. .. Ssr, 178 7.1.3.1. La structuration chez S. pimpinellifolium semble être expliquée par des différences du taux d"autogamie des accessions, 176 7.1. Structuration des ressources génétiques de tomate, intérêts et limites des, vol.7

.. .. Accessions-cultivées,

«. Les and .. .. ,

. .. , 2.3. Inférence à partir d"une étude focalisée sur le chromosome 2, Theor Appl Genet, vol.109, pp.669-79, 2004.

L. S. Barrero, B. Cong, F. Wu, and S. D. Tanksley, Developmental characterization of the fasciated locus and mapping of Arabidopsis candidate genes involved in the control of floral meristem size and carpel number in tomato, Genome, vol.49, pp.991-1006, 2006.

M. Causse, V. Saliba-colombani, L. Lecomte, P. Duffé, P. Rousselle et al., QTL analysis of fruit quality in fresh market tomato: a few chromosome regions control the variation of sensory and instrumental traits, J Exp Bot, vol.53, pp.2089-2098, 2002.
URL : https://hal.archives-ouvertes.fr/hal-02680289

B. Cong, L. S. Barrero, and S. D. Tanksley, Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication, Nat Genet, vol.40, p.800, 2008.

R. M. Feldman, C. C. Correll, K. B. Kaplan, and R. J. Deshaies, A complex of Cdc4p, Skp1p, and Cdc53p/cullin catalyzes ubiquitination of the phosphorylated CDK inhibitor Sic1p, Cell, vol.91, issue.2, pp.221-251, 1997.

A. Frary, T. C. Nesbitt, S. Grandillo, E. Knaap, B. Cong et al., fw2.2: a quantitative trait locus key to the evolution of tomato fruit size, Science, vol.289, pp.85-93, 2000.

E. Fridman, F. Carrari, Y. S. Liu, A. R. Fernie, and D. Zamir, Zooming in on a quantitative trait for tomato yield using interspecific introgressions, Science, vol.305, pp.1786-1789, 2004.

T. Laux, K. F. Mayer, J. Berger, and G. Jürgens, The WUSCHEL gene is required for shoot and floral meristem integrity in Arabidopsis, Development, vol.122, issue.1, pp.87-96, 1996.

L. Lecomte, V. Saliba-colombani, A. Gautier, M. C. Gomez-jimenez, P. Duffé et al., Fine mapping of QTLs of chromosome 2 affecting the fruit architecture and composition of tomato, Mol. Breeding, vol.13, pp.1-14, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02675419

L. Paslier, M. C. Bounon, R. Chauveau, A. Thareau, V. Canaguier et al., High Throughput SNPs Discovery In Grapevine, Poplar And Tomato. Plant and Animal Genome XVII Conference, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02758232

Z. Lippman and S. D. Tanksley, Dissecting the genetic pathway to extreme fruit size in tomato using a cross between the small-fruited wild species Lycopersicum pimpinellifolium and L. esculentum var. Giant Heirloom, Genetics, vol.158, pp.413-435, 2001.

J. Liu, J. Van-eck, B. Cong, and S. D. Tanksley, A new class of regulatory genes underlying the cause of pear-shaped tomato fruit, PNAS, vol.99, pp.13302-13308, 2002.

K. Mayer, H. Schoof, A. Haecker, M. Lenhard, G. Jürgens et al., Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem, Cell, vol.95, p.805, 1998.

K. G. Ardlie and L. Kruglyak, Patterns of linkage disequilibrium in the human genome, vol.3, pp.299-309, 2002.

Y. Bai and P. Lindhout, Domestication and Breeding of Tomatoes: What have We Gained and What Can We Gain in the Future?, Ann Bot, p.150, 2007.

Y. Benjamini and Y. Hochberg, On the Adaptive Control of the False Discovery Rate in Multiple Testing With Independent Statistics, J. Edu. Behav. Stat, vol.25, issue.1, pp.60-83, 2000.

P. J. Bradbury and Z. Zhang, TASSEL: software for association mapping of complex traits in diverse samples, Bioinformatics, vol.23, pp.2633-2635, 2007.

C. Bres and J. P. Bouchet, CGIS: an information system used for designing primers of candidate genes using Arabidopsis whole genome and Solanaceae EST databases, Triennal Conference of the EAPR. Bilbao (ESP), vol.16, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02762016

I. Buckler, S. Edward, and J. M. Thornsberry, Plant molecular diversity and applications to genomics, Curr. Opin. Plant Bio, vol.5, issue.2, pp.107-111, 2002.

K. S. Caldwell and J. Russell, Extreme Population-Dependent Linkage Disequilibrium Detected in an Inbreeding Plant Species, Hordeum vulgare, Genetics, vol.172, issue.1, pp.557-567, 2006.

L. Camus-kulandaivelu and J. Veyrieras, Maize Adaptation to Temperate Climate: Relationship Between Population Structure and Polymorphism in the Dwarf8 Gene, Genetics, vol.172, issue.4, pp.2449-2463, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02664567

M. Causse and V. Saliba-colombani, QTL analysis of fruit quality in fresh market tomato: a few chromosome regions control the variation of sensory and instrumental traits, J. Exp. Bot, vol.53, issue.377, pp.2089-2098, 2002.
URL : https://hal.archives-ouvertes.fr/hal-02680289

M. J. Daly and J. D. Rioux, High-resolution haplotype structure in the human genome, Nat. Genet, vol.29, issue.2, pp.229-232, 2001.

A. Darvasi and S. Shifman, The beauty of admixture, Nat. Genet, vol.37, issue.2, pp.118-119, 2005.

M. Daunay and H. Laterrot, Iconography and History of Solanaceae: Antiquity to the 17 th Century, Hort. Rev. J. Janick, vol.34, pp.1-119, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02816240

J. Doebley and A. Stec, The evolution of apical dominance in maize, Nature, vol.386, issue.6624, pp.485-488, 1997.

J. Drouaud, Variation in crossing-over rates across chromosome4 of Arabidopsis thaliana reveals the presence of meiotic recombination hot spots, Genome Res, vol.16, pp.106-114, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00017439

G. Evanno and S. Regnaut, Detecting the number of clusters of individuals using the software structure: a simulation study, Mol. Ecol, vol.14, issue.8, pp.2611-2620, 2005.

S. A. Flint-garcia and J. M. Thornsberry, Structure of linkage disequilibrium in plants, Annu. Rev. Plant Biol, vol.54, issue.1, pp.357-374, 2003.

S. A. Flint-garcia and A. Thuillet, Maize association population: a high-resolution platform for quantitative trait locus dissection, The Plant Journal, vol.44, issue.6, pp.1054-1064, 2005.

S. Foissac and P. Bardou, EUGENE'HOM: a generic similarity-based gene finder using multiple homologous sequences, Nucl. Acids Res, vol.31, issue.13, pp.3742-3745, 2003.
URL : https://hal.archives-ouvertes.fr/hal-02675508

A. Frary and T. C. Nesbitt, fw2.2: A Quantitative Trait Locus Key to the Evolution of Tomato Fruit Size, Science, vol.289, issue.5476, pp.85-88, 2000.

P. K. Gupta and S. Rustgi, Linkage disequilibrium and association studies in higher plants: Present status and future prospects, Plant Mol. Biol, vol.57, issue.4, pp.461-485, 2005.

O. J. Hardy and X. Vekemans, SPAGeDI: a versatile computer program to analyse spatial genetic structure at the individual or population levels, Molecular Ecology Notes, vol.2, pp.618-620, 2002.

D. L. Hyten and I. Choi, Highly Variable Patterns of Linkage Disequilibrium in Multiple Soybean Populations, Genetics, vol.175, issue.4, pp.1937-1944, 2007.

H. Innan and W. Stephan, Distinguishing the Hitchhiking and Background Selection Models, Genetics, vol.165, issue.4, pp.2307-2312, 2003.

J. Jimenez-gomez and J. Maloof, Sequence diversity in three tomato species: SNPs, markers, and molecular evolution, BMC Plant Biology, vol.9, issue.1, p.85, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02662350

H. Kaya and K. Shibahara, FASCIATA Genes for Chromatin Assembly Factor-1 in Arabidopsis Maintain the Cellular Organization of Apical Meristems, Cell, vol.104, issue.1, p.131, 2001.

S. Kim and V. Plagnol, Recombination and linkage disequilibrium in Arabidopsis thaliana, Nat Genet, vol.39, issue.9, pp.1151-1155, 2007.

J. Labate and L. Robertson, EST, COSII, and arbitrary gene markers give similar estimates of nucleotide diversity in cultivated tomato ( Solanum lycopersicum L.), 2009.

, App. Genet, vol.118, issue.5, pp.1005-1014

J. A. Labate and A. Baldo, Tomato SNP Discovery by EST Mining and Resequencing, Mol. Breed, vol.16, issue.4, pp.343-349, 2005.

L. Lecomte and V. Saliba-colombani, , 2004.

J. Liu and J. Van-eck, A new class of regulatory genes underlying the cause of pear-shaped tomato fruit, Proc. Nat. Acad. Sci. USA, vol.99, issue.20, pp.13302-13306, 2002.

A. D. Long and C. H. Langley, The Power of Association Studies to Detect the Contribution of Candidate Genetic Loci to Variation in Complex Traits, Genome Res, vol.9, issue.8, pp.720-731, 1999.

K. Manning and M. Tor, A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening, Nat. Genet, vol.38, issue.8, pp.948-952, 2006.

S. Muños and N. Ranc, Increases in tomato fruit size and locule number is controlled by two key SNP located near Wuschel

T. C. Nesbitt and S. D. Tanksley, Comparative Sequencing in the Genus Lycopersicon: Implications for the Evolution of Fruit Size in the Domestication of Cultivated Tomatoes, Genetics, vol.162, issue.1, pp.365-379, 2002.

M. Nordborg, Linkage Disequilibrium, Gene Trees and Selfing: An Ancestral Recombination Graph With Partial Self-Fertilization, Genetics, vol.154, issue.2, pp.923-929, 2000.

M. Nordborg and J. O. Borevitz, The extent of linkage disequilibrium in Arabidopsis thaliana, Nat. Genet, vol.30, issue.2, pp.190-193, 2002.

M. Nordborg and S. Tavare, Linkage disequilibrium: what history has to tell us, Trends Genet, vol.18, pp.83-90, 2002.

C. Paulus and B. Köllner, Physiological and biochemical characterization of glyoxalase I, a general marker for cell proliferation, from a soybean cell suspension, Planta, vol.189, issue.4, pp.561-566, 1993.

A. L. Price and N. J. Patterson, Principal components analysis corrects for stratification in genome-wide association studies, Nat. Genet, vol.38, issue.8, pp.904-909, 2006.

J. K. Pritchard and M. Stephens, Inference of Population Structure Using Multilocus Genotype Data, Genetics, vol.155, issue.2, pp.945-959, 2000.

J. K. Pritchard and M. Stephens, Association Mapping in Structured Populations, Am. J. Hum. Genet, vol.67, pp.170-181, 2000.

, R: A language and environment for statistical computing, reference index version 2.2.1. F. f. S. Computing, 2005.

A. Rafalski, Applications of single nucleotide polymorphisms in crop genetics, Curr. Opin. Plant Biol, vol.5, pp.94-100, 2002.

N. Ranc and S. Munos, A clarified position for solanum lycopersicum var. cerasiforme in the evolutionary history of tomatoes (solanaceae), BMC Plant Biol, vol.8, issue.1, p.130, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02668658

K. Ritland, Estimators for pairwise relatedness and individual inbreeding coefficients, Genetics Research, vol.67, issue.02, pp.175-185, 1996.

V. Saliba-colombani and M. Causse, Genetic analysis of organoleptic quality in fresh market tomato. 1. Mapping QTLs for physical and chemical traits, Theo. App. Genet, vol.102, issue.2, pp.259-272, 2001.
URL : https://hal.archives-ouvertes.fr/hal-02674426

M. Takahashi and F. Matsuda, Automated identification of single nucleotide polymorphisms from sequencing data, J. Bioinform. Comput. Biol, vol.1, pp.253-265, 2003.

, Références bibliographiques

I. Y. Abdurakhmonov and A. Abdukarimov, Application of association mapping to understanding the genetic diversity of plant germplasm ressources, Int. J. Plant. Geno, vol.18, 2008.

M. D. Adams and J. J. Sekelsky, From sequence to phenotype: reverse genetics in Drosophila melanogaster, Nat Rev Genet, vol.3, issue.3, pp.189-198, 2002.

E. Aguayo and V. Escalona, Quality of fresh-cut tomato as affected by type of cut, packaging, temperature and storage time, European Food Research and Technology, vol.219, issue.5, pp.492-499, 2004.

A. E. Alvarez and C. C. Wiel, Use of microsatellites to evaluate genetic diversity and species relationships in the genus Lycopersicon, TAG Theoretical and Applied Genetics, vol.103, issue.8, pp.1283-1292, 2001.

M. I. Aranzana and S. Kim, , 2005.

K. G. Ardlie and L. Kruglyak, Patterns of linkage disequilibrium in the human genome, vol.3, pp.299-309, 2002.

T. Areshchenkova and M. W. Ganal, Long tomato microsatellites are predominantly associated with centromeric regions, Genome, vol.42, pp.536-544, 1999.

O. T. Avery and C. M. Mcleod, Induction of transformation by a desoxyribonucleic acid fraction isolated from Pneumococcus Type III, J. Exp. Med, vol.79, pp.137-158, 1944.

Y. Bai and P. Lindhout, Domestication and breeding of tomatoes: What have we gained and what can we gain in the future?, Ann Bot, p.150, 2007.

E. A. Baldwin and K. Goodner, Effect of volatiles and their concentration on perception of tomato descriptors, Journal of food science, vol.69, issue.8, pp.310-318, 2004.

E. A. Baldwin and M. O. Nisperos-carriedo, Quantitative analysis of flavor parameters in six Florida tomato cultivars (Lycopersicon esculentum Mill), Journal of Agricultural and Food Chemistry, vol.39, issue.6, pp.1135-1140, 2002.

H. Bandelt and A. W. , Split decomposition: A new and useful approach to phylogenetic analysis of distance data, Molecular Phylogenetics and Evolution, vol.1, issue.3, pp.242-252, 1992.

J. Bao and H. Corke, Microsatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.), TAG Theoretical and Applied Genetics, vol.113, issue.7, pp.1185-1196, 2006.

A. Barnaud and T. Lacombe, Linkage disequilibrium in cultivated grapevine, Vitis vinifera L, vol.112, pp.708-716, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02668093

L. S. Barrero and B. Cong, Developmental characterization of the fasciated locus and mapping of Arabidopsis candidate genes involved in the control of floral meristem size and carpel number in tomato, Genome, vol.49, issue.8, pp.991-1006, 2006.

L. S. Barrero and S. D. Tanksley, Evaluating the genetic basis of multiple-locule fruit in a broad cross section of tomato cultivars, TAG Theoretical and Applied Genetics, vol.109, issue.3, pp.669-679, 2004.

C. Barry and J. Giovannoni, Ethylene and fruit ripening, Journal of Plant Growth Regulation, vol.26, issue.2, pp.143-159, 2007.

C. S. Barry and J. J. Giovannoni, Ripening in the tomato Green-ripe mutant is inhibited by ectopic expression of a protein that disrupts ethylene signaling, vol.103, p.7923, 2006.

T. M. Bataillon and J. L. David, Neutral genetic markers and conservation genetics: Simulated germplasm collections, Genetics, vol.144, issue.1, pp.409-417, 1996.
URL : https://hal.archives-ouvertes.fr/hal-02696077

K. Belkir and P. Borsa, GENETIX, logiciel sous WindowsTM pour la génétique des populations. Laboratoire Génome, Populations, Interactions CNRS UMR 5000, 2004.

E. M. Belle and U. Ramakrishnan, Serial coalescent simulations suggest a weak genealogical relationship between Etruscans and modern Tuscans, vol.103, p.8012, 2006.

Y. Benjamini and Y. Hochberg, On the adaptive control of the false discovery rate in multiple testing with independent statistics, J. Edu. Behav. Stat, vol.25, issue.1, pp.60-83, 2000.

L. Bermudez and U. Urias, A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit, J. Exp. Bot, p.146, 2008.

D. Bernacchi and T. Beck-bunn, Advanced backcross QTL analysis in tomato. I. Identification of QTLs for traits of agronomic importance from Lycopersicon hirsutum, TAG Theoretical and Applied Genetics, vol.97, issue.3, pp.381-397, 1998.

L. Bohs and R. G. Olmstead, Phylogenetic relationships in Solanum (Solanaceae) based on ndhF sequences, Systematic Botany, vol.22, issue.1, pp.5-17, 1997.

P. J. Bradbury and Z. Zhang, TASSEL: software for association mapping of complex traits in diverse samples, Bioinformatics, vol.23, pp.2633-2635, 2007.

U. Brand and J. C. Fletcher, SPAGeDI: a versatile computer program to analyse spatial genetic structure at the individual or population levels, Molecular Ecology Notes, vol.2, pp.618-620, 2000.

A. D. Hershey and M. Chase, Independant functions of viral proteins and nucleic acid in growth of bacteriophage, J. Gen. Physiol, vol.36, pp.39-56, 1952.

H. Y. Hirano and M. Eiguchi, A single base change altered the regulation of the Waxy gene at the posttranscriptional level during the domestication of rice, Mol Biol Evol, vol.15, issue.8, pp.978-987, 1998.

K. E. Holsinger and W. L. , Bayesian approaches for the analysis of population genetic structure: an example from Platanthera leucophaea (Orchidaceae), Mol. Ecol, vol.13, issue.4, pp.887-894, 2004.

K. E. Holsinger and P. O. Lewis, A Bayesian approach to inferring population structure from dominant markers, Mol. Ecol, vol.11, issue.7, pp.1157-1164, 2002.

D. H. Huson, SplitsTree: analyzing and visualizing evolutionary data, Bioinformatics, vol.14, issue.1, pp.68-73, 1998.

D. L. Hyten and I. Choi, Highly variable patterns of linkage disequilibrium in multiple soybean populations, Genetics, vol.175, issue.4, pp.1937-1944, 2007.

H. Innan and W. Stephan, Distinguishing the hitchhiking and background selection models, Genetics, vol.165, issue.4, pp.2307-2312, 2003.

T. Isaacson and G. Ronen, Cloning of tangerine from tomato reveals a carotenoid isomerase essential for the production of {beta}-carotene and xanthophylls in plants, Plant Cell, vol.14, issue.2, pp.333-342, 2002.

M. Isaksson and J. Stenberg, MLGA a rapid and cost-efficient assay for gene copy-number analysis, Nucl. Acids Res, vol.35, issue.17, p.115, 2007.

V. Ivandic and W. T. Thomas, Associations of simple sequence repeats with quantitative trait variation including biotic and abiotic stress tolerance in Hordeum spontaneum, Plant Breeding, vol.122, issue.4, pp.300-304, 2003.

H. Iwata and Y. Uga, Bayesian association mapping of multiple quantitative trait loci and its application to the analysis of genetic variation among Oryza sativa L. germplasms, TAG Theoretical and Applied Genetics, vol.114, issue.8, pp.1437-1449, 2007.

D. I. Jarvis and T. Hodgkin, Wild relatives and crop cultivars: detecting natural introgression and farmer selection of new genetic combinations in agroecosystems, Molecular Ecology, vol.8, issue.s1, pp.159-173, 1999.

J. Jenkins, The origin of the cultivated tomato, Economic Botany, vol.2, issue.4, pp.379-392, 1948.

J. Jimenez-gomez and J. Maloof, Sequence diversity in three tomato species: SNPs, markers, and molecular evolution, BMC Plant Biology, vol.9, issue.1, p.85, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02662350

P. A. Matthiolus, Di Pedacio Diascoride Anazarbeo libri einque della historia, et materia medicinale tradotti in lingua volgare Italiana, 1544.

R. Mauricio, Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology, Nat Rev Genet, vol.2, issue.5, pp.370-381, 2001.

K. F. Mayer and H. Schoof, Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem, Cell, vol.95, pp.805-815, 1998.

A. Mazzucato and R. Papa, Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces, TAG Theoretical and Applied Genetics, vol.116, issue.5, pp.657-669, 2008.

C. M. Mccallum and L. Comai, Targeting Induced Local Lesions IN Genomes (TILLING) for plant functional genomics, Plant Physiol, vol.123, issue.2, pp.439-442, 2000.

H. I. Mckhann and C. Camilleri, Nested core collections maximizing genetic diversity in Arabidopsis thaliana, The Plant Journal, vol.38, issue.1, pp.193-202, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02673930

D. Mcmeekin, Representations on pre-columbian spindle whorls of the floral and fruit structure of economic plants, Economic Botany, vol.46, issue.2, pp.171-180, 1992.

J. D. Mcpherson, Next-generation gap, Nat Meth, vol.6, issue.11s, pp.2-5, 2009.

R. Meissner and V. Chague, A high throughput system for transposon tagging and promoter trapping in tomato, The Plant Journal, vol.22, issue.3, pp.265-274, 2000.

N. Menda and Y. Semel, In silico screening of a saturated mutation library of tomato, The Plant Journal, vol.38, issue.5, pp.861-872, 2004.

G. Mendel, Experiments in plant hybridization: traduction originale de Versuche über Plflanzenhybriden par W. Bateson complétée par R, 1866.

M. A. Menz and R. R. Klein, Genetic diversity of public inbreds of Sorghum determined by mapped AFLP and SSR markers, Crop Science, vol.44, issue.4, pp.1236-1244, 2004.

J. C. Miller and S. D. Tanksley, RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon, TAG Theoretical and Applied Genetics, vol.80, issue.4, pp.437-448, 1990.

A. J. Monforte and S. D. Tanksley, Fine mapping of a quantitative trait locus (QTL) from Lycopersicon hirsutum chromosome 1 affecting fruit characteristics and agronomic traits: breaking linkage among QTLs affecting different traits and dissection of heterosis for yield, TAG Theoretical and Applied Genetics, vol.100, issue.3, pp.471-479, 2000.

S. Moore and J. Vrebalov, Use of genomics tools to isolate key ripening genes and analyse fruit maturation in tomato, J. Exp. Bot, vol.53, issue.377, pp.2023-2030, 2002.

T. H. Morgan and A. H. Sturtevant, The Mechanism of Mendelian Heredity, 1915.

A. Moses, Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites, BMC Evolutionary Biology, vol.9, issue.1, p.286, 2009.

L. A. Mueller and S. D. Tanksley, The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL), Comp Funct Genom, vol.6, issue.3, pp.153-158, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02680359

S. Muños and N. Ranc, Increases in tomato fruit size and locule number is controlled by two key SNP located near Wuschel

T. C. Nesbitt and S. D. Tanksley, Comparative sequencing in the genus Lycopersicon: Implications for the evolution of fruit size in the domestication of cultivated tomatoes, Genetics, vol.162, issue.1, pp.365-379, 2002.

M. L. Nguyen and S. J. Schwartz, Lycopene stability during food processing, Proc-Soc-Exp-Biol-Med, vol.218, issue.2, pp.101-105, 1998.

M. Nordborg, Linkage disequilibrium, gene trees and selfing: An ancestral recombination graph with partial self-fertilization, Genetics, vol.154, issue.2, pp.923-929, 2000.

M. Nordborg and J. O. Borevitz, The extent of linkage disequilibrium in Arabidopsis thaliana, Nat. Genet, vol.30, issue.2, pp.190-193, 2002.

M. Nordborg and T. T. Hu, The pattern of polymorphism in Arabidopsis thaliana, PLoS Biol, vol.3, issue.7, p.196, 2005.

M. Nordborg and S. Tavare, Linkage disequilibrium: what history has to tell us, Trends Genet, vol.18, pp.83-90, 2002.

M. Ostrowski and J. David, Evidence for a large-scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium, Molecular Ecology, vol.15, issue.6, pp.1507-1517, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02663382

K. Pajerowska-mukhtar and B. Stich, potato cultivars, Genetics, vol.181, issue.3, pp.1115-1127, 2009.

K. Palaisa and M. Morgante, , 2004.

I. Paran and I. Goldman, Recombinant inbred lines for genetic mapping in tomato, TAG Theoretical and Applied Genetics, vol.90, issue.3, pp.542-548, 1995.

I. Paran and E. Van-der-knaap, Genetic and molecular regulation of fruit and plant domestication traits in tomato and pepper, J. Exp. Bot, vol.58, issue.14, pp.3841-3852, 2007.

S. C. Parker and L. Hansen, Local DNA topography correlates with functional noncoding regions of the Human genome, Science, vol.324, issue.5925, pp.389-392, 2009.

A. H. Paterson and S. Damon, Mendelian factors underlying quantitative traits in tomato: Comparison across species, generations, and environments, Genetics, vol.127, issue.1, p.181, 1991.

A. H. Paterson and J. W. Deverna, Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato, Genetics, vol.124, issue.3, pp.735-742, 1990.

A. H. Paterson and E. S. Lander, , 1988.

C. Paulus and B. Köllner, Physiological and biochemical characterization of glyoxalase I, a general marker for cell proliferation, from a soybean cell suspension, Planta, vol.189, issue.4, pp.561-566, 1993.

I. E. Peralta and D. Spooner, History, origin and early cultivation of tomato (Solanaceae), Science Publisher, vol.2, pp.1-24, 2007.

I. E. Peralta and D. Spooner, Taxonomy of wild tomatoes and their relatives (Solanum sect. Lycopersicoides, sect. Juglandifolia, sect. Lycopersicon; Solanaceae), 2007.

I. E. Peralta and D. M. Spooner, Morphological characterization and relationships of wild tomatoes (Solanum L. Section Lycopersicon). A Festschrift for, 2005.

B. Croat, V. C. Hollowell, and R. C. Keating, , vol.104, pp.227-257

X. Perrier and A. Flori, Data analysis methods. Genetic diversity of cultivated tropical plants, pp.43-76, 2003.
URL : https://hal.archives-ouvertes.fr/halshs-00752878

X. Perrier and J. P. Jacquemoud-collet, DARwin software, 2006.

M. Pop and S. L. Salzberg, Bioinformatics challenges of new sequencing technology, Trends in Genetics, vol.24, issue.3, pp.142-149, 2008.

A. L. Price and N. J. Patterson, Principal components analysis corrects for stratification in genome-wide association studies, Nat. Genet, vol.38, issue.8, pp.904-909, 2006.

J. K. Pritchard and P. Donnelly, Case-control studies of association in structured or admixed populations, Theoretical Population Biology, vol.60, issue.3, pp.227-237, 2001.

J. K. Pritchard and M. Przeworski, Linkage disequilibrium in humans: models and data, The American Journal of Human Genetics, vol.69, issue.1, pp.1-14, 2001.

J. K. Pritchard and M. Stephens, Inference of population structure using multilocus genotype data, Genetics, vol.155, issue.2, pp.945-959, 2000.

J. K. Pritchard and M. Stephens, Association mapping in structured populations, Am. J. Hum. Genet, vol.67, pp.170-181, 2000.

M. Prudent, Analyse des variations de poids et de teneur en sucres du fruit de tomate par une approche intégrative combinant des études écophysiologique, génétique et moléculaire. Avignon, Université d'Avignon et des Pays de Vaucluse, p.152, 2008.

M. Prudent and M. Causse, Genetic and physiological analysis of tomato fruit weight and composition: influence of carbon availability on QTL detection, J. Exp. Bot, vol.60, issue.3, pp.923-937, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00600425

, R: A language and environment for statistical computing, reference index version 2.2.1. F. f. S. Computing, 2005.

A. Rafalski, Applications of single nucleotide polymorphisms in crop genetics, Curr. Opin. Plant Biol, vol.5, pp.94-100, 2002.

A. Rafalski and M. Morgante, Corn and humans: recombination and linkage disequilibrium in two genomes of similar size, Trends in Genetics, vol.20, issue.2, pp.103-111, 2004.

N. Ranc and S. Munos, A clarified position for Solanum lycopersicum var. cerasiforme in the evolutionary history of tomatoes (Solanaceae), BMC Plant Biol, vol.8, issue.1, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02668658

J. Ray and P. Moureau, Cloning and characterization of a gene involved in phytoene synthesis from tomato, Plant Molecular Biology, vol.19, issue.3, pp.401-404, 1992.

A. F. Reeves, An observation on natural outcrossing in the tomato (Lycopersicon esculentum L.) in Northwest Arkansas, Arkansas Academy of Science Proceedings XXVII, 1973.

D. E. Reich and M. Cargill, Linkage disequilibrium in the human genome, Nature, vol.411, issue.6834, pp.199-204, 2001.

D. Reinhardt and M. Frenz, Microsurgical and laser ablation analysis of interactions between the zones and layers of the tomato shoot apical meristem, Development, vol.130, issue.17, pp.4073-4083, 2003.

D. L. Remington and J. M. Thornsberry, Structure of linkage disequilibrium and phenotypic associations in the maize genome, Proceedings of the National Academy of Sciences of the United States of America, vol.98, pp.11479-11484, 1920.

C. M. Rick, Tomato Lycopersicon esculentum (Solanaceae), N. W. Simmonds, pp.268-273, 1976.

C. M. Rick and R. T. Chetelat, Utilization of related wild species for tomato improvement, Acta Horticulturae, vol.412, pp.21-38, 1995.

C. M. Rick and F. Fobes, Allozyme variation in the cultivated tomato and closely related species, Bulletin of the Torrey Botanical Club, vol.102, issue.6, pp.376-384, 1975.

C. M. Rick and J. F. Fobes, Genetic variation in Lycopersicon pimpinellifolium: Evidence of evolutionary change in mating systems, Plant Systematics and Evolution, vol.127, issue.2, pp.139-170, 1977.

C. M. Rick and M. Holle, Andean Lycopersicum esculentum var. cerasiforme: Genetic Varaition and Its Evolutionary Significance, Economic Botany, vol.44, pp.69-78, 1990.

C. M. Rick and H. Latterot, A revised key for the Lycopersicum and related Solanum species, Tomato Genetics Cooperative Report, vol.40, p.31, 1990.

L. H. Rieseberg and C. A. Buerkle, Genetic mapping in hybrid zones, The American Naturalist, vol.159, issue.s3, pp.36-50, 2002.

K. Ritland, Estimators for pairwise relatedness and individual inbreeding coefficients, Genet. Res, vol.67, issue.02, pp.175-185, 1996.

G. Ronen and L. Carmel-goren, An alternative pathway to beta-carotene formation in plant chromoplasts discovered by map-based cloning of Beta and old-gold color mutations in tomato, Proceedings of the National Academy of Sciences, vol.97, p.11102, 1920.

G. Ronen and M. Cohen, Regulation of carotenoid biosynthesis during tomato fruit development: expression of the gene for lycopene epsilon-cyclase is down-regulated during ripening and is elevated in the mutant Delta, The Plant Journal, vol.17, issue.4, pp.341-351, 1999.

J. Ronfort and T. Bataillon, Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula, BMC Plant Biology, vol.6, issue.1, p.28, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02659572

N. A. Rosenberg, Distruct: a program for the graphical display of population structure, 2007.

N. A. Rosenberg and J. K. Pritchard, Genetic structure of human populations, Science, vol.298, issue.5602, pp.2381-2385, 2002.

J. Ross-ibarra and P. L. Morrell, Plant domestication, a unique opportunity to identify the genetic basis of adaptation, PNAS, vol.104, issue.suppl_1, pp.8641-8648, 2007.

N. Rostoks and L. Ramsay, Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties, Proceedings of the National Academy of Sciences, vol.103, issue.49, pp.18656-18661, 2006.

S. Rozen and H. Skaletsky, Primer3 on the WWW for general users and for biologist programmers, Bioinformatics Methods and Protocols: Methods in Molecular Biology. S. Krawetz and S. Misener, vol.132, pp.365-386, 2000.

V. Saliba-colombani and M. Causse, Efficiency of AFLP, RAPD, and RFLP markers for the construction of an intraspecific map of the tomato genome, Genome, vol.43, issue.1, pp.29-40, 2000.
URL : https://hal.archives-ouvertes.fr/hal-02697767

V. Saliba-colombani and M. Causse, Genetic analysis of organoleptic quality in fresh market tomato. 1. Mapping QTLs for physical and chemical traits, Theo. App. Genet, vol.102, issue.2, pp.259-272, 2001.
URL : https://hal.archives-ouvertes.fr/hal-02674426

D. Schoen and A. Brown, Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers, PNAS, vol.90, issue.22, pp.10623-10627, 1993.

H. Schoof and M. Lenhard, , 2000.

M. F. Seldin, Admixture mapping as a tool in gene discovery, Current Opinion in Genetics & Development, vol.17, issue.3, pp.177-181, 2007.

S. Sim and M. Robbins, Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding, BMC Genomics, vol.10, issue.1, p.466, 2009.

I. Simko and S. Costanzo, Linkage disequilibrium mapping of a Verticillium dahliae resistance quantitative trait locus in tetraploid potato (Solanum tuberosum) through a candidate gene approach, TAG Theoretical and Applied Genetics, vol.108, issue.2, pp.217-224, 2004.

I. Simko and K. G. Haynes, Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers, Genetics, vol.173, issue.4, pp.2237-2245, 2006.

M. Simon and O. Loudet, polymorphism markers, Genetics, vol.178, issue.4, pp.2253-2264, 2008.

L. Skøt and J. Humphreys, Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.), Genetics, vol.177, issue.1, pp.535-547, 2007.

L. Skøt and M. O. Humphreys, , 2005.

T. F. Smith and C. Gaitatzes, The WD repeat: a common architecture for diverse functions, Trends in Biochemical Sciences, vol.24, issue.5, pp.181-185, 1999.

M. J. Smulders and G. Bredemeijer, Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species, TAG Theoretical and Applied Genetics, vol.94, issue.2, pp.264-272, 1997.

P. H. Sneath and R. R. Sokal, Numerical Taxonomy. The Principles and Practice of Numerical Classification, 1973.

G. Watterson, On the number of segregating sites in genetical models without recombination, Theor. Popul. Biol, vol.7, issue.2, pp.256-276, 1975.

A. L. Weber and W. H. Briggs, The genetic architecture of complex traits in teosinte (Zea mays ssp. parviglumis): New evidence from association mapping, Genetics, vol.180, issue.2, pp.1221-1232, 2008.

D. Weigel and M. Nordborg, Natural variation in Arabidopsis. How do we find the causal genes?, Plant Physiol, vol.138, issue.2, pp.567-568, 2005.

G. Weiss and A. Haeseler, Inference of population history using a likelihood approach, Genetics, vol.149, issue.3, pp.1539-1546, 1998.

S. R. Whitt and E. S. Buckler, Using natural allelic diversity to evaluate gene function, Methods in Molecular Biology, vol.236, pp.123-139, 2003.

J. Q. Wilkinson and M. B. Lanahan, An ethylene-inducible component of signal transduction encoded by never-ripe, Science, vol.270, issue.5243, pp.1807-1809, 1995.

S. I. Wright and B. S. Gaut, Molecular population genetics and the search for adaptive evolution in plants, Mol Biol Evol, vol.22, issue.3, pp.506-519, 2005.

Q. Xia and Y. Guo, Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx), Science, vol.326, issue.5951, pp.433-436, 2009.

M. Yamasaki and S. G. Schroeder, , 2008.

M. Yamasaki and M. I. Tenaillon, A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement, Plant Cell, vol.17, issue.11, pp.2859-2872, 2005.