Costa F, Alba R, Schouten H, Soglio V, Gianfranceschi L, Serra S, Musacchi S, Sansavini S, Costa G, Fei ZJ, Giovannoni J: Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening. BMC Plant Biol. 2010, 10: 229-10.1186/1471-2229-10-229.
Article
PubMed Central
PubMed
Google Scholar
Giovannoni JJ: Fruit ripening mutants yield insights into ripening control. Curr Opin Plant Biol. 2007, 10: 283-289. 10.1016/j.pbi.2007.04.008.
Article
CAS
PubMed
Google Scholar
Moore S, Vrebalov J, Payton P, Giovannoni J: Use of genomics tools to isolate key ripening genes and analyse fruit maturation in tomato. J Exp Bot. 2002, 53: 2023-2030. 10.1093/jxb/erf057.
Article
CAS
PubMed
Google Scholar
Zouine M, Latché A, Rousseau C, Regad F, Pech JC, Philippot M, Bouzayen M, Delalande C, Frasse P, Schiex T, Noirot C, Bellec A, Klopp C, Berges H, Mariette J, Vautrin S, Causse M, Rothan C: The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012, 485: 635-641. 10.1038/nature11119.
Article
Google Scholar
Grierson D: Ethylene and the control of fruit ripening. Molecular Biology and Biochemistry of Fruit Ripening. Edited by: Seymour GB, Giovannoni JJ, Tucker GA, Poole M. 2013, Wiley In Press, Boston
Google Scholar
Bleecker AB, Kende H: Ethylene: a gaseous signal molecule in plants. Annu Rev Cell Dev Biol. 2000, 16: 1-18. 10.1146/annurev.cellbio.16.1.1.
Article
CAS
PubMed
Google Scholar
Klee HJ: Control of ethylene-mediated processes in tomato at the level of receptors. J Exp Bot. 2002, 53: 2057-2063. 10.1093/jxb/erf062.
Article
CAS
PubMed
Google Scholar
Stepanova AN, Ecker JR: Ethylene signaling: from mutants to molecules. Curr Opin Plant Biol. 2000, 3: 353-360. 10.1016/S1369-5266(00)00096-0.
Article
CAS
PubMed
Google Scholar
Wilkinson JQ, Lanahan MB, Yen HC, Giovannoni JJ, Klee HJ: An ethylene-inducible component of signal transduction encoded by never-ripe. Science. 1995, 270: 1807-1809. 10.1126/science.270.5243.1807.
Article
CAS
PubMed
Google Scholar
Lincoln JE, Campbell AD, Oetiker J, Rottmann WH, Oeller PW, Shen NF, Theologis A: LE-ACS4, a fruit ripening and wound-induced 1-aminocyclopropane-1-carboxylate synthase gene of tomato (Lycopersicon esculentum). expression in Escherichia coli, structural characterization, expression characteristics, and phylogenetic analysis. J Biol Chem. 1993, 268: 19422-19430.
CAS
PubMed
Google Scholar
Olson DC, White JA, Edelman L, Harkins RN, Kende H: Differential expression of two genes for 1-aminocyclopropane-1-carboxylate synthase in tomato fruits. Proc Natl Acad Sci U S A. 1991, 88: 5340-5344. 10.1073/pnas.88.12.5340.
Article
PubMed Central
CAS
PubMed
Google Scholar
Barry CS, Llop-Tous MI, Grierson D: The regulation of 1-aminocyclopropane-1-carboxylic acid synthase gene expression during the transition from system-1 to system-2 ethylene synthesis in tomato. Plant Physiol. 2000, 123: 979-986. 10.1104/pp.123.3.979.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nambara E, Marion-Poll A: ABA action and interactions in seeds. Trends Plant Sci. 2003, 8: 213-217. 10.1016/S1360-1385(03)00060-8.
Article
CAS
PubMed
Google Scholar
Finkelstein RR: Studies of abscisic acid perception finally flower. Plant Cell. 2006, 18: 786-791. 10.1105/tpc.106.041129.
Article
PubMed Central
CAS
PubMed
Google Scholar
Shinozaki K, Yamaguchi-Shinozaki K: Gene networks involved in drought stress response and tolerance. J Exp Bot. 2007, 58: 221-227. 10.1093/jxb/erl164.
Article
CAS
PubMed
Google Scholar
Galpaz N, Wang Q, Menda N, Zamir D, Hirschberg JP: Abscisic acid deficiency in the tomato mutant high-pigment 3 leading to increased plastid number and higher fruit lycopene content. Plant J. 2008, 53: 717-730. 10.1111/j.1365-313X.2007.03362.x.
Article
CAS
PubMed
Google Scholar
Ren J, Chen P, Dai SJ, Li P, Li Q, Ji K, Wang YP, Leng P: Role of abscisic acid and ethylene in sweet cherry fruit maturation: molecular aspects. NZ J Crop Hort. 2011, 39: 1-14. 10.1080/01140671.2010.508819.
Article
Google Scholar
Zhang M, Yuan B, Leng P: The role of ABA in triggering ethylene biosynthesis and ripening of tomato fruit. J Exp Bot. 2009, 60: 1579-1588. 10.1093/jxb/erp026.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sun L, Yuan B, Zhang M, Wang L, Cui M, Wang Q, Leng P: Fruit-specific RNAi-mediated suppression of SlNCED1 increases both lycopene and β-carotene contents in tomato fruit. J Exp Bot. 2012, 63: 3097-3108. 10.1093/jxb/ers026.
Article
PubMed Central
CAS
PubMed
Google Scholar
Seymour GB, Ostergaard L, Chapman NH, Knapp S, Martin C: Fruit development and ripening. Annu Rev Plant Biol. 2013, 64: 219-241. 10.1146/annurev-arplant-050312-120057.
Article
CAS
PubMed
Google Scholar
Vrebalov J, Ruezinsky D, Padmanabhan V, White R, Medrano D, Drake R, Schuch W, Giovannoni J: A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science. 2002, 296: 343-346. 10.1126/science.1068181.
Article
CAS
PubMed
Google Scholar
Martel C, Vrebalov J, Tafelmeyer P, Giovannoni JJ: The tomato MADS-box transcription factor RIPENING INHIBITOR interacts with promoters involved in numerous ripening processes in a COLORLESS NONRIPENING-dependent manner. Plant Physiol. 2011, 157: 1568-1579. 10.1104/pp.111.181107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fujisawa M, Nakano T, Shima Y, Ito Y: A large-scale identification of direct targets of the tomato MADS box transcription factor RIPENING INHIBITOR reveals the regulation of fruit ripening. Plant Cell. 2013, 25: 371-386. 10.1105/tpc.112.108118.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fujisawa M, Nakano T, Ito Y: Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation. BMC Plant Biol. 2011, 11: 26-10.1186/1471-2229-11-26.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fujisawa M, Shima Y, Higuchi N, Nakano T, Koyama Y, Kasumi T, Ito Y: Direct targets of the tomato-ripening regulator RIN identified by transcriptome and chromatin immunoprecipitation analyses. Planta. 2012, 235: 1107-1122. 10.1007/s00425-011-1561-2.
Article
CAS
PubMed
Google Scholar
Qin G, Wang Y, Cao B, Wang W, Tian S: Unraveling the regulatory network of the MADS box transcription factor RIN in fruit ripening. Plant J. 2012, 70: 243-255. 10.1111/j.1365-313X.2011.04861.x.
Article
CAS
PubMed
Google Scholar
Bemer M, Karlova R, Ballester AR, Tikunov YM, Bovy AG, Wolters-Arts M, Rossetto PB, Angenent GC, Maagd RA: The tomato FRUITFULL homologs TDR4/FUL1 and MBP7/FUL2 regulate ethylene-independent aspects of fruit ripening. Plant Cell. 2012, 24: 4437-4451. 10.1105/tpc.112.103283.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chung MY, Vrebalov J, Alba R, Lee J, McQuinn R, Chung JD, Klein P, Giovannoni J: A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening. Plant J. 2010, 64: 936-947. 10.1111/j.1365-313X.2010.04384.x.
Article
CAS
PubMed
Google Scholar
Dong TT, Hu ZL, Deng L, Wang Y, Zhu MK, Zhang JL, Chen GP: A tomato MADS-box transcription factor, SlMADS1, acts as a negative regulator of fruit ripening. Plant Physiol. 2013, 163: 1026-1036. 10.1104/pp.113.224436.
Article
PubMed Central
CAS
PubMed
Google Scholar
Itkin M, Seybold H, Breitel D, Rogachev I, Meir S, Aharoni A: TOMATO AGAMOUS-LIKE 1 is a component of the fruit ripening regulatory network. Plant J. 2009, 60: 1081-1095. 10.1111/j.1365-313X.2009.04064.x.
Article
CAS
PubMed
Google Scholar
Karlova R, Rosin FM, Busscher-Lange J, Parapunova V, Do PT, Fernie AR, Fraser PD, Baxter C, Angenent GC, Maagd RA: Transcriptome and metabolite profiling show that APETALA2a is a major regulator of tomato fruit ripening. Plant Cell. 2011, 23: 923-941. 10.1105/tpc.110.081273.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lee JM, Joung JG, McQuinn R, Chung MY, Fei Z, Tieman D, Klee H, Giovannoni J: Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation. Plant J. 2012, 70: 191-204. 10.1111/j.1365-313X.2011.04863.x.
Article
CAS
PubMed
Google Scholar
Lin Z, Hong Y, Yin M, Li C, Zhang K, Grierson D: A tomato HD-Zip homeobox protein, LeHB-1, plays an important role in floral organogenesis and ripening. Plant J. 2008, 55: 301-310. 10.1111/j.1365-313X.2008.03505.x.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pan Y, Bradley G, Pyke K, Ball G, Lu CG, Fray R, Marshall A, Jayasuta S, Baxter C, Wijk R, Boyden L, Cade R, Chapman NH, Fraser PD, Hodgman C, Seymour GB: Network inference analysis identifies an APRR2-Like gene linked to pigment accumulation in tomato and pepper fruits. Plant Physiol. 2013, 161: 1476-1485. 10.1104/pp.112.212654.
Article
PubMed Central
CAS
PubMed
Google Scholar
Shima Y, Kitagawa M, Fujisawa M, Nakano T, Kato H, Kimbara J, Kasumi T, Ito Y: Tomato FRUITFULL homologues act in fruit ripening via forming MADS-box transcription factor complexes with RIN . Plant Mol Biol. 2013, 82: 427-438. 10.1007/s11103-013-0071-y.
Article
CAS
PubMed
Google Scholar
Vrebalov J, Pan IL, Arroyo AJ, McQuinn R, Chung M, Poole M, Rose J, Seymour G, Grandillo S, Giovannoni J, Irish VF: Fleshy fruit expansion and ripening are regulated by the Tomato SHATTERPROOF gene TAGL1 . Plant Cell. 2009, 21: 3041-3062. 10.1105/tpc.109.066936.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhu M, Chen G, Zhou S, Tu Y, Wang Y, Dong T, Hu Z: A new tomato NAC (NAM/ATAF1/2/CUC2) transcription factor, SlNAC4, functions as a positive regulator of fruit ripening and carotenoid accumulation. Plant Cell Physiol. 2014, 55 (1): 119-135. 10.1093/pcp/pct162.
Article
CAS
PubMed
Google Scholar
Selth LA, Dogra SC, Rasheed MS, Healy H, Randles JW, Rezaian MA: A NAC domain protein interacts with tomato leaf curl virus replication accessory protein and enhances viral replication. Plant Cell. 2005, 17: 311-325. 10.1105/tpc.104.027235.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ma NN, Zuo YQ, Liang XQ, Yin B, Wang GD, Meng QW: The multiple stress-responsive transcription factor SlNAC1 improves the chilling tolerance of tomato. Physiol Plant. 2013, 149: 474-486. 10.1111/ppl.12049.
Article
CAS
Google Scholar
Ouyang B, Yang T, Li H, Zhang L, Zhang Y, Zhang J, Fei Z, Ye Z: Identification of early salt stress response genes in tomato root by suppression subtractive hybridization and microarray analysis. J Exp Bot. 2007, 58: 507-520. 10.1093/jxb/erl258.
Article
CAS
PubMed
Google Scholar
Huang W, Miao M, Kud J, Niu X, Ouyang B, Zhang J, Ye Z, Kuhl JC, Liu Y, Xiao F: SlNAC1, a stress-related transcription factor, is fine-tuned on both the transcriptional and the post-translational level. New Phytol. 2013, 197: 1214-1224. 10.1111/nph.12096.
Article
CAS
PubMed
Google Scholar
Jin JP, Zhang H, Kong L, Gao G, Luo JC: PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res. 2014, 42: D1182-D1187. 10.1093/nar/gkt1016.
Article
PubMed Central
CAS
PubMed
Google Scholar
Alba R, Payton P, Fei Z, McQuinn R, Debbie P, Martin GB, Tanksley SD, Giovannoni J: Transcriptome and selected metabolite analyses reveal multiple points of ethylene control during tomato fruit development. Plant Cell. 2005, 17: 2954-2965. 10.1105/tpc.105.036053.
Article
PubMed Central
CAS
PubMed
Google Scholar
Burns J, Fraser PD, Bramley PM: Identification and quantification of carotenoids, tocopherols and chlorophylls in commonly consumed fruits and vegetables. Phytochemistry. 2003, 62: 939-947. 10.1016/S0031-9422(02)00710-0.
Article
CAS
PubMed
Google Scholar
Fraser PD, Bramley PM: The purification of phytoene dehydrogenase from Phycomyces blakesleeanus. Biochim Biophys Acta. 1994, 1212: 59-66. 10.1016/0005-2760(94)90189-9.
Article
CAS
PubMed
Google Scholar
Fraser PD, Romer S, Shipton CA, Mills PB, Kiano JW, Misawa N, Drake RG, Schuch W, Bramley PM: Evaluation of transgenic tomato plants expressing an additional phytoene synthase in a fruit-specific manner. Proc Natl Acad Sci U S A. 2002, 99: 1092-1097. 10.1073/pnas.241374598.
Article
PubMed Central
CAS
PubMed
Google Scholar
Maunders MJ, Holdsworth MJ, Slater A, Knapp JE, Bird CR, Schuch W, Grierson D: Ethylene stimulates the accumulation of ripening-related mRNAs in tomatoes. Plant Cell Environ. 1987, 10: 177-184.
CAS
Google Scholar
Puranik S, Sahu PP, Srivastava PS, Prasad M: NAC proteins: regulation and role in stress tolerance. Trends Plant Sci. 2012, 17: 369-381. 10.1016/j.tplants.2012.02.004.
Article
CAS
PubMed
Google Scholar
Tran LS, Nakashima K, Sakuma Y, Simpson SD, Fujita Y, Maruyama K, Fujita M, Seki M, Shinozaki K, Yamaquchi-Shinozaki K: Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought responsive cis-element in the early reponsive to dehydration stress 1 promoter. Plant Cell. 2004, 16: 2481-2498. 10.1105/tpc.104.022699.
Article
PubMed Central
CAS
PubMed
Google Scholar
Olsen AN, Ernst HA, Leggio LL, Skriver K: DNA-binding specificity and molecular functions of NAC transcription factors. Plant Sci. 2005, 169: 785-797. 10.1016/j.plantsci.2005.05.035.
Article
CAS
Google Scholar
Sun L, Sun Y, Zhang M, Wang L, Ren J, Cui M, Wang Y, Ji K, Li P, Li Q, Chen P, Dai S, Duan C, Wu Y, Leng P: Suppression of 9-cis-epoxycarotenoid dioxygenase, which encodes a key enzyme in abscisic acid biosynthesis, alters fruit texture in transgenic tomato. Plant Physiol. 2012, 158: 283-298. 10.1104/pp.111.186866.
Article
PubMed Central
PubMed
Google Scholar
Fraser PD, Truesdale MR, Bird CR, Schuch W, Bramley PM: Carotenoid biosynthesis during tomato fruit development (evidence for tissue-specific gene expression). Plant Physiol. 1994, 105: 405-413.
PubMed Central
CAS
PubMed
Google Scholar
Lincoln J, Fischer R: Regulation of gene expression by ethylene in wild-type and rin tomato (Lycopersicon esculentum) fruit. Plant Physiol. 1988, 88: 370-374. 10.1104/pp.88.2.370.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ronen G, Carmel-Goren L, Zamir D, Hirschberg J: An alternative pathway to beta-carotene formation in plant chromoplasts discovered by map-based cloning of beta and old-gold colour mutations in tomato. Proc Natl Acad Sci U S A. 2000, 97: 11102-11107. 10.1073/pnas.190177497.
Article
PubMed Central
CAS
PubMed
Google Scholar
Barry CS, Giovannoni JJ: Ethylene and fruit ripening. J Plant Growth Regul. 2007, 26: 143-159. 10.1007/s00344-007-9002-y.
Article
CAS
Google Scholar
Oeller PW, Lu MW, Taylor LP, Pike DA, Theologis A: Reversible inhibition of tomato fruit senescence by antisense RNA. Science. 1991, 254: 437-439. 10.1126/science.1925603.
Article
CAS
PubMed
Google Scholar
Barry CS, Blume B, Bouzayen M, Cooper W, Hamilton AJ, Grierson D: Differential expression of the 1-aminocyclopropane-1-carboxylate oxidase gene family of tomato. Plant J. 1996, 9: 525-535. 10.1046/j.1365-313X.1996.09040525.x.
Article
CAS
PubMed
Google Scholar
Ito Y, Kitagawa M, Ihashi N, Yabe K, Kimbara J, Yasuda J, Ito H, Inakuma T, Hiroi S, Kasumi T: DNA-binding specificity, transcriptional activation potential, and the rin mutation effect for the tomato fruit-ripening regulator RIN . Plant J. 2008, 55: 212-223. 10.1111/j.1365-313X.2008.03491.x.
Article
CAS
PubMed
Google Scholar
Kumar R, Sharma MK, Kapoor S, Tyagi AK, Sharma AK: Transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes provides insight into LeMADS-RIN-regulated ethylene-dependent as well as ethylene-independent aspects of ripening in tomato. Mol Genet Genomics. 2012, 287: 189-203. 10.1007/s00438-011-0671-7.
Article
CAS
PubMed
Google Scholar
Manning K, Tör M, Poole M, Hong Y, Thompson AJ, King GJ, Giovannoni JJ, Seymour GB: A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet. 2006, 38: 948-952. 10.1038/ng1841.
Article
CAS
PubMed
Google Scholar
Ergun M, Jeong J, Huber DJ, Cantliffe DJ: Suppression of ripening and softening of ‘Galia’ melons by 1-methylcyclopropene applied at preripe or ripe stages of development. Hort Sci. 2005, 40: 170-175.
CAS
Google Scholar
Hiwasa K, Kinugasa Y, Amano S, Hashimoto A, Nakno R, Inaba A, Kubo Y: Ethylene is required for both the initiation and progression of softening in pear (Pyrus communis L.) fruit. J Exp Bot. 2003, 54: 771-779. 10.1093/jxb/erg073.
Article
CAS
PubMed
Google Scholar
Nishiyama K, Guis M, Rose JK, Kubo Y, Bennett KA, Wangjin L, Kato K, Ushijima K, Nakano R, Inaba A, Bouzayen M, Latche A, Pech JC, Bennett AB: Ethylene regulation of fruit softening and cell wall disassembly in Charentais melon . J Exp Bot. 2007, 58: 1281-1290. 10.1093/jxb/erl283.
Article
CAS
PubMed
Google Scholar
Saladié M, Matas AJ, Isaacson T, Jenks MA, Goodwin SM, Niklas KJ, Xiaolin R, Labavitch JM, Shackel KA, Fernie AR, Lytovchenko A, O’Neill MA, Watkins CB, Rose JK: A reevaluation of the key factors that influence tomato fruit softening and integrity. Plant Physiol. 2007, 144 (2): 1012-1028. 10.1104/pp.107.097477.
Article
PubMed Central
PubMed
Google Scholar
Yan LH, Zhai QZ, Wei JN, Li SY, Wang B, Huang TT, Du MM, Sun JQ, Kang L, Li CB, Li CY: Role of tomato lipoxygenase D in wound-induced jasmonate biosynthesis and plant immunity to insect herbivores. PLoS Genet. 2013, 9 (12): e1003964-10.1371/journal.pgen.1003964. doi: 10.1371/journal.pgen.1003964
Article
PubMed Central
PubMed
Google Scholar
Fraser PD, Pinto ME, Holloway DE, Bramley PM: Technical advance: application of high-performance liquid chromatography with photodiode array detection to the metabolic profiling of plant isoprenoids. Plant J. 2000, 24: 551-558. 10.1046/j.1365-313x.2000.00896.x.
Article
CAS
PubMed
Google Scholar
Bino RJ, de Vos CH R, Lieberman M, Hall RD, Bovy A, Jonker HH, Tikunov Y, Lommen A, Moco S, Levin I: The light-hyperresponsive high pigment -2dg mutation of tomato: alterations in the fruit metabolome. New Phytol. 2005, 166: 427-438. 10.1111/j.1469-8137.2005.01362.x.
Article
CAS
PubMed
Google Scholar
Livak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods. 2001, 25: 402-408. 10.1006/meth.2001.1262.
Article
CAS
PubMed
Google Scholar
Wu T, Abbott JA: Firmness and force relaxation characteristics of tomatoes stored intact or as slices. Postharvest Biol Tec. 2002, 24: 59-68. 10.1016/S0925-5214(01)00133-8.
Article
Google Scholar
Fu J, Chu J, Sun X, Wang J, Yan C: Simple, rapid, and simultaneous assay of multiple carboxyl containing phytohormones in wounded tomatoes by UPLC-MS/MS using single SPE purification and isotope dilution. Anal Sci. 2012, 28: 1081-1087. 10.2116/analsci.28.1081.
Article
CAS
PubMed
Google Scholar