P. Abbal and G. Planton, La mesure objective de la fermeté des fruits et légumes, un pénétromètre électronique automatique et programmable, le système Pénélaup, Infos-Ctifl, vol.62, pp.27-30, 1990.

J. A. Abbott, Textural quality assessment for fresh fruits and vegetables, Quality of Fresh and Processed Foods, vol.542, pp.265-279, 2004.

C. J. Baxter, M. Sabar, W. P. Quick, and L. J. Sweetlove, Comparison of changes in fruit gene expression in tomato introgression lines provides evidence of genome-wide transcriptional changes and reveals links to mapped QTLs and described traits, J. Exp. Bot, vol.56, pp.1591-1604, 2005.

J. D. Bendtsen, L. J. Jensen, N. Blom, G. Von-heijne, and S. Brunak, Feature-based prediction of non-classical and leaderless protein secretion, Protein Engineering Design & Selection, vol.17, pp.349-356, 2004.

J. Bergervoet, H. A. Verhoeven, L. Gilissen, and R. J. Bino, High amounts of nuclear DNA in tomato (Lycopersicon esculentum Mill) pericarp, Plant Science, vol.116, pp.141-145, 1996.

D. Bernacchi, T. Beck-bunn, D. Emmatty, Y. Eshed, S. Inai et al., Advanced backcross QTL analysis of tomato. II. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild QTL-alleles derived from Lycopersicon hirsutum and L. pimpinellifolium, Theoretical and Applied Genetics, vol.97, pp.170-180, 1998.

D. Bernacchi and S. D. Tanksley, An interspecific backross of Lycopersicon esculentum x L. hirsutum : linkage analysis and a QTL study of sexual compatibility factors and floral traits, Genetics, vol.147, pp.861-877, 1997.

R. Bernatzky and S. D. Tanksley, Genetics of actin-related sequences in tomato, Theoretical and Applied Genetics, vol.72, pp.314-321, 1986.

A. B. Bleecker and H. Kende, Ethylene: A gaseous signal molecule in plants, Annual Review of Cell and Developmental Biology, vol.16, p.1, 2000.

J. Bohner and F. Bangerth, Cell number, cell size and hormone levels in semi-isogenic mutants of Lycopersicon pimpinellifolium differing in fruit size, Physiologia Plantarum, vol.72, pp.316-320, 1988.

A. Bouchez, F. Hospital, M. Causse, A. Gallais, and A. Charcosset, Marker-assisted introgression of favorable alleles at quantitative trait loci between maize elite lines, Genetics, vol.162, pp.1945-1959, 2002.
URL : https://hal.archives-ouvertes.fr/hal-02670246

D. Bouchez and H. Hofte, Functional genomics in plants, Plant Physiology, vol.118, pp.725-732, 1998.
URL : https://hal.archives-ouvertes.fr/hal-02691458

M. C. Bourne, Food texture and viscosity. Concept and measurement, vol.325, p.pp, 1982.

M. M. Bradford, A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding, Analytical Biochemistry, vol.72, pp.248-254, 1976.

D. A. Brummell, Regulation and genetic manipulation of ripening in climacteric fruit, Stewart Postharvest Review, vol.3, issue.1, pp.1-19, 2005.

D. A. Brummell, Cell wall disassembly in ripening fruit, Functional Plant Biology, vol.33, pp.103-119, 2006.

D. A. Brummell and M. H. Harpster, Cell wall metabolism in fruit softening and quality and its manipulation in transgenic plants, Plant Molecular Biology, vol.47, pp.311-340, 2001.

D. A. Brummell, M. H. Harpster, and P. Dunsmuir, Differential expression of expansin gene family members during growth and ripening of tomato fruit, Plant Molecular Biology, vol.39, pp.161-169, 1999.

M. A. Budiman, L. Mao, T. C. Wood, and R. A. Wing, A Deep-Coverage Tomato BAC Library and Prospects Toward Development of an STC Framework for Genome Sequencing, Genome Res, vol.10, pp.129-136, 2000.

L. Butler, The linkage map of the tomato, The Journal of Heredity, vol.43, pp.25-35, 1952.

R. G. Buttery, Quantitative and sensory aspects of flavour of tomato and other vegetables and fruits, Flavor Science: Sensory Principles and Techniques, pp.259-286, 1993.

F. M. Cánovas, E. Dumas-gaudot, G. Recorbet, J. Jorrin, H. P. Mock et al., Plant proteome analysis, Proteomics, vol.4, pp.285-298, 2004.

N. Carpita and D. Gibeaut, Structural models of primary cell walls in flowering plants: consistency of molecular structure with the physical properties of the walls during growth, The Plant Journal, vol.3, p.1, 1993.

F. Carrari and A. R. Fernie, Metabolic regulation underlying tomato fruit development, J. Exp. Bot, 2006.

F. Carrari, A. Nunes-nesi, Y. Gibon, A. Lytovchenko, M. E. Loureiro et al., Reduced Expression of Aconitase Results in an Enhanced Rate of Photosynthesis and Marked Shifts in Carbon Partitioning in Illuminated Leaves of Wild Species Tomato, Plant Physiol, vol.133, pp.1322-1335, 2003.

C. Catala, J. Rose, and A. B. Bennett, Auxin-Regulated Genes Encoding Cell Wall-Modifying Proteins Are Expressed during Early Tomato Fruit Growth, Plant Physiol, vol.122, pp.527-534, 2000.

M. Causse, Genetic background of fresh-market tomato flavour, Fruit and vegetable flavour: recent advances and future prospects

M. Causse, M. Buret, K. Robini, and P. Verschave, Inheritance of nutritional and sensory quality traits in fresh market tomato and relation to consumer preferences, Journal of Food Science, vol.68, pp.2342-2350, 2003.
URL : https://hal.archives-ouvertes.fr/hal-02676797

M. Causse, P. Duffe, M. C. Gomez, M. Buret, R. Damidaux et al., A genetic map of candidate genes and QTLs involved in tomato fruit size and composition, Journal of Experimental Botany, vol.55, pp.1671-1685, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02679748

M. Causse, L. Lecomte, N. Baffert, P. Duffé, and F. Hospital, Marker-assisted selection for the transfer of QTLs controlling fruit quality traits into tomato elite lines, Acta Horticulturae, vol.546, pp.557-564, 2001.
URL : https://hal.archives-ouvertes.fr/hal-02758647

M. Causse, V. Saliba-colombani, L. Lecomte, P. Duffe, 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, Journal of Experimental Botany, vol.53, pp.2089-2098, 2002.
URL : https://hal.archives-ouvertes.fr/hal-02680289

M. Causse, V. Saliba-colombani, I. Lesschaeve, and M. Buret, Genetic analysis of organoleptic quality in fresh market tomato. 2. Mapping QTLs for sensory attributes, Theoretical and Applied Genetics, vol.102, pp.273-283, 2001.
URL : https://hal.archives-ouvertes.fr/hal-02674426

J. Chaïb, L. Lecomte, M. Buret, and M. Causse, Stability over genetic backgrounds, generations and years of quantitative trait locus (QTLs) for organoleptic quality in tomato, Theoretical and Applied Genetics, vol.112, pp.934-944, 2006.

Y. Chambroy, M. Souty, G. Jacquemin, R. M. Gomez, and J. M. Audergon, Research on the suitability of modified atmosphere packaging for shelf-life and quality improvement of apricot fruit, 1995.

, Acta Horticulturae, vol.384, pp.633-638

H. D. Chapman, V. J. Morris, R. R. Selvendran, and M. A. O'neill, Static and dynamic light-scattering studies of pectic polysaccharides from the middle lamellae and primary cell walls of ciders apples, Carbohydrate research, vol.165, pp.53-68, 1987.

G. Chen, R. Hackett, D. Walker, A. Taylor, Z. Lin et al., Identification of a Specific Isoform of Tomato Lipoxygenase (TomloxC) Involved in the Generation of Fatty Acid-Derived Flavor Compounds, Plant Physiol, vol.136, pp.2641-2651, 2004.

C. Cheniclet, W. Y. Rong, M. Causse, N. Frangne, L. Bolling et al., Cell expansion and endoreduplication show a large genetic variability in pericarp and contribute strongly to tomato fruit growth, Plant Physiology, vol.139, 1984.
URL : https://hal.archives-ouvertes.fr/hal-02679827

R. F. Chuaqui, R. F. Bonner, C. Best, J. W. Gillespie, M. J. Flaig et al., Post-analysis follow-up and validation of microarray experiments, Nature Genetics, vol.32, pp.509-514, 2002.

G. A. Churchill, Fundamentals of experimental design for cDNA microarrays, Nature Genetics, vol.32, pp.490-495, 2002.

J. D. Clarke and T. Zhu, Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: practical considerations and perspectives, The Plant Journal, vol.45, pp.630-650, 2006.

C. Collazo, P. L. Ramos, O. Chacon, C. J. Borroto, Y. Lopez et al.,

O. Hidalgo, Phenotypical and molecular characterization of the Tomato mottle Taino virus-Nicotiana megalosiphon interaction, Physiological and Molecular Plant Pathology, vol.67, pp.231-236, 2005.

L. Consoli, A. Lefevre, M. Zivy, D. Devienne, and C. Damerval, QTL analysis of proteome and transcriptome variations for dissecting the genetic architecture of complex traits in maize, Plant Molecular Biology, vol.48, pp.575-581, 2002.
URL : https://hal.archives-ouvertes.fr/hal-02672605

B. G. Coombe, The Development of Fleshy Fruits, Annual Review of Plant Physiology, vol.27, pp.207-228, 1976.

D. J. Cosgrove, Loosening of plant cell walls by expansins, vol.407, pp.321-326, 2000.

P. Costa and C. Plomion, Genetic analysis of needle proteins in maritime pine: 2. Variation of protein accumulation, Silvae Genetica, vol.48, 1999.
URL : https://hal.archives-ouvertes.fr/hal-02689441

J. Couzin, Genomics -Microarray data reproduced, but some concerns remain, Science, vol.313, pp.1559-1559, 2006.

P. R. Crookes and D. Grierson, Ultrastructure of tomato fruit ripening and the role of polygalacturonase isoenzymes in cell wall degradation, Plant Physiology, vol.72, pp.1088-1093, 1983.

C. Damerval, A. Maurice, J. M. Josse, and V. Dd, Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression, Genetics, vol.137, 1994.
URL : https://hal.archives-ouvertes.fr/hal-02702036

A. Darvasi, A. Weinreb, V. Minke, J. I. Weller, and M. Soller, Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map, Genetics, vol.134, pp.943-951, 1993.

J. N. Davies and G. E. Hobson, The constituents of tomato fruit -the influence of environment, nutrition, and genotype, CRC Critical Reviews in Food Science and Nutrition, vol.15, pp.205-280, 1981.

D. De-vienne and M. Causse, La cartographie et la caractérisation des locus contrôlant la variation des caractères quantitatifs, Les marqueurs moléculaires en génétique et biotechnologies végétales: INRA, 1998.

D. De-vienne, A. Leonardi, C. Damerval, and M. Zivy, Genetics of proteome variation for QTL characterization: application to drought-stress responses in maize, J. Exp. Bot, vol.50, pp.303-309, 1999.
URL : https://hal.archives-ouvertes.fr/hal-02691692

J. Dekkers and F. Hospital, The use of molecular genetics in the improvement of agricultural populations, Nature Rev Genet, vol.3, pp.22-32, 2002.
URL : https://hal.archives-ouvertes.fr/hal-02670794

M. F. Devaux, A. Barakat, P. Robert, B. Bouchet, F. Guillon et al., Mechanical breakdown and cell wall structure of mealy tomato pericarp tissue, Postharvest Biology and Technology, vol.37, pp.209-221, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02682493

S. Doganlar, A. Frary, H. M. Ku, and S. D. Tanksley, Mapping quantitative trait loci in inbred backcross lines of Lycopersicon pimpinellifolium (LA1589), Genome, vol.45, pp.1189-1202, 2002.

N. Dudareva, E. Pichersky, and J. Gershenzon, Biochemistry of plant volatiles, Plant Physiology, vol.135, pp.1893-1902, 2004.

F. Duprat, F. Roudot, M. Grotte-nicolas, and A. C. Roudot, Non-homogeneity of fruits, Sciences des Aliments, vol.11, pp.613-626, 1991.

M. Eisenstein, Microarrays: Quality control, vol.442, pp.1067-1070, 2006.

O. Emanuelsson, H. Nielsen, S. Brunak, V. Heijne, and G. , Predicting subcellular localization of proteins based on their N-terminal amino acid sequence, Journal of Molecular Biology, vol.300, pp.1005-1016, 2000.

J. K. Eng, A. L. Mccormack, and J. R. Yates, An approach to correlate tandem mass spectral of peptides with amino acid sequences in a protein database, J. Am. Soc. Mass spectrum, vol.5, pp.976-989, 1994.

Y. Eshed and D. Zamir, A genomic library of Lycopersicon pennellii in L. esculentum: a tool for fine mapping of genes, Euphytica, vol.79, pp.175-179, 1994.

Y. Eshed and D. Zamir, An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL, Genetics, vol.141, pp.1147-1162, 1995.

Y. Eshed and D. Zamir, Less-than-additive epistatic interactions of quantitative trait loci in tomato, Genetics, vol.143, pp.1807-1817, 1996.

M. V. Faria, W. R. Maluf, A. Smd, A. Junior, V. C. Gomes et al., Yield and post-harvest quality of tomato hybrids heterozygous at the loci alcobaca, old goldcrimson or high pigment, Genetics and Molecular Research, vol.2, pp.317-327, 2003.

M. Faurobert, C. Mihr, N. Bertin, T. Pawlowski, L. Negroni et al., Major proteome variations associated with cherry tomato pericarp development and ripening, Plant Physiol
URL : https://hal.archives-ouvertes.fr/hal-02667189

M. Faurobert, E. Pelpoir, and J. Chaïb, Phenol extraction of proteins for proteomic studies of recalcitrant plant tissues, Methods in Molecular Biology, pp.9-14, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02822879

Z. Fei, X. Tang, A. R. Giovannoni, and J. , Tomato Expression Database (TED): a suite of data presentation and analysis tools, Nucl. Acids Res, vol.34, pp.766-770, 2006.

Z. Fei, X. Tang, R. M. Alba, J. A. White, C. M. Ronning et al.,

, Comprehensive EST analysis of tomato and comparative genomics of fruit ripening, The Plant Journal, vol.40, pp.47-59

L. Fernandez, L. Torregrosa, N. Terrier, L. Sreekantan, J. Grimplet et al., Identification of genes associated with flesh morphogenesis during grapevine fruit development, Plant Molecular Biology eFIRST, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02667292

B. J. Ferrie, N. Beaudoin, W. Burkhart, C. G. Bowsher, and S. J. Rothstein, The Cloning of Two Tomato Lipoxygenase Genes and Their Differential Expression during Fruit Ripening, Plant Physiol, vol.106, pp.109-118, 1994.

M. L. Fishman, D. T. Gillespie, and S. M. Sondey, Intrinsinc viscosity and molecular weight of pectin components, Carbohydrate research, vol.215, pp.91-104, 1991.

R. Michelmore, I. Paran, and R. Kesseli, Identification of Markers Linked to Disease-Resistance Genes by Bulked Segregant Analysis: A Rapid Method to Detect Markers in Specific Genomic Regions by Using Segregating Populations, PNAS, vol.88, pp.9828-9832, 1991.

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

N. Mir and R. Beaudry, Atmosphere control using oxygen and carbon dioxide. Fruit Quality and Its Biological Basis, pp.122-156, 2002.

D. Miron, M. Petreikov, N. Carmi, S. Shen, I. Levin et al., , 2002.

, Sucrose uptake, invertase localization and gene expression in developing fruit of Lycopersicon esculentum and the sucrose-accumulating Lycopersicon hirsutum, Physiologia Plantarum, vol.115, pp.35-47

S. Moco, R. J. Bino, O. Vorst, H. A. Verhoeven, J. De-groot et al.,

, A Liquid Chromatography-Mass Spectrometry-Based Metabolome Database for Tomato, Plant Physiol, vol.141, pp.1205-1218

M. Mohan, S. Nair, A. Bhagwat, T. G. Krishna, M. Yano et al., Genome mapping, molecular markers and marker-assisted selection in crop plants, Molecular Breeding, vol.3, pp.87-103, 1997.

A. J. Monforte and S. D. Tanksley, Fine mapping of a quantitative trait locus (QTL) from, 2000.

, Lycopersicon hirsutum chromosome 1 affecting fruit characteristics and agronomic traits: breaking linkage among QTLs affecting different traits and dissection of heterosis for yield, Theoretical and Applied Genetics, vol.100, pp.471-479

S. Moore, P. Payton, M. Wright, S. Tanksley, and J. Giovannoni, Utilization of tomato microarrays for comparative gene expression analysis in the Solanaceae, J. Exp. Bot, vol.56, pp.2885-2895, 2005.

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

L. A. Mueller, T. H. Solow, N. Taylor, B. Skwarecki, R. Buels et al., The SOL Genomics Network. A comparative resource for Solanaceae biology and beyond, Plant Physiology, vol.138, pp.1310-1317, 2005.

L. A. Mueller, S. D. Tanksley, J. J. Giovannoni, J. Van-eck, S. Stack et al., The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL), Comparative and Functional Genomics, vol.6, pp.153-158, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02680359

C. Muller, A revision of the genus Lycopersicon, 1940.

A. M. Munoz, Development and application of texture reference scales, Journal of Sensory Studies, vol.1, pp.55-83, 1986.

M. A. Mutschler, D. W. Wolfe, E. D. Cobb, and K. S. Yourstone, Tomato fruit quality and shelf life in hybrids heterozygous for the alc ripening mutant, HortScience, vol.27, pp.352-355, 1992.

A. Nakatsuka, S. Murachi, H. Okunishi, S. Shiomi, R. Nakano et al., Differential Expression and Internal Feedback Regulation of 1-Aminocyclopropane-1-Carboxylate Synthase, 1-Aminocyclopropane-1-Carboxylate Oxidase, and Ethylene Receptor Genes in Tomato Fruit during Development and Ripening, Plant Physiol, vol.118, pp.1295-1305, 1998.

D. Nettleton, A Discussion of Statistical Methods for Design and Analysis of Microarray Experiments for Plant Scientists, Plant Cell, vol.18, pp.2112-2121, 2006.

V. Neuhoff, N. Arold, D. Taube, and W. Ehrhardt, Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie Brilliant Blue G-250 and R-250, Electrophoresis, vol.9, pp.255-262, 1988.

B. Nguyen-quoc and C. H. Foyer, A role for 'futile cycles' involving invertase and sucrose synthase in sucrose metabolism of tomato fruit, Journal of Experimental Botany, vol.52, pp.881-889, 2001.

S. Noir, A. Brautigam, T. Colby, J. Schmidt, and R. Panstruga, A reference map of the Arabidopsis thaliana mature pollen proteome, Biochemical and Biophysical Research Communications, vol.337, pp.1257-1266, 2005.

S. Odanaka, A. B. Bennett, and Y. Kanayama, Distinct physiological roles of fructokinase isozymes revealed by gene-specific suppression of Frk1 and Frk2 expression in tomato, Plant Physiology, vol.129, pp.1119-1126, 2002.

K. Oh, K. Hardeman, M. G. Ivanchenko, M. Ellard-ivey, A. Nebenfuhr et al.,

, Fine mapping in tomato using microsynteny with the Arabidopsis genome: the Diageotropica (Dgt) locus, Genome Biology, vol.3

R. C. O'malley, F. I. Rodriguez, J. J. Esch, B. M. Binder, O. Donnell et al., Ethylene-binding activity, gene expression levels, and receptor system output for ethylene receptor family members from Arabidopsis and tomato, The Plant Journal, vol.41, pp.651-659, 2005.

F. Paoletti, E. Moneta, A. Bertone, and F. Sinesio, Mechanical properties and sensory evaluation of selected apple cultivars, Lebensmittel-Wissenschaft und -Technologie, vol.26, pp.264-270, 1993.

A. H. Paterson, J. W. De-verna, B. Lanini, and S. D. Tanksley, Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato, Genetics, vol.124, pp.735-742, 1990.

A. H. Paterson, E. S. Lander, J. D. Hewitt, S. Peterson, S. E. Lincoln et al., Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms, Nature, vol.335, pp.721-726, 1988.

D. G. Peterson, H. J. Price, J. S. Johnston, and S. M. Stack, DNA content of heterochromatin and euchromatin in tomato (Lycopersicon esculentum) pachytene chromosomes, Genome, vol.39, pp.77-82, 1996.

M. Petro-turza, Flavor of tomato and tomato products, Food Reviews International, vol.2, pp.309-351, 1986.

S. Pflieger, V. Lefebvre, and M. Causse, The candidate gene approach in plant genetics: a review, 2001.
URL : https://hal.archives-ouvertes.fr/hal-02681845

, Molecular Breeding, vol.7, pp.275-291

M. Pigliucci, From molecules to phenotypes? The promise and limits of integrative biology, Basic and Applied Ecology, vol.4, pp.297-306, 2003.

R. E. Pitt, Models for the rheology and statistical strength of uniformly stressed vegetative tissue, Transactions of the ASAE, vol.25, pp.1776-1784, 1982.

R. E. Pitt and H. L. Chen, Time-dependent aspects of the strength and rheology of vegetative tissue, Transactions of the ASAE, vol.26, pp.1275-1280, 1983.

G. Planton, Tomate, Mesure de la fermeté au Durofel 25, Infos-Ctifl, vol.74, pp.17-20, 1991.

B. W. Poovaiah, Y. Mizrahi, H. C. Dostal, J. H. Cherry, and A. C. Leopold, Water permeability during tomato fruit development in normal and rin nonripening mutant, Plant Physiology, vol.56, pp.813-815, 1975.

R. Pressey, Extraction and assay of tomato polygalacturonases, HortScience, vol.21, pp.490-492, 1986.

S. Prestage, R. Linforth, A. J. Taylor, E. Lee, J. Speirs et al., Volatile production in tomato fruit with modified alcohol dehydrogenase activity, Journal of the Science of Food and Agriculture, vol.79, pp.131-136, 1999.

A. H. Price, Believe it or not, QTLs are accurate!, Trends in Plant Science, vol.11, pp.213-216, 2006.

S. E. Prussia, J. J. Astleford, Y. C. Hung, and R. Hewlett, Non-destructive firmness measuring device, 1994.

U. S. Patent, , vol.372, p.30

B. Quéméner, D. Bertrand, M. I. Causse, M. Lahaye, and M. , Tomato near-isogenic lines differing in QTLs for fruit texture show affected cell wall: structural analysis by enzymatic oligosaccharide fingerprinting, Journal of Chromatography, vol.1141, pp.41-49, 2007.

B. Ratanachinakorn, A. Klieber, and D. H. Simons, Effect of short-term control atmospheres and maturity on ripening and eating quality of tomatoes, Postharvest Biol Technol, vol.11, pp.149-154, 1997.

R. J. Redgwell and M. Fischer, Fruit texture, cell wall metabolism and consumer perceptions. Fruit Quality and Its Biological Basis, pp.46-88, 2002.

N. Reyna and C. H. Sneller, Evaluation of marker-assisted introgression of yield QTL alleles into adapted soybean, Crop Science, vol.41, pp.1317-1321, 2001.

C. Rick, H. Laterrot, and J. Philouze, A revised key for the Lycopersicon species, Tomato Genetics Cooperative Report, vol.40, 1990.
URL : https://hal.archives-ouvertes.fr/hal-02712754

C. M. Rick, New mutants, Report of the Tomato Genetics Cooperative, vol.6, pp.22-23, 1956.

V. Robert, M. West, S. Inai, A. Caines, L. Arntzen et al., Markerassisted introgression of blackmold resistance QTL alleles from wild Lycopersicon cheesmanii to cultivated tomato (L. esculentum) and evaluation of QTL phenotypic effects, Molecular Breeding, vol.8, pp.217-233, 2001.

R. Robinson and M. Tomes, Ripening inhibitor: a gene with multiple effect on ripening, Report of the Tomato Genetics Cooperative, vol.18, pp.36-37, 1968.

M. Rocco, D. 'ambrosio, C. Arena, S. Faurobert, M. Scaloni et al., Proteomic analysis of tomato fruits from two ecotypes during ripening, PROTEOMICS, vol.6, pp.3781-3791, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02656588

G. R. Rodriguez and G. R. Pratta, Recombinant lines obtained from an intraspecific cross between Lycopersicon species selected by fruit weight and fruit shelf life, Journal Of The American Society For Horticulture Science, vol.131, pp.651-656, 2006.

I. Romagosa, F. Han, S. E. Ullrich, P. M. Hayes, and D. M. Wesenberg, Verification of yield QTL through realized molecular marker-assisted selection responses in a barley cross, Molecular Breeding, vol.5, pp.143-152, 1999.

G. Ronen, L. Carmel-goren, D. Zamir, and J. Hirschberg, An alternative pathway to betacarotene 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 of the United States of America, vol.97, pp.11102-11107, 2000.

J. Rose, S. Bashir, J. J. Giovannoni, M. M. Jahn, and R. S. Saravanan, Tackling the plant proteome: practical approaches, hurdles and experimental tools, Plant Journal, vol.39, pp.715-733, 2004.

J. Rose and A. B. Bennett, Cooperative disassembly of the cellulose-xyloglucan network of plant cell walls: parallels between cell expansion and fruit ripening, Trends in Plant Science, vol.4, pp.176-183, 1999.

J. Rose, H. H. Lee, and A. B. Bennett, Expression of a divergent expansion gene is fruit-specific and ripening-regulated, Proceedings of the National Academy of Sciences of the United States of America, vol.94, pp.5955-5960, 1997.

M. Rossignol, Analysis of the plant proteome, Current Opinion in Biotechnology, vol.12, pp.131-134, 2001.
URL : https://hal.archives-ouvertes.fr/hal-02671651

S. Roy, A. Jauneau, and B. Vian, Analytical detection of calcium ions and immunocytochemical visualization of homogalacturonic sequences in the ripe cherry tomato, Plant Physiology and Biochemistry, vol.32, pp.633-640, 1994.
URL : https://hal.archives-ouvertes.fr/hal-02705352

S. Roy, A. E. Watada, and W. P. Wergin, Characterization of the cell wall microdomain surrounding plasmodesmata in apple fruit, Plant Physiology, vol.114, pp.539-547, 1997.

Y. L. Ruan and J. W. Patrick, The cellular pathway of postphloem sugar transport in developing tomato fruit, Planta, vol.196, pp.434-444, 1995.

M. Saladie, J. Rose, and C. B. Watkins, Characterization of DFD (delayed fruit deterioration): a new tomato mutant, Acta Horticulturae, pp.79-84, 2005.

E. Salentijn, A. Aharoni, J. G. Schaart, M. J. Boone, and F. A. Krens, Differential gene expression analysis of strawberry cultivars that differ in fruit-firmness, Physiologia Plantarum, vol.118, pp.571-578, 2003.

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

V. Saliba-colombani, M. Causse, D. Langlois, J. Philouze, and M. Buret, Genetic analysis of organoleptic quality in fresh market tomato. 1. Mapping QTLs for physical and chemical traits, Theoretical and Applied Genetics, vol.102, pp.259-272, 2001.
URL : https://hal.archives-ouvertes.fr/hal-02674426

J. Sampedro and D. J. Cosgrove, The expansin superfamily, Genome Biology, vol.6, pp.241-242, 2005.

R. S. Saravanan and J. Rose, A critical evaluation of sample extraction techniques for enhanced proteomic analysis of recalcitrant plant tissues, proteomics, vol.4, pp.2522-2532, 2004.

J. E. Sarry, N. Sommerer, F. X. Sauvage, A. Bergoin, M. Rossignol et al., , 2004.

, Grape berry biochemistry revisited upon proteomic analysis of the mesocarp, SAS Institute. 1988. SAS users guide: statistics, vol.4, pp.201-215

A. A. Schaffer and M. Petreikov, Sucrose-to-Starch Metabolism in Tomato Fruit Undergoing Transient Starch Accumulation, Plant Physiol, vol.113, pp.739-746, 1997.

N. Schauer, Y. Semel, U. Roessner, A. Gur, I. Balbo et al., Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement, Nature Biotechnology, vol.24, pp.447-454, 2006.

W. Schuch, C. R. Bird, J. Ray, C. Smith, C. F. Watson et al., Control and manipulation of gene expression during tomato fruit ripening, Plant Molecular Biology, vol.13, pp.303-311, 1989.

A. M. Sebolt, R. C. Shoemaker, and B. W. Diers, Analysis of a quantative trait locus allele from wild soybean that increases seed protein concentration in soybean, Crop Science, vol.40, pp.1438-1444, 2000.

M. Serrano-megias and J. M. Lopez-nicolas, Application of agglomerative hierarchical clustering to identify consumer tomato preferences: influence of physicochemical and sensory characteristics on consumer response, Journal of the Science of Food and Agriculture, vol.86, pp.493-499, 2006.

B. Servin, C. Dillmann, G. Decoux, and F. Hospital, MDM: a program to compute fully informative genotype frequencies in complex breeding schemes, The Journal of Heredity, vol.93, pp.227-228, 2002.

G. B. Seymour, I. J. Colquhoun, M. S. Dupont, K. R. Parsley, R. Selvendran et al., Composition and structural features of cell wall polysaccharides from tomato fruits, Phytochemistry, vol.29, pp.725-731, 1990.

G. B. Seymour, S. E. Harding, A. J. Taylor, G. E. Hobson, and G. A. Tucker, Polyuronide solubilization during ripening of normal and mutant tomato fruit, Phytochemistry, vol.26, pp.1871-1875, 1987.

G. B. Seymour and K. Manning, Genetic control of fruit ripening. Fruit Quality and Its Biological Basis, pp.253-274, 2002.

G. B. Seymour, K. Manning, E. M. Eriksson, A. H. Popovich, and G. J. King, Genetic identification and genomic organization of factors affecting fruit texture, J. Exp. Bot, vol.53, pp.2065-2071, 2002.

K. A. Shackel, C. Greve, J. M. Labavitch, and H. Ahmadi, Cell turgor changes associated with ripening in tomato pericarp tissue, Plant Physiology, vol.97, pp.814-816, 1991.

L. Shen, B. Courtois, K. L. Mcnally, S. Robin, and Z. Li, Evaluation of near-isogenic lines of rice introgressed with QTLs for root depth through marker-aided selection, Theoretical and Applied Genetics, vol.103, pp.75-83, 2001.

J. D. Sherman and S. M. Stack, Two-Dimensional Spreads of Synaptonemal Complexes from Solanaceous Plants. VI. High-Resolution Recombination Nodule Map for Tomato (Lycopersicon esculentum), Genetics, vol.141, pp.683-708, 1995.

H. Shiota, T. Sudoh, and I. Tanaka, Expression analysis of genes encoding plasma membrane aquaporins during seed and fruit development in tomato, Plant Science, vol.171, pp.277-285, 2006.

J. J. Smith, E. P. Muldoon, J. J. Willard, and D. Lamport, Tomato extensin precursors P1 and P2 are highly periodic structures, Phytochemistry, vol.25, pp.1021-1030, 1986.

G. K. Smyth, Limma: Linear models for microarray data, Bioinformatics and Computational Biology Solution Using R and Bioconductor, pp.397-420, 2005.

G. K. Smyth, J. Michaud, and H. S. Scott, Use of within-array replicate spots for assessing differential expression in microarray experiments, Bioinformatics, vol.21, pp.2067-2075, 2005.

P. Soille, Morphological image analysis. Principles and applications, 1993.

D. M. Spooner, I. E. Peralta, and S. Knapp, Comparison of AFLPs with other markers for phylogenetic inference in wild tomatoes Solanum L. section, Lycopersicon (Mill.) Wettst. Taxon, vol.54, pp.43-61, 2005.

D. W. Stanley, Biological membrane deterioration and associated quality losses in food tissues, 1991.

, CRC Critical Reviews in Food Science and Nutrition, vol.30, pp.487-553

W. Stephan and C. H. Langley, DNA Polymorphism in Lycopersicon and Crossing-Over per Physical Length, Genetics, vol.150, pp.1585-1593, 1998.

M. A. Stevens, Citrate and malate concentrations in tomato fruits: genetic control and maturational effects, Journal of the American Society for Horticultural Science, vol.97, pp.655-658, 1972.

M. A. Stevens, A. A. Kader, M. Albright-holton, and M. Algazi, Genotypic variation for flavor and composition in fresh market tomatoes, Journal of the American Society for Horticultural Science, vol.102, pp.680-689, 1977.

H. Stone, J. Sidel, S. Oliver, A. Woolsey, and R. C. Singleton, Sensory evaluation by quantitative descriptive analysis, Food Technology, vol.28, pp.24-29, 1974.

J. D. Storey, A direct approach to false discovery rates, Journal of the Royal Statistical Society Series B-Statistical Methodology, vol.64, pp.479-498, 2002.

C. W. Stuber and P. H. Sisco, Marker-facilitated transfer of QTL alleles between elite inbred lines and responses in hybrids, th Annual Corn and Sorghum Research Conference, vol.46, pp.104-113, 1992.

D. Sugar, Management of postharvest diseases. Fruit Quality and Its Biological Basis, pp.225-252, 2002.

A. S. Szczesniak, Texture is a sensory property, Food Quality and Preference, vol.13, pp.215-225, 2002.

A. S. Szczesniak and R. Ilker, The meaning of textural characteristics -juiciness in plant foodstuffs, Journal of Texture Studies, vol.19, pp.61-78, 1988.

A. S. Szczesniak and E. Z. Skinner, Meaning of texture words to the consumer, Journal of Texture Studies, vol.4, pp.378-384, 1973.

S. M. Tam, C. Mhiri, A. Vogelaar, M. Kerkveld, S. R. Pearce et al., Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposonbased SSAP, AFLP and SSR. Theoretical and Applied Genetics, vol.110, pp.819-831, 2005.

S. D. Tanksley, The Genetic, Developmental, and Molecular Bases of Fruit Size and Shape Variation in Tomato, Plant Cell, vol.16, pp.181-189, 2004.

S. D. Tanksley, M. W. Ganal, and G. B. Martin, Chromosome landing : a paradigm for map-based gene cloning in plants with large genomes, Trends Genet, vol.11, pp.63-68, 1995.

S. D. Tanksley, M. W. Ganal, J. P. Prince, M. C. De-vicente, M. W. Bonierbale et al., High density molecular linkage maps of the tomato and potato genomes, Genetics, vol.132, pp.1141-1160, 1992.

S. D. Tanksley, S. Grandillo, T. M. Fulton, D. Zamir, Y. Eshed et al.,

, Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium, Theoretical and Applied Genetics, vol.92, pp.213-224

H. Thiellement, N. Bahrman, C. Damerval, C. Plomion, M. Rossignol et al.,

M. Zivy, Proteomics for genetic and physiological studies in plants, Electrophoresis, vol.20, pp.2013-2026, 1999.
URL : https://hal.archives-ouvertes.fr/hal-02694612

A. J. Thompson, M. Tor, C. S. Barry, J. Vrebalov, C. Orfila et al., Molecular and genetic characterization of a novel pleiotropic tomato-ripening mutant, Plant Physiology, vol.120, pp.383-389, 1999.

A. K. Thybo, I. E. Bechmann, and K. Brandt, Integration of sensory and objective measurements of tomato quality: quantitative assessment of the effect of harvest date as compared with growth medium (soil versus rockwool), electrical conductivity, variety and maturity, Journal of the Science of Food and Agriculture, vol.85, pp.2289-2296, 2005.

D. M. Tieman, J. A. Ciardi, M. G. Taylor, and H. J. Klee, Members of the tomato LeEIL (EIN3-like) gene family are functionally redundant and regulate ethylene responses throughout plant development, The Plant Journal, vol.26, pp.47-58, 2001.

D. M. Tieman, M. Zeigler, E. A. Schmelz, M. G. Taylor, P. Bliss et al., Identification of loci affecting flavour volatile emissions in tomato fruits, Journal of Experimental Botany, vol.57, pp.887-896, 2006.

E. C. Tigchelaar, M. Tomes, E. Kerr, and R. Barman, A new ripening mutant, non-ripening (nor), 1973.

, Report of the Tomato Genetics Cooperative, vol.35, p.20

P. Tonutti and C. Bonghi, Genomics approaches for better understanding the biological basis of fruit ripening and quality, Proceedings of the Ivth International Conference on Managing Quality in Chains, Vols 1 and 2 -the Integrated View on Fruits and Vegetables Quality, pp.307-316, 2006.

T. Toojinda, E. Baird, A. Booth, L. Broers, P. Hayes et al.,

, Introgression of quantitative trait loci (QTLs) determining stripe rust resistance in barley: an example of marker-assisted line development, Theoretical and Applied Genetics, vol.96, pp.123-131

G. A. Tucker, G. B. Seymour, . Tje, and G. A. Tucker, Introduction, Biochemistry of fruit ripening, pp.1-51, 1993.

R. Van-berloo, H. Aalbers, A. Werkman, and R. E. Niks, Resistance QTL confirmed through development of QTL-NILs for barley leaf rust resistance, Molecular Breeding, vol.8, pp.187-195, 2001.

R. Van-der-hoeven, C. Ronning, J. Giovannoni, G. Martin, and S. Tanksley, Deductions about the Number, Organization, and Evolution of Genes in the Tomato Genome Based on Analysis of a, 2002.

, Large Expressed Sequence Tag Collection and Selective Genomic Sequencing, Plant Cell, vol.14, pp.1441-1456

A. Varga and J. Bruisma, CRC Handbook of Fruit Set and Development, Tomato. In: Monselise S, pp.461-491, 1986.

W. Verkerke, J. Janse, and M. Kersten, Instrumental measurement and modelling of tomato fruit taste, Acta Horticulturae, pp.199-205, 1998.

A. R. Vicente, C. Greve, and J. M. Labavitch, Recent findings in plant cell wall structure and metabolism: future challenges and potential implications for softening, Stewart Postharvest Review, vol.2, p.9, 2006.

R. D. Vierstra, Protein-Degradation in Plants, Annual Review of Plant Physiology and Plant Molecular Biology, vol.44, pp.385-410, 1993.

P. M. Visscher and C. S. Haley, Detection of putative quantitative trait loci in line crosses under infinitesimal genetic models, Theoretical and Applied Genetics, vol.93, pp.691-702, 1996.

J. Vrebalov, D. Ruezinsky, V. Padmanabhan, R. White, D. Medrano et al., A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus, Science, vol.296, pp.343-346, 2002.

M. J. Wade, R. G. Winther, A. F. Agrawal, and C. J. Goodnight, Alternative definitions of epistasis: dependence and interaction, Trends in Ecology & Evolution, vol.16, pp.498-504, 2001.

K. W. Waldron, M. L. Parker, and A. C. Smith, Plant cell walls and food quality, Comprehensive Reviews in Food Science and Food Safety, vol.2, pp.101-119, 2003.

P. G. Walley and G. B. Seymour, Investigating the polygenic nature of texture traits in tomato fruit, 2006.

, VI International Solanaceae Conference

X. Wang, M. J. Hessner, Y. Wu, N. Pati, and S. Ghosh, Quantitative quality control in microarray experiments and the application in data filtering, normalization and false positive rate prediction, 2003.

, Bioinformatics, vol.19, pp.1341-1347

Y. Wang, R. Van-der-hoeven, R. Nielsen, L. Mueller, and S. Tanksley, Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments, TAG Theoretical and Applied Genetics, vol.112, pp.72-84, 2005.

V. C. Wasinger, S. J. Cordwell, A. Cerpapoljak, J. X. Yan, A. A. Gooley et al., , 1995.

. Mollicutes--mycoplasma-genitalium, Electrophoresis, vol.16, pp.1090-1094

G. O. Wasteneys and M. E. Galway, Remodelling the cytoskeleton for growth and form: An overview with some new views, Annual Review of Plant Biology, vol.54, pp.691-722, 2003.

C. B. Watkins, Ethylene synthesis, mode of action, consequences and control. Fruit Quality and Its Biological Basis, pp.180-224, 2002.

J. White, T. Pacey-miller, A. Crawford, G. Cordeiro, D. Barbary et al., Abundant transcripts of malting barley identified by serial analysis of gene expression (SAGE), Plant Biotechnology Journal, vol.4, pp.289-301, 2006.

P. J. White, Recent advances in fruit development and ripening: an overview, Journal of Experimental Botany, vol.53, 1995.

W. Willats, P. Knox, and J. D. Mikkelsen, Pectin: new insights into an old polymer are starting to gel, Trends in Food Science & Technology, vol.17, pp.97-104, 2006.

J. Q. Wilkinson, M. B. Lanahan, H. C. Yen, J. J. Giovannoni, and H. J. Klee, An Ethylene-Inducible Component of Signal-Transduction Encoded by Never-Ripe, Science, vol.270, pp.1807-1809, 1995.

F. Wu, L. A. Mueller, D. Crouzillat, V. Petiard, and S. D. Tanksley, Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative, Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade, Genetics, vol.174, p.1407, 2006.

Y. H. Yang, S. Dudoit, P. Luu, and T. P. Speed, Normalization for cDNA microarray data, SPIE BiOS, vol.4266, 2001.

K. Y. Yeung, R. E. Bumgarner, and A. E. Raftery, Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data, Bioinformatics, vol.21, pp.2394-2402, 2005.

G. G. Yousef and J. A. Juvik, Enhancement of seedling emergence in sweet corn by marker-assisted backcrossing of beneficial QTL, Crop Science, vol.42, pp.96-104, 2002.

Z. B. Zeng, Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci, Proc Natl Acad Sci, vol.90, pp.10972-10976, 1993.

Z. B. Zeng, Precision mapping of quantitative trait loci, Genetics, vol.136, pp.1457-1468, 1994.

H. Zhu, G. Briceño, R. Dovel, P. M. Hayes, B. H. Liu et al., Molecular breeding for grain yield in barley: an evaluation of QTL effects in a spring barley cross, Theoretical and Applied Genetics, vol.98, pp.772-779, 1999.

M. Zivy and D. De-vienne, Proteomics: a link between genomics, genetics and physiology, Plant Molecular Biology, vol.44, pp.575-580, 2000.
URL : https://hal.archives-ouvertes.fr/hal-02685500

, ANNEXES Annexe 1: Carte génétique représentant les 75 IL de M82 dans LA716 (Eshed and Zamir, 1994.

, Annexe 2: Protocole d'extraction d'ADN en format 96 sans solvant (d'après Stéphane Muños

, Annexe 3: Protocole d'extraction des protéines totales au phénol

, Liste de l'ensemble des marqueurs testés pour la densification en marqueurs des régions d, Annexe, vol.4

, Localisation des spots différentiellement exprimés (Tableaux VI.3 et VI.4) sur les gels d'électrophorèse bidimensionnelle, Annexe, vol.6

, Gènes candidats issus du criblage différentiel Lxl/Levovil à quatre stades de développement réalisé sur des puces à oligonucléotides dédiées texture, vol.7

, Article présentant l'étude des effets épistatiques contrôlant les variations phénotypique de six composantes de la qualité du fruit de tomate: poids du fruit, nombre de loge, fermeté instrumentale, acidité titrable, teneurs en sucres et en solides solubles, Annexe, vol.8, p.141

, Localisation des spots différentiellement exprimés (Tableaux VI.3 et VI.4) sur les gels d'électrophorèse bidimensionnelle, colorés au nitrate d'argent, réalisés à partir d'extraits de protéines totales du péricarpe de tomate. Les cercles indiquent la position de spots absents chez Lx mais présents pour d'autres génotypes, Annexe, vol.6

, Article présentant l'étude des effets épistatiques contrôlant les variations phénotypique de six composantes de la qualité du fruit de tomate: poids du fruit, nombre de loge, fermeté instrumentale, acidité titrable, teneurs en sucres et en solides solubles, Annexe, vol.8

M. Causse, *. , J. Chaïb, and L. Lecomte, Michel Buret ? and Frédéric Hospital ?, p.1

, Unité de Génétique et Amélioration des Fruits et Légumes, INRA, vol.84143

F. Montfavet, Author for correspondence

?. Inra, . Sécurité, D. Qualité-des-produits-d'origine-végétale, . Saint-paul-;-avignon, ?. France et al., Epistasis may exert important effect on the dynamics of evolving populations (Cheverud and Routman 1996; Elena and Lenski 2001). In the evolutionary history of species, complementary epistatic interactions due to the isolation of subspecies explain some epistatic interactions (Fenster et al. 1997) for instance for female sterility in rice (Kubo and Yoshimura 2005) or seed yield in bean, Bâtiment, vol.84914, 1909.

. Doebley, This could result in a restricted genetic gain from markerassisted selection (Liu et al. 2003) as well as some difficulties when trying to characterize the QTL. Ignoring the epistatic interactions also leads to underestimate genetic variance and to overestimate individual QTL effects (Carlborg and Haley 2004). chance (Tanksley 1993). Nevertheless, several cases of epistatic interactions have been detected in plants, for flowering time, Its presence may have important consequences on the success of detection, introgression and characterization of the genes controlling quantitative traits, 1995.

. Mahmood, Several cases of epistasis were also detected for disease resistance, Thabuis et al, 2003.

C. , In tomato, significant interactions were detected for fruit shape (Van Der Knaap et al. 2002), locule number (Lippman and Tanksley 2001), colour (Kabelka et al. 2004), soluble solid content (Monforte et al. 2001), fructose to glucose ratio (Levin et al. 2004) and aroma production (Causse et al. 2002). its effect is rarely significant, except when specific designs are used, 2001.

, Thus many QTL detected in this study (with additive or epistatic effect) corresponded to main effect QTL in other studies on tomato, confirming that QTL are consistent over species, but that some QTL may be detected tomato (Grandillo et al. 1999). In the CL-RIL population, five QTL were mapped and two other

, Fruit weight QTL have already been found in all these regions, in at least two other progenies (Grandillo et al. 1999), except on chromosome 12. In CL-RIL, a duplicate epistatic interaction was shown between Q 2 and a region of chromosome 6 where a QTL was detected by, and Q 9a ) were detected in QTL-CIL, 1999.

, For locule number, at least eight QTL were previously detected in four progenies, Lippman and Tanksley, 2001.

T. Van-der-knaap, five of which being detected in at least two progenies. Interactions between QTL were detected only in certain progenies, and three new putative epistatic interactions involving five other fragments were, 2003.

. Seymour, Many biological processes control fruit firmness: the change of color during ripening, the ethylene synthesis partly responsible of cell wall loosening, cell adhesion and osmotic pressure modifications, 2002.

, firmness has a low heritability and is generally quantitatively inherited. A comparison of previously mapped QTL for firmness in progenies of S. pimpinellifolium, p.28, 2001.

. Fulton, For this trait the epistatic interactions appeared much more important than additive effects in both CL-RIL and QTL-CIL. In QTL-CIL the four regions exhibited significant epistatic interactions and ten interactions were significant in the CL-RIL, among which four involved Q 4 or Q 9a , three Q 2 and one Q 1 , highlighting the consistency of results in QTL-CIL and CL-RIL. Overall, 13 of QTL controlling this trait, and more than 20 QTL were mapped, QTL in 18 regions. Firmness had the lowest heritability and the lowest number of QTL detected in CL-RIL. QTL on chromosome 4 and 9 were already detected twice in the same regions in studies of advanced backcross progenies involving wild species, 1995.

. Fulton, All the QTL regions detected with CL-RIL and QTL-NIL have already been detected with other populations, QTL for sugars have been mapped in at least 35 regions, 2002.

. Fulton, Acidity relies on the content of citric and malic acids, for which at least 29 QTL have been detected

. Causse, All the additive QTL detected in CL-RIL or QTL-NIL have already been mapped in another progeny. Four of the 6 loci involved in interactions corresponded to QTL in other progenies, 2004.

N. Ahmadi, L. Albar, G. Pressoir, A. Pinel, D. Fargette et al., Genetic basis and mapping of the resistance to Rice yellow mottle virus. III. Analysis of QTL efficiency in introgressed progenies confirmed the hypothesis of complementary epistasis between two resistance QTLs, Theor Appl Genet, vol.103, pp.1084-1092, 2001.

R. Anholt, C. L. Dilda, S. Chang, J. J. Fanara, N. H. Kulkarni et al., The genetic architecture of odor-guided behavior in Drosophila: epistasis and the transcriptome, Nature Genet, vol.35, pp.180-184, 2003.

L. S. Barrero and S. D. Tanksley, Evaluating the genetic basis of multiple-locule fruit in a broad cross section of tomato cultivars, Theor Appl Genet, vol.109, pp.669-679, 2004.

D. Bernacchi, T. Beck-bunn, Y. Eshed, J. Lopez, V. Petiard et al., Advanced backross QTL analysis in tomato. I. Identification of QTL for traits of agronomic importance from Lycopersicon hirsutum, Theor Appl Genet, vol.97, pp.381-397, 1998.

R. B. Brem and L. Kruglyak, The landscape of genetic complexity across 5,700 gene expression traits in yeast, Proc Natl Acad Sci, vol.102, pp.1572-1577, 2005.

A. L. Caicedo, J. R. Stinchcombe, K. M. Olsen, J. Schmitt, and M. D. Purugganan, Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait, Proc Natl Acad Sci, vol.101, pp.15670-15675, 2004.

F. Calenge, D. Drouet, C. Denance, W. E. Van-de-weg, M. Brisset et al., Genet, vol.111, pp.128-135, 2005.

O. Carlborg and C. S. Haley, Epistasis: too often neglected in complex trait studies?, Nature Rev Genet, vol.5, pp.618-624, 2004.

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

M. Causse, P. Duffe, M. C. Gomez, M. Buret, R. Damidaux et al., A Genetic map of candidate genes and QTL involved in tomato fruit size and composition, J Exp Bot, vol.55, pp.1671-85, 2004.

A. Charcosset, M. Causse, M. Moreau, and A. Gallais, Investigation into the effect of genetic background on QTL expression using three connected maize recombinant inbred lines (RIL) populations, Biometrics in Plant Breeding: Applications of molecular markers, pp.83-89, 1995.
URL : https://hal.archives-ouvertes.fr/hal-02773329

J. M. Cheverud and E. J. Routman, Epistasis as a source of increased additive genetic variance at population bottlenecks, Evolution, vol.50, pp.1042-1051, 1996.

J. D. Clarke, N. Aarts, B. J. Feys, X. N. Dong, and J. E. Parker, Constitutive disease resistance requires EDS1 in the Arabidopsis mutants cpr1 and cpr6 and is partially EDS1-dependent in cpr5, Plant J, vol.26, pp.409-420, 2001.

G. L. Coaker and D. M. Francis, Mapping, genetic effects, and epistatic interaction of two bacterial canker resistance QTLs from Lycopersicon hirsutum, Theor Appl Genet, vol.108, pp.1047-1055, 2004.

C. C. Cockerham and Z. B. Zeng, Design III with marker loci, Genetics, vol.143, pp.1437-1456, 1996.

H. J. Cordell, J. A. Todd, N. J. Hill, C. J. Lord, P. A. Lyons et al., Statistical modeling of interlocus interactions in a complex disease: Rejection of the multiplicative model of epistasis in type 1 diabetes, Genetics, vol.158, pp.357-367, 2001.

J. Doebley, A. Stec, and C. Gustus, Teosinte Branched 1 and the origin of maize -evidence for epistasis and the evolution of dominance, Genetics, vol.141, pp.333-346, 1995.

S. F. Elena and R. E. Lenski, Epistasis between new mutations and genetic background and a test of genetic canalization, Evolution, vol.55, pp.1746-1752, 2001.

Y. Eshed and D. Zamir, An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL, Genetics, vol.141, pp.1147-1162, 1995.

Y. Eshed and D. Zamir, Less-than-additive epistatic interactions of quantitative trait loci in tomato, Genetics, vol.143, pp.1807-1817, 1996.

C. Fenster, . Gallowaylf, and L. Chao, Epistasis and its consequences for the evolution of natural populations, Trends Ecol Evol, vol.12, pp.282-286, 1997.

R. A. Fisher, The correlation between relatives on the supposition of Mendelian inheritance, Trans Roy Soc Edinburgh, vol.52, pp.399-433, 1918.

T. M. Fulton, T. Beckbunn, D. Emmatty, Y. Eshed, J. Lopez et al., QTL analysis of an advanced backcross of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTLs found in other wild species, Theor Appl Genet, vol.95, pp.881-894, 1997.

T. M. Fulton, S. Grandillo, T. Beck-bunn, E. Fridman, A. Frampton et al., Advanced backcross QTL analysis of a Lycopersicon esculentum x Lycopersicon parviflorum cross, Theor Appl Genet, vol.100, pp.1025-1042, 2000.

T. M. Fulton, P. Bucheli, E. Voirol, J. Lopez, V. Petiard et al., Quantitative trait loci (QTL) affecting sugars, organic acids and other biochemical properties possibly contributing to flavor, identified in four advanced backcross populations of tomato, Euphytica, vol.127, pp.163-177, 2002.

J. Giovannoni, Molecular biology of fruit maturation and ripening, Ann Rev Plant Phys Plant Mol Biol, vol.52, pp.725-749, 2001.

S. Grandillo, H. M. Ku, and S. D. Tanksley, Identifying the loci responsible for natural variation in fruit size and shape in tomato, Theor Appl Genet, vol.99, pp.978-987, 1999.

T. Jack, Molecular and Genetic mechanisms of floral control, The Plant Cell, vol.16, pp.1-17, 2004.

J. L. Jannink and R. Jansen, Mapping epistatic quantitative trait loci with one-dimensional genome searches, Genetics, vol.157, pp.445-454, 2001.

W. C. Johnson and P. Gepts, The Role of epistasis in controlling seed yield and other agronomic traits in an Andean x Mesoamerican cross of common bean (Phaseolus vulgaris L.), Euphytica, vol.125, pp.69-79, 2002.

E. Kabelka, W. C. Yang, and D. M. Francis, Improved tomato fruit color within an inbred backcross line derived from Lycopersicon esculentum and L. hirsutum involves the interaction of loci, J Amer Soc Hort Sci, vol.129, pp.250-257, 2004.

C. H. Kao, Z. B. Zeng, and R. D. Teasdale, Multiple interval mapping for quantitative trait loci, Genetics, vol.152, pp.1203-1216, 1999.

M. J. Kearsey, H. S. Pooni, and N. H. Syed, Genetics of quantitative traits in Arabidopsis thaliana, Heredity, vol.91, pp.456-464, 2003.

P. D. Keightley, Metabolic models of selection response, J Theor Biol, vol.182, pp.311-316, 1996.

J. Kroymann and T. Mitchell-olds, Epistasis and balanced polymorphism influencing complex trait variation, Nature, vol.435, pp.95-98, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02104679

T. Kubo and A. Yoshimura, Epistasis underlying female sterility detected in hybrid breakdown in a Japonica-Indica cross of rice, Oryza sativa L.). Theor Appl Genet, vol.110, pp.346-355, 2005.

K. G. Lark, K. Chase, F. Adler, L. M. Mansur, and J. H. Orf, Interactions between quantitative trait loci in soybean in which trait variation at one locus is conditional upon a specific allele at another, Proc Natl Acad Sci, vol.92, pp.4656-4660, 1995.

L. Lecomte, P. Duffé, M. Buret, B. Servin, F. Hospital et al., Marker-assisted introgression of five QTLs controlling fruit quality traits into three tomato lines revealed interactions between QTLs and genetic background, Theor Appl, vol.109, pp.658-668, 2004.

J. Li, G. Brader, and E. T. Palva, The WRKY70 transcription factor: A node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense, Plant Cell, vol.16, pp.319-331, 2004.

Z. K. Li, L. J. Luo, H. W. Mei, D. L. Wang, Q. Y. Shu et al., Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. I. Biomass and grain yield, Genetics, vol.158, pp.1737-1753, 2001.

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 Lycopersicon pimpinellifolium and L-esculentum var. giant heirloom, Genetics, vol.158, pp.413-422, 2001.

P. Y. Liu, J. Zhu, X. Y. Lou, and Y. Lu, A method for marker-assisted selection based on QTLs with epistatic effects, Genetica, vol.119, pp.75-86, 2003.

T. Mahmood, U. Ekuere, F. Yeh, A. G. Good, and G. R. Stringam, RFLP linkage analysis and mapping genes controlling the fatty acid profile of Brassica juncea using reciprocal DH populations, Theor Appl Genet, vol.107, pp.283-290, 2003.

M. D. Mcmullen, M. Snook, E. A. Lee, P. F. Byrne, H. Kross et al., , p.The, 2001.

H. W. Mei, L. J. Luo, C. S. Ying, Y. P. Wang, X. Q. Yu et al., Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two testcross populations, Theor Appl Genet, vol.107, pp.89-101, 2003.

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, Theor Appl Genet, vol.100, pp.471-479, 2000.

A. J. Monforte, E. Friedman, D. Zamir, and S. D. Tanksley, Comparison of a set of allelic QTL-NILs for chromosome 4 of tomato: Deductions about natural variation and implications for germplasm utilization, Theor Appl Genet, vol.102, pp.572-590, 2001.

L. Monna, H. X. Lin, S. Kojima, T. Sasaki, and M. Yano, Genetic dissection of a genomic region for a quantitative trait locus, Hd3, into two loci, Hd3a and Hd3b, controlling heading date in rice, Theor Appl Genet, vol.104, pp.772-778, 2002.

L. A. Mueller, S. D. Tanksley, J. J. Giovannoni, J. Van-eck, S. Stack et al., The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL), Compar. Funct. Genomics, vol.6, pp.153-158, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02680359

P. C. Phillips, The language of gene interaction, Genetics, vol.149, pp.1167-1171, 1998.

S. Purcell and P. C. Sham, Epistasis in quantitative trait locus linkage analysis: Interaction or main effect?, Behavior Genetics, vol.34, pp.143-152, 2004.

B. Quilot, M. Génard, J. Kervella, and F. Lescourret, Analysis of genotypic variations in flesh total sugar content via a modelling approach applied to peach fruit, Theor Appl Genet, vol.109, pp.440-449, 2004.

V. Robert, M. West, S. Inai, A. Caines, L. Arntzen et al., Marker-assisted introgression of blackmold resistance QTL alleles from wild Lycopersicon cheesmanii to cultivated tomato (L. esculentum) and evaluation of QTL phenotypic effects, Mol Breed, vol.8, pp.217-233, 2001.

V. Saliba-colombani, M. Causse, D. Langlois, J. Philouze, and M. Buret, Genetic analysis of organoleptic quality in fresh market tomato. 1. Mapping QTLs for physical and chemical traits, SAS users guide: statistics (SAS Institute, vol.102, pp.259-272, 1988.
URL : https://hal.archives-ouvertes.fr/hal-02674426

D. Segre, A. Deluna, G. M. Church, and R. Kishony, Modular epistasis in yeast metabolism, Nature Genetics, vol.37, pp.77-83, 2005.

G. Seymour, K. Manning, E. M. Eriksson, A. H. Popovich, and G. J. King, Genetic identification and genomic organization of factors affecting fruit texture, J Exp Bot, vol.53, pp.2065-2071, 2002.

L. M. Steinmetz, H. Sinha, D. R. Richards, J. I. Spiegelman, P. J. Oefner et al., Dissecting the architecture of a quantitative trait locus in yeast, Nature, vol.416, pp.326-330, 2002.

N. H. Syed and Z. J. Chen, Molecular marker genotypes, heterozygosity and genetic interactions explain heterosis in Arabidopsis thaliana, Heredity, vol.94, pp.295-304, 2005.

S. D. Tanksley, M. W. Ganal, J. P. Prince, M. C. De-vicente, M. W. Bonierbale et al., High density molecular linkage maps of the tomato and potato genomes, Genetics, vol.132, pp.1141-1160, 1992.

S. D. Tanksley, Mapping polygenes, Annu Rev Genet, vol.27, pp.205-233, 1993.

S. D. Tanksley, S. Grandillo, T. M. Fulton, D. Zamir, Y. Eshed et al., Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium, Theor Appl Genet, vol.92, pp.213-224, 1996.

A. Thabuis, A. Palloix, B. Servin, A. M. Daubèze, P. Signoret et al., Marker-assisted introgression of 4 Phytophthora capsici resistance QTL alleles into a bell pepper line: validation of additive and epistatic effects, Mol Br, vol.14, pp.9-20, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02671845

M. C. Ungerer, S. S. Halldorsdottir, J. L. Modliszewski, T. Mackay, and M. D. Purugganan, Quantitative trait loci for inflorescence development in Arabidopsis thaliana, Genetics, vol.160, pp.1133-1151, 2002.

R. Van-berloo, H. Aalbers, A. Werkman, and R. E. Niks, Resistance QTL confirmed through development of QTL-NILs for barley leaf rust resistance, Mol Breed, vol.8, pp.187-195, 2001.

E. Van-der-knaap and S. D. Tanksley, The making of a bell pepper-shaped tomato fruit: identification of loci controlling fruit morphology in Yellow Stuffer tomato, Theor Appl Genet, vol.107, pp.139-147, 2003.

E. Van-der-knaap, Z. B. Lippman, and S. D. Tanksley, Extremely elongated tomato fruit controlled by four quantitative trait loci with epistatic interactions, Theor Appl Genet, vol.104, pp.241-247, 2002.

M. Visker, L. Keizer, H. J. Van-eck, E. Jacobsen, L. T. Colon et al., Can the QTL for late blight resistance on potato chromosome 5 be attributed to foliage maturity type?, Theor. Appl. Genet, vol.106, pp.317-325, 2003.

M. J. Wade, R. G. Winther, A. F. Agrawal, and C. J. Goodnight, Alternative definitions of epistasis: dependence and interaction, Trends Ecol Evol, vol.16, pp.498-504, 2001.

G. G. Yousef and J. A. Juvik, Enhancement of seedling emergence in sweet corn by marker-assisted backcrossing of beneficial QTL, Crop Sci, vol.42, pp.96-104, 2002.

J. W. Zhao and J. L. Meng, Genetic analysis of loci associated with partial resistance to Sclerotinia sclerotiorum in rapeseed (Brassica napus L.), Theor. Appl. Genet, vol.106, issue.4, pp.759-764, 2003.

J. Y. Zhao, H. C. Becker, D. Q. Zhang, Y. F. Zhang, and W. Ecke, Oil content in a European x Chinese rapeseed population: QTL with additive and epistatic effects and their genotype-environment interactions, Crop Sci, vol.45, pp.51-59, 2005.