Skip to main content
SpringerLink
Log in

Tomato Resources for Functional Genomics

  • Chapter
  • First Online:
The Tomato Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

Tomato is currently the model species for fleshy fruit development and for Solanaceae species. The recent completion of a high-quality genome sequence of the inbred tomato (Solanum lycopersicum) cultivar ‘Heinz 1706’ allowed the prediction and in silico annotation of ca 35,000 genes. Assigning a biological function to these genes is among the priorities of the tomato community, especially for genes contributing to fleshy fruit development and quality, and to other major agronomical traits in tomato and Solanaceae. More than a decade of research using genomic tools, mostly transcriptome and metabolome, combined with genetic mapping approaches, provided first cues on the possible function of tomato genes by describing where, when, and with which other gene/metabolite these genes are expressed. Current advances in sequencing technologies now allow the exhaustive inventory of tomato transcripts in various plant organs, tissues and even cell types. To cope with the need to assign biological functions to a large number of genes, tomato mutant resources based on several technologies [T-DNA and transposon insertional mutants, fast-neutron, γ-ray and ethyl methanesulfonate (EMS) mutants] have been developed in the recent years. Among them, the Targeting Induced Local Lesions In Genomes (TILLING) technology, based on the generation by EMS of high density point mutations evenly distributed in the genome and on the subsequent detection of mutations in target genes is presently the most established. The present chapter will describe the main resources, strategies and tools currently available for linking genes to phenotype in tomato.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30:174–178

    Article  CAS  PubMed  Google Scholar 

  • Alonso JM, Ecker JR (2006) Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat Rev Genet 7:524–536

    Article  CAS  PubMed  Google Scholar 

  • Baldet P, Bres C, Mauxion J-P, Just D, Bournonville C, Ferrand C, Mori K, Okabe Y, Ezura H, Rothan C (2013) TILLING identification of ascorbate biosynthesis tomato mutants for investigating vitamin C in tomato. Plant Biotechnol 30:309–314

    Article  CAS  Google Scholar 

  • Busch BL, Schmitz G, Rossmann S, Piron F, Ding J, Bendahmane A, Theres K (2011) Shoot branching and leaf dissection in tomato are regulated by homologous gene modules. Plant Cell 23:3595–3609

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Causse M, Desplat N, Pascual L, Le Paslier MC, Sauvage C, Bauchet G, Bérard A, Bounon R, Tchoumakov M, Brunel D, Bouchet JP (2013) Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genom 14:791

    Article  Google Scholar 

  • Causse M, Duffe P, Gomez MC, Buret M, Damidaux R, Zamir D, Gur A, Chevalier C, Lemaire-Chamley M, Rothan C (2004) A Genetic map of candidate genes and QTLs involved in tomato fruit size and composition. J Exp Bot 55:1671–1685

    Article  CAS  PubMed  Google Scholar 

  • Chakrabarti M, Zhang N, Sauvage C, Muños S, Blanca J, Cañizares J, Diez MJ, Schneider R, Mazourek M, McClead J, Causse M, van der Knaap E (2013) A cytochrome P450 regulates a domestication trait in cultivated tomato. Proc Natl Acad Sci USA 110:17125–17130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Colbert T, Till BJ, Tompa R, Reynolds S, Steine MN, Yeung AT, McCallum CM, Comai L, Henikoff S (2001) High-throughput screening for induced point mutations. Plant Physiol 126:480–484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dan Y, Fei Z, Rothan C (2007) Micro-Tom—a new model plant for genomics. Genes Genomes Genomics 1:167–179

    Google Scholar 

  • David-Schwartz R, Badani H, Smadar W, Levy AA, Galili G, Kapulnik Y (2001) Identification of a novel genetically controlled step in mycorrhizal colonization: plant resistance to infection by fungal spores but not extra-radical hyphae. Plant J 27:561–569

    Article  CAS  PubMed  Google Scholar 

  • Diévart A, Clark SE (2003) Using mutant alleles to determine the structure and function of leucine-rich repeat receptor-like kinases. Curr Opin Plant Biol 6:507–516

    Article  PubMed  Google Scholar 

  • Di Matteo A, Ruggieri V, Sacco A, Rigano MM, Carriero F, Bolger A, Fernie AR, Frusciante L, Barone A (2013) Identification of candidate genes for phenolics accumulation in tomato fruit. Plant Sci 205–206:87–96

    Article  PubMed  Google Scholar 

  • Dor E, Yoneyama K, Wininger S, Kapulnik Y, Yoneyama K, Koltai H, Xie X, Hershenhorn J (2011) Strigolactone deficiency confers resistance in tomato line SL-ORT1 to the parasitic weeds Phelipanche and Orobanche spp. Phytopathology 101:213–222

    Article  CAS  PubMed  Google Scholar 

  • Emmanuel E, Levy AA (2002) Tomato mutants as tools for functional genomics. Curr Opin Plant Biol 5:112–117

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fernandez AI, Viron N, Alhagdow M, Karimi M, Jones M, Amsellem Z, Sicard A, Czerednik A, Angenent G, Grierson D, May S, Seymour G, Eshed Y, Lemaire-Chamley M, Rothan C, Hilson P (2009) Flexible tools for gene expression and silencing in tomato. Plant Physiol 151:1729–1740

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fernie AR, Klee HJ (2011) The use of natural genetic diversity in the understanding of metabolic organization and regulation. Front Plant Sci 2:59

    CAS  PubMed  PubMed Central  Google Scholar 

  • Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88

    Article  CAS  PubMed  Google Scholar 

  • Fridman E, Pleban T, Zamir D (2000) A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene. Proc Natl Acad Sci USA 97:4718–4723

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gady AL, Hermans FW, Van de Wal MH, van Loo EN, Visser RG, Bachem CW (2009) Implementation of two high through-put techniques in a novel application: detecting point mutations in large EMS mutated plant populations. Plant Methods 5:13

    Article  PubMed  PubMed Central  Google Scholar 

  • Gady AL, Vriezen WH, Van de Wal MH, Huang P, Bovy AG, Visser RG, Bachem CW (2012) Induced point mutations in the phytoene synthase 1 gene cause differences in carotenoid content during tomato fruit ripening. Mol Breed 29:801–812

    Article  CAS  PubMed  Google Scholar 

  • Gidoni D, Fuss E, Burbidge A, Speckmann GJ, James S, Nijkamp D, Mett A, Feiler J, Smoker M, de Vroomen MJ et al (2003) Multi-functional T-DNA/Ds tomato lines designed for gene cloning and molecular and physical dissection of the tomato genome. Plant Mol Biol 51:83–98

    Article  CAS  PubMed  Google Scholar 

  • Greene EA, Codomo CA, Taylor NE, Henikoff JG, Till BJ, Reynolds SH, Enns LC, Burtner C, Johnson JE, Odden AR, Comai L, Henikoff S (2003) Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics 164:731–740

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hartwig B, James GV, Konrad K, Schneeberger K, Turck F (2012) Fast isogenic mapping-by-sequencing of ethyl methanesulfonate-induced mutant bulks. Plant Physiol 160:591–600

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Henikoff S, Comai L (2003) Single-nucleotide mutations for plant functional genomics. Annu Rev Plant Biol 54:375–401

    Article  CAS  PubMed  Google Scholar 

  • Hirakawa H, Shirasawa K, Ohyama A, Fukuoka H, Aoki K, Rothan C, Sato S, Isobe S, Tabata S (2013) Genome-wide SNP genotyping to infer the effects on gene functions in tomato. DNA Res 20:221–233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ichihashi Y, Sinha NR (2014) From genome to phenome and back in tomato. Curr Opin Plant Biol 18C:9–15

    Article  Google Scholar 

  • Isaacson T, Kosma DK, Matas AJ, Buda GJ, He Y, Yu B, Pravitasari A, Batteas JD, Stark RE, Jenks MA, Rose JKC (2009) Cutin deficiency in the tomato fruit cuticle consistently affects resistance to microbial infection and biomechanical properties, but not transpirational water loss. Plant J 60:363–377

    Article  CAS  PubMed  Google Scholar 

  • Jones MO, Piron-Prunier F, Marcel F, Piednoir-Barbeau E, Alsadon AA, Wahb-Allah MA, Al-Doss AA, Bowler C, Bramley PM, Fraser PD, Bendahmane A (2012) Characterisation of alleles of tomato light signalling genes generated by TILLING. Phytochemistry 79:78–86

    Article  CAS  PubMed  Google Scholar 

  • Julio E, Laporte F, Reis S, Rothan C, Dorlhac de Borne F (2008) Targeted mutation breeding as a tool for tobacco crop improvement. Mol Breed 21:369–381

    Article  CAS  Google Scholar 

  • Just D, Garcia V, Fernandez L, Bres C, Mauxion J, Petit J, Jorly J, Assali J, Bournonville C, Ferrand C, Baldet P, Lemaire-Chamley M, Mori K, Okabe Y, Ariizumi T, Asamizu E, Ezura H, Rothan C (2013) Micro-Tom mutants for functional analysis of target genes and discovery of new alleles in tomato. Plant Biotechnol 30:225–231

    Article  CAS  Google Scholar 

  • Kharkwal MC, Shu QY (2009) The role of induced mutations in world food security. In: Shu QY (ed) induced plant mutations in the genomics era. Food and Agricultural Organization of the United nations, Rome, pp 33–38

    Google Scholar 

  • Kimbara J, Yoshida M, Ito H, Kitagawa M, Takada W, Hayashi K, Shibutani Y, Kusano M, Okazaki Y, Nakabayashi R, Mori T, Saito K, Ariizumi T, Ezura H (2013) Inhibition of CUTIN DEFICIENT 2 causes defects in cuticle function and structure and metabolite changes in tomato fruit. Plant Cell Physiol 54:1535–1548

    Article  CAS  PubMed  Google Scholar 

  • Klee HJ, Giovannoni JJ (2011) Genetics and control of tomato fruit ripening and quality attributes. Annu Rev Genet 45:41–59

    Article  CAS  PubMed  Google Scholar 

  • Kobayashi M, Nagasaki H, Garcia V, Just D, Bres C, Mauxion JP, Le Paslier MC, Brunel D, Suda K, Minakuchi Y, Toyoda A, Fujiyama A, Toyoshima H, Suzuki T, Igarashi K, Rothan C, Kaminuma E, Nakamura Y, Yano K, Aoki K (2014) Genome-wide analysis of intraspecific DNA polymorphism in ‘Micro-Tom’, a model cultivar of tomato (Solanum lycopersicum). Plant Cell Physiol 55:445–454

    Article  CAS  PubMed  Google Scholar 

  • Krieger U, Lippman ZB, Zamir D (2010) The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato. Nat Genet 42:459–463

    Article  CAS  PubMed  Google Scholar 

  • Leide J, Hildebrandt U, Reussing K, Riederer M, Vogg G (2007) The developmental pattern of tomato fruit wax accumulation and its impact on cuticular transpiration barrier properties: effects of a deficiency in a beta-ketoacyl-coenzyme A synthase (LeCER6). Plant Physiol 144:1667–1679

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li X, Song Y, Century K, Straight S, Ronald P, Dong X, Lassner M, Zhang Y (2001) A fast neutron deletion mutagenesis-based reverse genetics system for plants. Plant J 27:235–242

    Article  CAS  PubMed  Google Scholar 

  • Li X, Zhang Y (2002) Reverse genetics by fast neutron mutagenesis in higher plants. Funct Integr Genom 2:254–258

    Article  CAS  Google Scholar 

  • MacAlister CA, Park SJ, Jiang K, Marcel F, Bendahmane A, Izkovich Y, Eshed Y, Lippman ZB (2012) Synchronization of the flowering transition by the tomato TERMINATING FLOWER gene. Nat Genet 44:1393–1398

    Article  CAS  PubMed  Google Scholar 

  • Martín-Trillo M, Grandío EG, Serra F, Marcel F, Rodríguez-Buey ML, Schmitz G, Theres K, Bendahmane A, Dopazo H, Cubas P (2011) Role of tomato BRANCHED1-like genes in the control of shoot branching. Plant J 67:701–714

    Article  PubMed  Google Scholar 

  • Mathews H, Clendennen SK, Caldwell CG, Liu XL, Connors K, Matheis N, Schuster DK, Menasco DJ, Wagoner W, Lightner J, Wagner DR (2003) Activation tagging in tomato identifies a transcriptional regulator of anthocyanin biosynthesis, modification, and transport. Plant Cell 15:1689–1703

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matas AJ, Yeats TH, Buda GJ, Zheng Y, Chatterjee S, Tohge T, Ponnala L, Adato A, Aharoni A, Stark R, Fernie AR, Fei Z, Giovannoni JJ, Rose JK (2011) Tissue- and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation. Plant Cell 23:3893–3910

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matsukura C, Yamaguchi I, Inamura M, Ban Y, Kobayashi Y, Yin YG, Saito T, Kuwata C, Imanishi S, Nishimura S (2007) Generation of gamma irradiation-induced mutant lines of the miniature tomato (Solanum lycopersicum L.) cultivar ‘Micro-Tom’. Plant Biotechnol 24:39–44

    Article  Google Scholar 

  • Ménard G, Biais B, Prodhomme D, Ballias P, Petit J, Just D, Rothan C, Rolin D, Gibon Y (2013) High throughput biochemical phenotyping for plants. Adv Bot Res 67:407–439

    Article  Google Scholar 

  • Menda N, Semel Y, Peled D, Eshed Y, Zamir D (2004) In silico screening of a saturated mutation library of tomato. Plant J 38:861–872

    Article  CAS  PubMed  Google Scholar 

  • Meissner R, Jacobson Y, Melamed S, Levyatov S, Shalev G, Ashri A, Elkind Y, Levy AA (1997) A new model system for Tomato Genetics. Plant J 12:1465–1472

    Article  CAS  Google Scholar 

  • Meissner R, Chague V, Zhu Q, Emmanuel E, Elkind Y, Levy AA (2000) A high throughput system for transposon tagging and promoter trapping in tomato. Plant J 38:861–872

    Google Scholar 

  • Minoia S, Petrozza A, D’Onofrio O, Piron F, Mosca G, Sozio G, Cellini F, Bendahmane A, Carriero F (2010) A new mutant genetic resource for tomato crop improvement by TILLING technology. BMC Res Notes 3:69

    Article  PubMed  PubMed Central  Google Scholar 

  • Mounet F, Moing A, Garcia V, Petit J, Maucourt M, Deborde C, Bernillon S, Le Gall G, Colquhoun I, Defernez M, Giraudel J-L, Rolin D, Rothan C, Lemaire-Chamley M (2009) Gene and metabolite regulatory network analysis of early developing fruit tissues highlights new candidate genes for the control of tomato fruit composition and development. Plant Physiol 149:1505–1528

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Okabe Y, Asamizu E, Saito T, Matsukura C, Ariizumi T, Brès C, Rothan C, Mizoguchi T, Ezura H (2011) Tomato TILLING technology: development of a reverse genetics tool for the efficient isolation of mutants from Micro-Tom mutant libraries. Plant Cell Physiol 52:1994–2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Orzaez D, Medina A, Torre S, Fernández-Moreno JP, Rambla JL, Fernández-Del-Carmen A, Butelli E, Martin C, Granell A (2009) A visual reporter system for virus-induced gene silencing in tomato fruit based on anthocyanin accumulation. Plant Physiol 150:1122–1134

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ostergaard L, Yanofsky MF (2004) Establishing gene function by mutagenesis in Arabidopsis thaliana. Plant J 39:682–696

    Article  CAS  PubMed  Google Scholar 

  • Ozaki S, Ogata Y, Suda K, Kurabayashi A, Suzuki T, Yamamoto N, Iijima Y, Tsugane T, Fujii T, Konishi C, Inai S, Bunsupa S, Yamazaki M, Shibata D, Aoki K (2010) Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module. DNA Res 17:105–116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Park SJ, Jiang K, Schatz MC, Lippman ZB (2012) Rate of meristem maturation determines inflorescence architecture in tomato. Proc Natl Acad Sci USA 109:639–644

    Article  CAS  PubMed  Google Scholar 

  • Petit J, Bres C, Just D, Garcia V, Marion D, Bakan B, Joubes J, Domergue F, Rothan C (2014) Analyses of tomato fruit brightness mutants uncover strong cutin-deficient mutants among which a new allele of GDSL lipase. Plant Physiol 164:888–906

    Article  CAS  PubMed  Google Scholar 

  • Piron F, Nicolaï M, Minoïa S, Piednoir E, Moretti A, Salgues A, Zamir D, Caranta C, Bendahmane A (2010) An induced mutation in tomato eIF4E leads to immunity to two potyviruses. PLoS ONE 5:e11313

    Article  PubMed  PubMed Central  Google Scholar 

  • Ranc N, Muños S, Xu J, Le Paslier MC, Chauveau A, Bounon R, Rolland S, Bouchet JP, Brunel D, Causse M (2012) Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme. Genes Genom Genet 2:853–864

    CAS  Google Scholar 

  • Rigola D, van Oeveren J, Janssen A, Bonné A, Schneiders H, van der Poel HJ, van Orsouw NJ, Hogers RC, de Both MT, van Eijk MJ (2009) High-throughput detection of induced mutations and natural variation using KeyPoint technology. PLoS ONE 4:e4761

    Article  PubMed  PubMed Central  Google Scholar 

  • Rohrmann J, Tohge T, Alba R, Osorio S, Caldana C, McQuinn R, Arvidsson S, Van der Merwe MJ, Riaño-Pachón DM, Mueller-Roeber B, Fei Z, Nesi AN, Giovannoni JJ, Fernie AR (2011) Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. Plant J 68:999–1013

    Article  CAS  PubMed  Google Scholar 

  • Saito T, Ariizumi T, Okabe Y, Asamizu E, Hiwasa-Tanase K, Fukuda N, Mizoguchi T, Yamazaki Y, Aoki K, Ezura H (2011) TOMATOMA: a novel tomato mutant database distributing Micro-Tom mutant collections. Plant Cell Physiol 52:283–296

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sato S, Shirasawa K, Tabata S (2013) Structural analyses of the tomato genome. Plant Biotechnol 30:257–263

    Article  CAS  Google Scholar 

  • Schauer N, Semel Y, Roessner U, Gur A, Balbo I, Carrari F, Pleban T, Perez-Melis A, Brudigam C, Kopka J, Willmitzer L, Zamir D, Fernie AR (2006) Genetics of metabolite in fruits of interspecific introgressions of tomato. Nat Biotechnol 24:447–454

    Article  CAS  PubMed  Google Scholar 

  • Shi JX, Adato A, Alkan N, He Y, Lashbrooke J, Matas AJ, Meir S, Malitsky S, Isaacson T, Prusky D, Leshkowitz D, Schreiber L, Granell AR, Widemann E, Grausem B, Pinot F, Rose JK, Rogachev I, Rothan C, Aharoni A (2013) The tomato SlSHINE3 transcription factor regulates fruit cuticle formation and epidermal patterning. New Phytol 197:468–480

    Article  CAS  PubMed  Google Scholar 

  • Shirasawa K, Isobe S, Hirakawa H, Asamizu E, Fukuoka H, Just D, Rothan C, Sasamoto S, Fujishiro T, Kishida Y, Kohara M, Tsuruoka H, Wada T, Nakamura Y, Sato S, Tabata S (2010) SNP discovery and linkage map construction in cultivated tomato. DNA Res 17:381–391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sikder S, Biswas P, Hazra P, Akhtar S, Chattopadhyay A, Badigannavar AM, D’Souza SF (2013) Induction of mutation in tomato (Solanum lycopersicum L.) by gamma irradiation and EMS. Indian J Genet Plant Breeding 73:392–399

    Article  Google Scholar 

  • Sikora P, Chawade A, Larsson M, Olsson J, Olsson O (2011) Mutagenesis as a tool in plant genetics, functional genomics, and breeding. Int J Plant Genom. doi:10.1155/2011/314829

    Google Scholar 

  • Sim SC, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Van Deynze A, Hamilton JP, Buell CR, Causse M, Wijeratne S, Francis DM (2012) Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS ONE 7:e40563

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Slade AJ, Fuerstenberg SI, Loeffler D, Steine MN, Facciotti D (2005) A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nat Biotechnol 23:75–81

    Article  CAS  PubMed  Google Scholar 

  • Sreelakshmi Y, Gupta S, Bodanapu R, Chauhan VS, Hanjabam M, Thomas S, Mohan V, Sharma S, Srinivasan R, Sharma R (2010) NEATTILL: a simplified procedure for nucleic acid extraction from arrayed tissue for TILLING and other high-throughput reverse genetic applications. Plant Methods 6:3

    Article  PubMed  PubMed Central  Google Scholar 

  • Tomato Genome Consortium TG (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641

    Article  Google Scholar 

  • Triques K, Sturbois B, Gallais S, Dalmais M, Chauvin S, Clepet C, Aubourg S, Rameau C, Caboche M, Bendahmane A (2007) Characterization of Arabidopsis thaliana mismatch specific endonucleases: application to mutation discovery by TILLING in pea. Plant J 51:1116–1125

    Article  CAS  PubMed  Google Scholar 

  • Tsai H, Howell T, Nitcher R, Missirian V, Watson B, Ngo KJ, Lieberman M, Fass J, Uauy C, Tran RK, Khan AA, Filkov V, Tai TH, Dubcovsky J, Comai L (2011) Discovery of rare mutations in populations: TILLING by sequencing. Plant Physiol 156:1257–1268

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tsai H, Missirian V, Ngo KJ, Tran RK, Chan SR, Sundaresan V, Comai L (2013) Production of a high-efficiency TILLING population through polyploidization. Plant Physiol 161:1604–1614

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Urbanczyk-Wochniak E, Usadel B, Thimm O, Nunes-Nesi A, Carrari F, Davy M, Blasing O, Kowalczyk M, Weicht D, Polinceusz A, Meyer S, Stitt M, Fernie AR (2005) Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: effects of genetic and environmental alterations in energy metabolism in the leaf. Plant Mol Biol 60:773–792

    Article  Google Scholar 

  • Vankudavath RN, Bodanapu R, Sreelakshmi Y, Sharma R (2012) High-throughput phenotyping of plant populations using a personal digital assistant. Methods Mol Biol 918:97–116

    Article  CAS  PubMed  Google Scholar 

  • Vogg G, Fischer S, Leide J, Emmanuel E, Jetter R, Levy AA, Riederer M (2004) Tomato fruit cuticular waxes and their effects on transpiration barrier properties: functional characterization of a mutant deficient in a very-long-chain fatty acid beta-ketoacyl-CoA synthase. J Exp Bot 55:1401–1410

    Article  CAS  PubMed  Google Scholar 

  • Xu J, Ranc N, Muños S, Rolland S, Bouchet JP, Desplat N, Le Paslier MC, Liang Y, Brunel D, Causse M (2013) Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species. Theor Appl Genet 126:567–581

    Article  PubMed  Google Scholar 

  • Yeats TH, Martin LB, Viart HM, Isaacson T, He Y, Zhao L, Matas AJ, Buda GJ, Domozych DS, Clausen MH, Rose JK (2012) The identification of cutin synthase: formation of the plant polyester cutin. Nat Chem Biol 8:609–611

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yuan L, Dou Y, Kianian SF, Zhang C, Holding DR (2014) Deletion mutagenesis identifies a haploinsufficient role for γ-zein in opaque2 endosperm modification. Plant Physiol 164:119–130

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. INRA, UMR 1332 Biologie du Fruit et Pathologie, 71 Av Edouard Bourleaux, 33140, Villenave d’Ornon, France

    Christophe Rothan, Cécile Bres, Virginie Garcia & Daniel Just

  2. UMR 1332 Biologie du Fruit et Pathologie, Université de Bordeaux, 33140, Villenave d’Ornon, France

    Christophe Rothan, Cécile Bres, Virginie Garcia & Daniel Just

Authors
  1. Christophe Rothan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Cécile Bres
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Virginie Garcia
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Daniel Just
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Christophe Rothan .

Editor information

Editors and Affiliations

  1. GAFL, INRA, Montfavet Cedex, France

    Mathilde Causse

  2. Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA

    Jim Giovannoni

  3. INRA-INP Toulouse, Castanet Tolosan, France

    Mondher Bouzayen

  4. INRA-INP Toulouse, Castanet Tolosan, France

    Mohamed Zouine

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Rothan, C., Bres, C., Garcia, V., Just, D. (2016). Tomato Resources for Functional Genomics. In: Causse, M., Giovannoni, J., Bouzayen, M., Zouine, M. (eds) The Tomato Genome. Compendium of Plant Genomes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-53389-5_5

Download citation

Publish with us

Policies and ethics

Search

Navigation