G. Angenent, J. Franken, M. Busscher, A. Van-dijken, J. Van-went et al., A Novel Class of MADS Box Genes Is Involved in Ovule Development in Petunia, THE PLANT CELL ONLINE, vol.7, issue.10, pp.1569-1582, 1995.
DOI : 10.1105/tpc.7.10.1569

C. Audran-delalande, C. Bassa, I. Mila, F. Regad, M. Zouine et al., Genome-Wide Identification, Functional Analysis and Expression Profiling of the Aux/IAA Gene Family in Tomato, Plant and Cell Physiology, vol.53, issue.4, pp.659-672
DOI : 10.1093/pcp/pcs022

M. Bemer, R. Karlova, A. Ballester, Y. Tikunov, A. Bovy et al., The Tomato FRUITFULL Homologs TDR4/FUL1 and MBP7/FUL2 Regulate Ethylene-Independent Aspects of Fruit Ripening, The Plant Cell, vol.24, issue.11, pp.4437-4451, 2012.
DOI : 10.1105/tpc.112.103283

D. Brummell, M. Harpster, P. Civello, J. Palys, A. Bennett et al., Modification of Expansin Protein Abundance in Tomato Fruit Alters Softening and Cell Wall Polymer Metabolism during Ripening, THE PLANT CELL ONLINE, vol.11, issue.11, pp.2203-2216, 1999.
DOI : 10.1105/tpc.11.11.2203

L. Colombo, J. Franken, E. Koetje, J. Van-went, H. Dons et al., The Petunia MADS Box Gene FBP11 Determines Ovule Identity, THE PLANT CELL ONLINE, vol.7, issue.11, pp.1859-1868, 1995.
DOI : 10.1105/tpc.7.11.1859

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC161044/pdf

L. Colombo, J. Franken, A. Van-der-krol, P. Wittich, H. Dons et al., Downregulation of Ovule-Specific MADS Box Genes from Petunia Results in Maternally Controlled Defects in Seed Development, THE PLANT CELL ONLINE, vol.9, issue.5, pp.703-715, 1997.
DOI : 10.1105/tpc.9.5.703

S. De-folter, A. Shchennikova, J. Franken, M. Busscher, R. Baskar et al., MADS-box gene involved in ovule and seed development in petunia and Arabidopsis, The Plant Journal, vol.33, issue.Suppl., pp.934-946, 2006.
DOI : 10.3109/10520297509117081

T. Dong, Z. Hu, L. Deng, Y. Wang, M. Zhu et al., A Tomato MADS-Box Transcription Factor, SlMADS1, Acts as a Negative Regulator of Fruit Ripening, PLANT PHYSIOLOGY, vol.163, issue.2, pp.1026-1036, 2013.
DOI : 10.1104/pp.113.224436

L. Dreni and M. Kater, subfamily genes, New Phytologist, vol.8, issue.3, pp.717-732, 2014.
DOI : 10.1111/j.1525-142X.2006.05073.x

L. Dreni, A. Pilatone, D. Yun, S. Erreni, A. Pajoro et al., Functional Analysis of All AGAMOUS Subfamily Members in Rice Reveals Their Roles in Reproductive Organ Identity Determination and Meristem Determinacy, The Plant Cell, vol.23, issue.8, pp.2850-2863, 2011.
DOI : 10.1105/tpc.111.087007

K. Earley, J. Haag, O. Pontes, K. Opper, T. Juehne et al., Gateway-compatible vectors for plant functional genomics and proteomics, The Plant Journal, vol.38, issue.4, pp.616-629, 2006.
DOI : 10.1016/j.tplants.2005.01.008

URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2005.02617.x/pdf

M. Ecarnot, P. B?czyk, L. Tessarotto, and C. Chervin, Rapid phenotyping of the tomato fruit model, Micro-Tom, with??a??portable VIS???NIR spectrometer, Plant Physiology and Biochemistry, vol.70, pp.159-163, 2013.
DOI : 10.1016/j.plaphy.2013.05.019

I. Ezquer, C. Mizzotti, and E. Nguema-ona, The Developmental Regulator SEEDSTICK Controls Structural and Mechanical Properties of the Arabidopsis Seed Coat, The Plant Cell, vol.28, issue.10, pp.2478-2492, 2016.
DOI : 10.1105/tpc.16.00454

URL : https://hal.archives-ouvertes.fr/hal-01601979

R. Favaro, A. Pinyopich, R. Battaglia, M. Kooiker, L. Borghi et al., MADS-Box Protein Complexes Control Carpel and Ovule Development in Arabidopsis, THE PLANT CELL ONLINE, vol.15, issue.11, pp.2603-2611, 2003.
DOI : 10.1105/tpc.015123

URL : http://www.plantcell.org/content/plantcell/15/11/2603.full.pdf

M. Fujisawa, T. Nakano, Y. Shima, and Y. Ito, A Large-Scale Identification of Direct Targets of the Tomato MADS Box Transcription Factor RIPENING INHIBITOR Reveals the Regulation of Fruit Ripening, The Plant Cell, vol.25, issue.2, pp.371-386, 2013.
DOI : 10.1105/tpc.112.108118

E. Giménez, L. Castañeda, B. Pineda, I. Pan, V. Moreno et al., TOMATO AGAMOUS1 and ARLEQUIN/TOMATO AGAMOUS-LIKE1 MADS-box genes have redundant and divergent functions required for tomato reproductive development, Plant Molecular Biology, vol.346, issue.3, pp.513-531, 2016.
DOI : 10.1038/346035a0

E. Giménez, B. Pineda, and J. Capel, Functional Analysis of the Arlequin Mutant Corroborates the Essential Role of the ARLEQUIN/TAGL1 Gene during Reproductive Development of Tomato, PLoS ONE, vol.126, issue.12, 2010.
DOI : 10.1371/journal.pone.0014427.s006

D. Grierson, G. Tucker, J. Keen, J. Ray, C. Bird et al., Sequencing and identification of a cDNA done for tomato polygalacturonase, Nucleic Acids Research, vol.14, issue.21, pp.8595-8603, 1986.
DOI : 10.1093/nar/14.21.8595

Y. Hao, G. Hu, D. Breitel, M. Liu, I. Mila et al., Auxin Response Factor SlARF2 Is an Essential Component of the Regulatory Mechanism Controlling Fruit Ripening in Tomato, PLOS Genetics, vol.47, issue.12, 2015.
DOI : 10.1371/journal.pgen.1005649.s003

K. Heijmans, K. Ament, A. Rijpkema, J. Zethof, M. Wolters-arts et al., Redefining C and D in the Petunia ABC, The Plant Cell, vol.24, issue.6, pp.2305-2317, 2012.
DOI : 10.1105/tpc.112.097030

G. Hu, J. Fan, Z. Xian, W. Huang, D. Lin et al., Overexpression of SlREV alters the development of the flower pedicel abscission zone and fruit formation in tomato, Plant Science, vol.229, pp.86-95, 2014.
DOI : 10.1016/j.plantsci.2014.08.010

M. Itkin, H. Seybold, D. Breitel, I. Rogachev, S. Meir et al., TOMATO AGAMOUS-LIKE??????1 is a component of the fruit ripening regulatory network, The Plant Journal, vol.26, issue.6, pp.1081-1095, 2009.
DOI : 10.1093/treephys/27.5.649

R. Karlova, N. Chapman, K. David, G. Angenent, G. Seymour et al., Transcriptional control of fleshy fruit development and ripening, Journal of Experimental Botany, vol.65, issue.16, pp.4527-4541, 2014.
DOI : 10.1093/jxb/eru316

URL : https://academic.oup.com/jxb/article-pdf/65/16/4527/18025367/eru316.pdf

M. Kater, L. Colombo, J. Franken, M. Busscher, S. Masiero et al., Multiple AGAMOUS Homologs from Cucumber and Petunia Differ in Their Ability to Induce Reproductive Organ Fate, THE PLANT CELL ONLINE, vol.10, issue.2, pp.171-182, 1998.
DOI : 10.1105/tpc.10.2.171

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC143982/pdf

S. Kempin, M. Mandel, and M. Yanofsky, Conversion of Perianth into Reproductive Organs by Ectopic Expression of the Tobacco Floral Homeotic Gene NAG1, Plant Physiology, vol.103, issue.4, pp.1041-1046, 1993.
DOI : 10.1104/pp.103.4.1041

B. Langmead and S. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012.
DOI : 10.1093/bioinformatics/btp352

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381/pdf

J. Leclercq, B. Ranty, and M. Sanchez-ballesta, Molecular and biochemical characterization of LeCRK1, a ripening-associated tomato CDPK-related kinase, Journal of Experimental Botany, vol.56, pp.25-35, 2005.
DOI : 10.1093/jxb/eri003

S. Liljegren, G. Ditta, Y. Eshed, B. Savidge, J. Bowman et al., SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis, Nature, vol.404, pp.766-770, 2000.

M. Liu, G. Diretto, J. Pirrello, J. Roustan, Z. Li et al., , shows contrasting effects on tomato fruit ripening, New Phytologist, vol.195, issue.Suppl, pp.206-218, 2014.
DOI : 10.1111/j.1469-8137.2012.04160.x

M. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biology, vol.14, issue.12, p.550, 2014.
DOI : 10.1186/gb-2013-14-4-r36

A. Lovisetto, B. Baldan, A. Pavanello, and G. Casadoro, Characterization of an AGAMOUS gene expressed throughout development of the fleshy fruit-like structure produced by Ginkgo biloba around its seeds, BMC Evolutionary Biology, vol.32, issue.5, p.139, 2015.
DOI : 10.1007/BF02670468

T. Løvdal and C. Lillo, Reference gene selection for quantitative real-time PCR normalization in tomato subjected to nitrogen, cold, and light stress, Analytical Biochemistry, vol.387, issue.2, pp.238-242, 2009.
DOI : 10.1016/j.ab.2009.01.024

J. Malabarba, V. Buffon, J. Mariath, M. Gaeta, M. Dornelas et al., The MADS-box gene Agamous-like 11 is essential for seed morphogenesis in grapevine, Journal of Experimental Botany, vol.68, issue.7, pp.1493-1506, 2017.
DOI : 10.1093/jxb/erx025

C. Martel, J. Vrebalov, P. Tafelmeyer, and J. Giovannoni, The Tomato MADS-Box Transcription Factor RIPENING INHIBITOR Interacts with Promoters Involved in Numerous Ripening Processes in a COLORLESS NONRIPENING-Dependent Manner, PLANT PHYSIOLOGY, vol.157, issue.3, pp.1568-1579, 2011.
DOI : 10.1104/pp.111.181107

E. Maza, RLE (DESeq2), and MRN normalization methods for a simple two-conditions-withoutreplicates RNA-seq experimental design, papyro comparison of TMM (edgeR), p.164, 2016.
DOI : 10.3389/fgene.2016.00164

URL : http://journal.frontiersin.org/article/10.3389/fgene.2016.00164/pdf

E. Maza, P. Frasse, P. Senin, M. Bouzayen, and M. Zouine, Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments, Communicative & Integrative Biology, vol.6, issue.6, 2013.
DOI : 10.1007/s13361-011-0237-2

URL : https://hal.archives-ouvertes.fr/hal-00982548

N. Mejía, B. Soto, and M. Guerrero, Molecular, genetic and transcriptional evidence for a role of VvAGL11 in stenospermocarpic seedlessness in grapevine, BMC Plant Biology, vol.11, issue.1, 2011.
DOI : 10.1093/nar/gkm306

R. Mellway and S. Lund, Interaction analysis of grapevine MIKCc-type MADS transcription factors and heterologous expression of putative v??raison regulators in tomato, Journal of Plant Physiology, vol.170, issue.16, pp.1424-1433, 2013.
DOI : 10.1016/j.jplph.2013.05.010

E. Miedes and E. Lorences, Xyloglucan endotransglucosylase/hydrolases (XTHs) during tomato fruit growth and ripening, Journal of Plant Physiology, vol.166, issue.5, pp.489-498, 2009.
DOI : 10.1016/j.jplph.2008.07.003

Y. Mizukami and H. Ma, Ectopic expression of the floral homeotic gene AGAMOUS in transgenic Arabidopsis plants alters floral organ identity, Cell, vol.71, issue.1, pp.119-131, 1992.
DOI : 10.1016/0092-8674(92)90271-D

Y. Mizukami and H. Ma, Determination of Arabidopsis floral meristem identity by AGAMOUS. The Plant Cell 9, pp.393-408, 1997.
DOI : 10.2307/3870490

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC156926/pdf

C. Mizzotti, I. Ezquer, and D. Paolo, SEEDSTICK is a Master Regulator of Development and Metabolism in the Arabidopsis Seed Coat, PLoS Genetics, vol.51, issue.12, 2014.
DOI : 10.1371/journal.pgen.1004856.s007

C. Mizzotti, M. Mendes, E. Caporali, A. Schnittger, M. Kater et al., The MADS box genes SEEDSTICK and ARABIDOPSIS Bsister play a maternal role in fertilization and seed development, The Plant Journal, vol.139, issue.3, pp.409-420, 2012.
DOI : 10.1104/pp.105.067314

URL : https://hal.archives-ouvertes.fr/hal-00700459

M. Ng and M. Yanofsky, Function and evolution of the plant MADS-box gene family, Nature Reviews Genetics, vol.2, issue.3, pp.186-195, 2001.
DOI : 10.1105/tpc.2.8.755

N. Ocarez and N. Mejía, Suppression of the D-class MADS-box AGL11 gene triggers seedlessness in fleshy fruits, Plant Cell Reports, vol.24, issue.Suppl, pp.239-254, 2016.
DOI : 10.1038/74238

I. Pan, R. Mcquinn, J. Giovannoni, and V. Irish, Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development, Journal of Experimental Botany, vol.61, issue.6, pp.1795-1806, 2010.
DOI : 10.1093/jxb/erq046

R. Pattison, F. Csukasi, Y. Zheng, Z. Fei, E. Van-der-knaap et al., Comprehensive Tissue-Specific Transcriptome Analysis Reveals Distinct Regulatory Programs during Early Tomato Fruit Development, Plant Physiology, vol.168, issue.4, pp.1684-1701, 2015.
DOI : 10.1104/pp.15.00287

URL : http://www.plantphysiol.org/content/plantphysiol/168/4/1684.full.pdf

A. Pinyopich, G. Ditta, B. Savidge, S. Liljegren, E. Baumann et al., Assessing the redundancy of MADS-box genes during carpel and ovule development, Nature, vol.424, issue.6944, pp.85-88, 2003.
DOI : 10.1038/nature01741

L. Pnueli, D. Hareven, S. Rounsley, M. Yanofsky, and E. Lifschitz, Isolation of the Tomato AGAMOUS Gene TAG1 and Analysis of Its Homeotic Role in Transgenic Plants, THE PLANT CELL ONLINE, vol.6, issue.2, pp.163-173, 1994.
DOI : 10.1105/tpc.6.2.163

G. Qin, Y. Wang, B. Cao, W. Wang, and S. Tian, Unraveling the regulatory network of the MADS box transcription factor RIN in fruit ripening, The Plant Journal, vol.9, issue.Suppl., pp.243-255, 2012.
DOI : 10.1046/j.1365-313X.1996.9050671.x

J. Riechmann and E. Meyerowitz, Determination of floral organ identity by Arabidopsis MADS domain homeotic proteins AP1, AP3, PI, and AG is independent of their DNA-binding specificity., Molecular Biology of the Cell, vol.8, issue.7, pp.1243-1259, 1997.
DOI : 10.1091/mbc.8.7.1243

G. Seymour, L. Østergaard, N. Chapman, S. Knapp, and C. Martin, Fruit Development and Ripening, Annual Review of Plant Biology, vol.64, issue.1, pp.219-241, 2013.
DOI : 10.1146/annurev-arplant-050312-120057

Y. Shima, M. Fujisawa, and M. Kitagawa, homologs regulate fruit ripening via ethylene biosynthesis, Bioscience, Biotechnology, and Biochemistry, vol.125, issue.2, pp.231-237, 2014.
DOI : 10.1104/pp.110.158279

URL : http://www.tandfonline.com/doi/pdf/10.1080/09168451.2014.878221?needAccess=true

R. Singh, E. Low, and L. Ooi, The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK, Nature, vol.39, issue.7462, pp.340-344, 2013.
DOI : 10.1186/1471-2229-9-114

C. Smaczniak, R. Immink, G. Angenent, and K. Kaufmann, Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies, Development, vol.139, issue.17, pp.3081-3098, 2012.
DOI : 10.1242/dev.074674

D. Smith, J. Abbott, and K. Gross, Down-Regulation of Tomato beta -Galactosidase 4 Results in Decreased Fruit Softening, PLANT PHYSIOLOGY, vol.129, issue.4, pp.1755-1762, 2002.
DOI : 10.1104/pp.011025

U. Sonnewald, M. Brauer, A. Von-schaewen, M. Stitt, and L. Willmitzer, Transgenic tobacco plants expressing yeast-derived invertase in either the cytosol, vacuole or apoplast: a powerful tool for studying sucrose metabolism and sink/source interactions, The Plant Journal, vol.26, issue.1, pp.95-106, 1991.
DOI : 10.1105/tpc.1.1.95

A. Tadiello, A. Pavanello, D. Zanin, E. Caporali, L. Colombo et al., A PLENA-like gene of peach is involved in carpel formation and subsequent transformation into a fleshy fruit, Journal of Experimental Botany, vol.60, issue.2, pp.651-661, 2009.
DOI : 10.1093/jxb/ern313

A. Terao, H. Hyodo, S. Satoh, and H. Iwai, Changes in the distribution of cell wall polysaccharides in early fruit pericarp and ovule, from fruit set to early fruit development, in tomato (Solanum lycopersicum), Journal of Plant Research, vol.139, issue.5, pp.719-728, 2013.
DOI : 10.1104/pp.105.065912

O. Thimm, O. Bläsing, and Y. Gibon, mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes, The Plant Journal, vol.132, issue.7, pp.914-939, 2004.
DOI : 10.1111/j.1365-313X.2004.02016.x

C. Trapnell, L. Pachter, and S. Salzberg, TopHat: discovering splice junctions with RNA-Seq, Bioinformatics, vol.25, issue.9, pp.1105-1111, 2009.
DOI : 10.1093/bioinformatics/btp120

URL : https://academic.oup.com/bioinformatics/article-pdf/25/9/1105/16892242/btp120.pdf

S. Uluisik, N. Chapman, and R. Smith, Genetic improvement of tomato by targeted control of fruit softening, Nature Biotechnology, vol.13, issue.9, pp.950-952, 2016.
DOI : 10.1104/pp.126.1.210

A. Van-der-krol and N. Chua, Flower Development in Petunia, THE PLANT CELL ONLINE, vol.5, issue.10, pp.1195-1203, 1993.
DOI : 10.1105/tpc.5.10.1195

J. Vrebalov, I. Pan, and A. Arroyo, Fleshy Fruit Expansion and Ripening Are Regulated by the Tomato SHATTERPROOF Gene TAGL1, The Plant Cell, vol.21, issue.10, pp.3041-3062, 2009.
DOI : 10.1105/tpc.109.066936

URL : http://www.plantcell.org/content/plantcell/21/10/3041.full.pdf

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, issue.5566, pp.343-346, 2002.
DOI : 10.1126/science.1068181

H. Wang, B. Jones, and Z. Li, The Tomato Aux/IAA Transcription Factor IAA9 Is Involved in Fruit Development and Leaf Morphogenesis, THE PLANT CELL ONLINE, vol.17, issue.10, pp.2676-2692, 2005.
DOI : 10.1105/tpc.105.033415

Q. Xie, Z. Hu, Z. Zhu, T. Dong, Z. Zhao et al., Overexpression of a novel MADS-box gene SlFYFL delays senescence, fruit ripening and abscission in tomato, Scientific Reports, vol.24, issue.1, p.4367, 2014.
DOI : 10.1104/pp.24.1.1

W. Xu, E. Fiume, O. Coen, C. Pechoux, L. Lepiniec et al., Endosperm and Nucellus Develop Antagonistically in Arabidopsis Seeds, The Plant Cell, vol.28, issue.6, pp.1343-1360, 2016.
DOI : 10.1105/tpc.16.00041

URL : http://www.plantcell.org/content/plantcell/28/6/1343.full.pdf

S. Zhong, Z. Fei, and Y. Chen, Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening, Nature Biotechnology, vol.57, issue.2, pp.154-159, 2013.
DOI : 10.1186/gb-2008-9-9-r137

M. Zouine, E. Maza, A. Djari, M. Lauvernier, P. Frasse et al., TomExpress, a unified tomato RNA-Seq platform for visualization of expression data, clustering and correlation networks, The Plant Journal, vol.10, issue.4, 2017.
DOI : 10.1038/nrg2484

URL : https://hal.archives-ouvertes.fr/hal-01607612