pp.11823-11826, 2008.

D. C. Koboldt, Q. Zhang, D. E. Larson, D. Shen, M. D. Mclellan et al., VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing, Genome Res, vol.22, pp.568-576, 2012.

J. Oksanen, F. G. Blanchet, M. Friendly, R. Kindt, P. Legendre et al., vegan: Community Ecology Package, 2016.

E. Paradis, J. Claude, and K. Strimmer, APE: Analyses of phylogenetics and evolution in R language, Bioinformatics, vol.20, pp.289-290, 2004.
URL : https://hal.archives-ouvertes.fr/ird-01887318

R. Pierik, L. Mommer, and L. Voesenek, Molecular mechanisms of plant competition: neighbour detection and response strategies, Funct Ecol, vol.27, pp.841-853, 2013.

A. Platt, M. Horton, Y. S. Huang, Y. Li, A. E. Anastasio et al.,

N. Warthmann, D. Weigel, L. Rivero, R. Scholl, M. Nordborg et al., The scale of population structure in Arabidopsis thaliana, Plos Genet, vol.6, p.1000843, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00457092

A. R. Pluess, A. Frank, C. Heiri, H. Lalagüe, G. G. Vendramin et al., Genomeenvironment association study suggests local adaptation to climate at the regional scale in Fagus sylvatica, New Phytol, vol.210, pp.589-601, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01309135

N. Provart and T. Zhu, A browser-based functional classification Superviewer for Arabidopsis genomics, Curr. Comput. Mol. Biol, pp.271-272, 2003.

I. Roig-villanova, J. Bou-torrent, A. Galstyan, L. Carretero-paulet, S. Portolés et al., Interaction of shade avoidance and auxin responses: a role for two novel atypical bHLH proteins, EMBO J, vol.26, pp.4756-4767, 2007.

F. Roux and J. Bergelson, Chapter Four -The genetics underlying natural variation in the biotic interactions of Arabidopsis thaliana: the challenges of linking evolutionary genetics and community ecology, Curr Top Dev Biol, vol.119, pp.111-156, 2016.

A. Sanon, Z. N. Andrianjaka, Y. Prin, R. Bally, J. Thioulouse et al., Rhizosphere microbiota interfers with plant-plant interactions, Plant Soil, vol.321, pp.259-278, 2009.
URL : https://hal.archives-ouvertes.fr/halsde-00525562

M. Scalfi, E. Mosca, D. Pierro, E. A. Troggio, M. Vendramin et al., Micro-and macro-geographic scale effect on the molecular imprint of selection and adaptation in Norway Spruce, PLoS ONE, vol.9, p.115499, 2014.

A. Singer, J. Travis, and K. Johst, Interspecific interactions affect species and community responses to climate shifts, Oikos, vol.122, pp.358-366, 2013.

H. J. Subrahmaniam, C. Libourel, E. P. Journet, J. B. Morel, . Muños et al., The genetics underlying natural variation of plant-plant interactions, a beloved but forgotten member of the family of biotic interactions, Plant J, vol.93, pp.747-770, 2018.

S. Swain, H. W. Jiang, and H. L. Hsieh, FAR-RED INSENSITIVE 219/JAR1 contributes to shade avoidance responses of Arabidopsis seedlings by modulating key shade signaling components, Front Plant Sci, vol.8, 1901.

S. T. Tan, C. Dai, H. T. Liu, and H. W. Xue, Arabidopsis Casein Kinase 1 proteins CK1.3 and CK1.4 phosphorylate Cryptochrome 2 to regulate blue light signaling, Plant Cell, vol.25, pp.2618-2632, 2013.

V. Trivellone, S. Bougeard, S. Giavi, P. Krebs, D. Balseiro et al., Factors shaping community assemblages and species co-occurrence of different trophic levels, vol.7, pp.4745-4754, 2017.

M. Wang, F. Roux, C. Bartoli, C. Huard-chauveau, C. Meyer et al., Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes, Proc. Nat. Acad. Sci. U.S.A, vol.115, pp.5440-5449, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01806895

G. J. Allan, S. P. Difazio, B. M. Potts, D. G. Fischer, C. A. Gehring et al., A framework for community and ecosystem genetics: from genes to ecosystems, Nat Rev Genet, vol.7, pp.510-523, 2006.

J. B. Wilson, R. K. Peet, J. Dengler, and M. Pärtel, Plant species richness: the world records, J Veg Sci, vol.24, pp.796-802, 2012.

M. Wrzaczek, J. P. Vainonen, S. Stael, L. Tsiatsiani, H. Help-rinta-rahko et al., GRIM REAPER peptide binds to receptor kinase PRK5 to trigger cell death in Arabidopsis, EMBO J, vol.34, pp.55-66, 2015.

D. H. Xing, Z. B. Lai, Z. Y. Zheng, K. M. Vinod, B. F. Fan et al., Stress-and pathogeninduced Arabidopsis WRKY48 is a transcriptional activator that represses plant basal defense, Mol. Plant, vol.1, pp.459-470, 2008.

C. R. Xu, C. Liu, Y. L. Wang, L. C. Li, W. Q. Chen et al., Histone acetylation affects expression of cellular patterning genes in the Arabidopsis root epidermis, Proc Natl Acad Sci, vol.102, pp.14469-14474, 2005.

T. Züst, C. Heichinger, U. Grossniklaus, R. Harrington, D. J. Kliebenstein et al., Natural enemies drive geographic variation in plant defenses, Science, vol.338, pp.116-119, 2012.