Skip to main content

Phenotyping of Tomatoes

  • Chapter
  • First Online:
Phenotyping for Plant Breeding

Abstract

Tomato is the most important vegetable crop after potato consumed worldwide. It is serving as model plant for fruit development and ripening biology. It is also serving as reference plant for genomics of other solanaceaous crops. Recently, tomato genome has been completely sequenced. As large amount of genetic and genomics resources are available in tomato. In-depth phenotyping of existing and generated variation in tomato may serve a valuable tool to correlate this huge data with agronomically important traits. For detailed phenotyping, IPGRI has developed tomato plant characteristics descriptors. By selecting few important descriptors, compact phenotypic catalog has been developed in tomato. Many mutant populations have been characterized using this catalog to store massive phenotyping data. Many wild species are naturally crossable with cultivated tomato; which are sources of many fruit quality traits along with biotic and abiotic stress tolerance alleles. Many researchers already used these species to introgressed agronomically important alleles into cultivated tomato. In future appropriate phenotyping of these lines along with mutant populations using new platforms like Tomato Analyzer software and new imaging technologies can help to intensify the phenotyping of tomato and thus availability of high throughput phenotyping platforms in future will hasten the speed of tomato breeding program and also help to correlate complex phenotypic data with genome.

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

Access this chapter

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

  • Alba R, Payton P, Fei Z, McQuinn R, Debbie P, Martin GB, Tanksley SD, Giovannoni JJ (2005) Transcriptome and selected metabolite analyses reveal multiple points of ethylene control during tomato fruit development. Plant Cell 17:2954–2965

    Article  PubMed  CAS  Google Scholar 

  • Alpert KB, Tanksley SD (1996) High-resolution mapping and isolation of a yeast artificial chromosome contig containing fw2.2: a major fruit weight quantitative trait locus in tomato. Proc Natl Acad Sci USA 93:15503–15507

    Article  PubMed  CAS  Google Scholar 

  • Ammiraju JS, Veremis JC, Huang X, Roberts PA, Kaloshian I (2003) The heat-stable root-knot nematode resistance gene Mi-9 from Lycopersicon peruvianum is localized on the short arm of chromosome 6. Theor Appl Genet 106:478–484

    PubMed  CAS  Google Scholar 

  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218

    Article  CAS  Google Scholar 

  • Bai Y, Lindhout P (2007) Domestication and breeding of tomatoes: what have we gained and what can we gain in the future? Ann Bot Lond 100:1085–1094

    Article  Google Scholar 

  • Bai Y, van der Hulst R, Huang CC, Wei L, Stam P, Lindhout P (2004) Mapping OI-4, a gene conferring resistance to Oidium neolycopersici and originating from Lycopersicon peruvianum LA2172, requires multi-allelic, single-locus markers. Theor Appl Genet 109:1215–1223

    Article  PubMed  CAS  Google Scholar 

  • Ballvora A, Pierre M, van den Ackerveken G, Schornack S, Rossier O, Ganal M, Lahaye T, Bonas U (2001) Genetic mapping and functional analysis of the tomato Bs4 locus governing recognition of the Xanthomonas campestris pv. vesicatoria AvrBs4 protein. Mol Plant Microbe Interact 14:629–638

    Article  PubMed  CAS  Google Scholar 

  • Basu A, Imrhan V (2007) Tomatoes versus lycopene in oxidative stress and carcinogenesis: conclusions from clinical trials. Eur J Clin Nutr 61:295–303

    Article  PubMed  CAS  Google Scholar 

  • Behringer FJ, Lomax TL (1999) High-resolution mapping and genetic characterization of the Lazy-2 gravitropic mutant of tomato. J Hered 90:489–493

    Article  PubMed  CAS  Google Scholar 

  • Beraldi D, Picarella ME, Soressi GP, Mazzucato A (2004) Fine mapping of the parthenocarpic fruit (pat) mutation in tomato. Theor Appl Genet 108:209–216

    Article  PubMed  CAS  Google Scholar 

  • Bernacchi D, Tanksley SD (1997) An interspecific backcross of Lycopersicon esculentum x L. hirsutum: linkage analysis and a QTL study of sexual compatibility factors and floral traits. Genetics 147:861–877

    PubMed  CAS  Google Scholar 

  • Bernatzky R (1993) Genetic mapping and protein product diversity of the self-incompatibility locus in wild tomato (Lycopersicon peruvianum). Biochem Genet 31:173–184

    Article  PubMed  CAS  Google Scholar 

  • Bonnema G, Hontelez J, Verkerk R, Zhang YQ, Daelen R, Kammen A, Zabel P (1996) An improved method of partially digesting plant megabase DNA suitable for YAC cloning: application to the construction of a 5.5 genome equivalent YAC library of tomato. Plant J 9:125–133

    Article  PubMed  CAS  Google Scholar 

  • Borevitz JO, Chory J (2004) Genomics tools for QTL analysis and gene discovery. Curr Opin Plant Biol 7:132–136

    Article  PubMed  CAS  Google Scholar 

  • Brewer MT, Lang L, Fujimura K, Dujmovic N, Gray S, van der Knaap E (2006) Development of a controlled vocabulary and software application to analyze fruit shape variation in tomato and other plant species. Plant Physiol 141:15–25

    Article  PubMed  CAS  Google Scholar 

  • Brommonschenkel SH, Tanksley SD (1997) Map-based cloning of the tomato genomic region that spans the Sw-5 tospovirus resistance gene in tomato. Mol Gen Genet 256:121–126

    Article  PubMed  CAS  Google Scholar 

  • Budiman MA, Mao L, Wood TC, Wing RA (2000) A deep-coverage tomato BAC library and prospects toward development of an STC framework for genome sequencing. Genome Res 10:129–136

    PubMed  CAS  Google Scholar 

  • Budiman MA, Chang SB, Lee S, Yang TJ, Zhang HB, Jong H, Wing RA (2004) Localization of jointless-2 gene in the centromeric region of tomato chromosome 12 based on high resolution genetic and physical mapping. Theor Appl Genet 108:190–196

    Article  PubMed  CAS  Google Scholar 

  • Canady MA, Meglic V, Chetelat RT (2005) A library of Solanum lycopersicoides introgression lines in cultivated tomato. Genome 48:685–697

    Article  PubMed  CAS  Google Scholar 

  • Carvalho RF, Campos ML, Pino LE, Crestana SL, Zsogon A, Lima JE, Benedito VA, Peres LE (2011) Convergence of developmental mutants into a single tomato model system: ‘Micro-Tom’ as an effective toolkit for plant development research. Plant Methods 7:18

    Article  PubMed  CAS  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  PubMed  CAS  Google Scholar 

  • Chetelat RT, DeVerna JW, Bennett AB (1995) Introgression into tomato (Lycopersicon esculentum) of the L. chmielewskii sucrose accumulator gene (sucr) controlling fruit sugar composition. Theor Appl Genet 91:327–333

    CAS  Google Scholar 

  • Chetelat RT, Meglic V, Cisneros P (2000) A genetic map of tomato based on BC(1) Lycopersicon esculentum x Solanum lycopersicoides reveals overall synteny but suppressed recombination between these homeologous genomes. Genetics 154:857–867

    PubMed  CAS  Google Scholar 

  • Churchill GA, Giovannoni JJ, Tanksley SD (1993) Pooled-sampling makes high-resolution mapping practical with DNA markers. Proc Natl Acad Sci USA 90:16–20

    Article  PubMed  CAS  Google Scholar 

  • Cuartero J, Bolarin MC, Asins MJ, Moreno V (2006) Increasing salt tolerance in the tomato. J Exp Bot 57:1045–1058

    Article  PubMed  CAS  Google Scholar 

  • Darrigues A, Hall J, van der Knaap E, Francis DM (2008) Tomato Analyzer-Color Test: a new tool for efficient digital phenotyping. J Am Soc Hort Sci 133:579–586

    Google Scholar 

  • Dixon RA (2005) A two-for-one in tomato nutritional enhancement. Nat Biotechnol 23:825–826

    Article  PubMed  CAS  Google Scholar 

  • Dixon MS, Jones DA, Keddie JS, Thomas CM, Harrison K, Jones JD (1996) The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat proteins. Cell 84:451–459

    Article  PubMed  CAS  Google Scholar 

  • Dorais M, Papadopoulos AP, Gosselin A (2001) Greenhouse tomato fruit quality. Horticult Rev 26:239–319

    CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Eshed Y, Zamir D (1994) A genomic library of Lycopersicon pennellii in L. esculentum: a tool for fine mapping of genes. Euphytica 79:175–179

    Article  CAS  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

    PubMed  CAS  Google Scholar 

  • Farrar RR, Barbour JD, Kennedy GG (1994) Field-evaluation of insect resistance in a wild tomato and its effects on insect parasitoids. Entomol Exp Appl 71:211–226

    Article  Google Scholar 

  • Foolad MR (2007) Genome mapping and molecular breeding of tomato. Int J Plant Genomics 2007:64358

    PubMed  Google Scholar 

  • Foolad MR, Lin GY (1998) Genetic analysis of low temperature tolerance during germination in tomato, Lycopersicon esculentum Mill. Plant Breed 117:171–176

    Article  Google Scholar 

  • Foolad MR, Zhang LP, Lin GY (2001) Identification and validation of QTLs for salt tolerance during vegetative growth in tomato by selective genotyping. Genome 44:444–454

    Article  PubMed  CAS  Google Scholar 

  • Foolad MR, Zhang LP, Subbiah P (2003) Genetics of drought tolerance during seed germination in tomato: inheritance and QTL mapping. Genome 46:536–545

    Article  PubMed  CAS  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

    Google Scholar 

  • Frary A, Xu Y, Liu J, Mitchell S, Tedeschi E, Tanksley S (2005) Development of a set of PCR-based anchor markers encompassing the tomato genome and evaluation of their usefulness for genetics and breeding experiments. Theor Appl Genet 111:291–312

    Article  PubMed  CAS  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  PubMed  CAS  Google Scholar 

  • Fridman E, Carrari F, Liu YS, Fernie AR, Zamir D (2004) Zooming in on a quantitative trait for tomato yield using interspecific introgressions. Science 305:1786–1789

    Article  PubMed  CAS  Google Scholar 

  • Ganal MW, Simon R, Brommonschenkel S, Arndt M, Phillips MS, Tanksley SD, Kumar A (1995) Genetic mapping of a wide spectrum nematode resistance gene (Hero) against Globodera rostochiensis in tomato. Mol Plant Microbe Interact 8:886–891

    Article  PubMed  CAS  Google Scholar 

  • Georgelis N, Scott JW, Baldwin EA (2004) Relationship of tomato fruit sugar concentration with physical and chemical traits and linkage of RAPD markers. J Am Soc Hort Sci 129:839–845

    CAS  Google Scholar 

  • Giovannoni JJ (2004) Genetic regulation of fruit development and ripening. Plant Cell 16(Suppl):170–180

    Google Scholar 

  • Giovannoni JJ (2007) Fruit ripening mutants yield insights into ripening control. Curr Opin Plant Biol 10:283–289

    Article  PubMed  CAS  Google Scholar 

  • Giovannoni JJ, Noensie EN, Ruezinsky DM, Lu XH, Tracy SL, Ganal MW, Martin GB, Pillen K, Alpert K, Tanksley SD (1995) Molecular-genetic analysis of the ripening-inhibitor and non-ripening loci of tomato - a first step in genetic map-based cloning of fruit ripening genes. Mol Gen Genet 248:195–206

    Article  PubMed  CAS  Google Scholar 

  • Giritch A, Ganal M, Stephan UW, Baumlein H (1998) Structure, expression and chromosomal localisation of the metallothionein-like gene family of tomato. Plant Mol Biol 37:701–714

    Article  PubMed  CAS  Google Scholar 

  • Gonzalo MJ, Brewer MT, Anderson C, Sullivan D, Gray S, van der Knaap E (2009) Tomato fruit shape analysis using morphometric and morphology attributes implemented in Tomato Analyzer software program. J Am Soc Hort Sci 134:77–87

    Google Scholar 

  • Gorman SW, Banasiak D, Fairley C, McCormick S (1996) A 610 kb YAC clone harbors 7 cM of tomato (Lycopersicon esculentum) DNA that includes the male sterile 14 gene and a hotspot for recombination. Mol Gen Genet 251:52–59

    PubMed  CAS  Google Scholar 

  • Grandillo S, Tanksley SD (1996) Genetic analysis of RFLPs, GATA microsatellites and RAPDs in a cross between L. esculentum and L. pimpinellifolium. Theor Appl Genet 92:957–965

    Article  CAS  Google Scholar 

  • Gupta V, Mathur S, Solanke AU, Sharma MK, Kumar R, Vyas S, Khurana P, Khurana JP, Tyagi AK, Sharma AK (2009) Genome analysis and genetic enhancement of tomato. Crit Rev Biotechnol 29:152–181

    Article  PubMed  CAS  Google Scholar 

  • Gur A, Semel Y, Cahaner A, Zamit D (2004) Real Time QTL of complex phenotypes in tomato interspecific introgression lines. Trends Plant Sci 9:107–109

    Article  PubMed  CAS  Google Scholar 

  • Gur A, Zamir D (2004) Unused natural variation can lift yield barriers in plant breeding. PLoS Biol 2(10): e245. doi:10.1371/journal.pbio.0020245

    Google Scholar 

  • Haanstra JP, Lauge R, Meijer-Dekens F, Bonnema G, de Wit PJ, Lindhout P (1999) The Cf-ECP2 gene is linked to, but not part of, the Cf-4/Cf-9 cluster on the short arm of chromosome 1 in tomato. Mol Gen Genet 262:839–845

    Article  PubMed  CAS  Google Scholar 

  • Hamilton AJ, Brown S, Yuanhai H, Ishizuka M, Lowe A, Solis A, Grierson D (1999) A transgene with repeated DNA causes high frequency, post-transcriptional suppression of ACC-oxidase gene expression in tomato. Plant J 15:737–746

    Article  Google Scholar 

  • Heuvelink E (2005) Tomatoes. CABI, Oxfordshire

    Book  Google Scholar 

  • IPGRI (1996) Descriptors of Tomato (Lycopersicon spp.). International Plant Genetic Resources Institute, Rome

    Google Scholar 

  • Kalloo G (1986) Tomato. Allied Publishers, New Delhi

    Google Scholar 

  • Kaloshian I, Yaghoobi J, Liharska T, Hontelez J, Hanson D, Hogan P, Jesse T, Wijbrandi J, Simons G, Vos P, Zabel P, Williamson VM (1998) Genetic and physical localization of the root-knot nematode resistance locus mi in tomato. Mol Gen Genet 257:376–385

    Article  PubMed  CAS  Google Scholar 

  • Kinzer SM, Schwager SJ, Mutschler MA (1990) Mapping of ripening-related or ripening-specific cDNA clones of tomato (Lycopersicon esculentum). Theor Appl Genet 79:489–496

    Article  CAS  Google Scholar 

  • Knapp S, Bohs L, Nee M, Spooner DM (2004) Solanaceae - a model for linking genomics with biodiversity. Comp Funct Genomics 5:285–291

    Article  PubMed  CAS  Google Scholar 

  • Kramer MG, Redenbaugh K (1994) Commercialization of a tomato with an antisense polygalacturonase gene: the FLAVR SAVRTM tomato story. Euphytica 79:293–297

    Article  Google Scholar 

  • Ku HM, Doganlar S, Chen KY, Tanksley SD (1999) The genetic basis of pear-shaped tomato fruit. Theor Appl Genet 9:844–850

    Article  Google Scholar 

  • Kuromori T, Takahashi S, Kondou Y, Shinozaki K, Matsui M (2009) Phenome analysis in plant species using loss-of-function and gain-of-function mutants. Plant Cell Physiol 50:1215–1231

    Article  PubMed  CAS  Google Scholar 

  • Larkan NJ, Smith SE, Barker SJ (2007) Position of the reduced mycorrhizal colonization (Rmc) locus on the tomato genome map. Mycorrhiza 17:311–318

    Google Scholar 

  • Levin I, Gilboa N, Yeselson E, Shen S, Schaffer AA (2000) Fgr, a major locus that modulate the fructose to glucose ratio in mature tomato fruits. Theor Appl Genet 100:256–262

    Article  CAS  Google Scholar 

  • Li C, Liu G, Xu C, Lee GI, Bauer P, Ling HQ, Ganal MW, Howe GA (2003) The tomato suppressor of prosystemin-mediated responses 2 gene encodes a fatty acid desaturase required for the biosynthesis of jasmonic acid and the production of a systemic wound signal for defense gene expression. Plant Cell 15:1646–1661

    Article  PubMed  CAS  Google Scholar 

  • Li C, Schilmiller AL, Liu G, Lee GI, Jayanty S, Sageman C, Vrebalov J, Giovannoni JJ, Yagi K, Kobayashi Y, Howe GA (2005) Role of beta-oxidation in jasmonate biosynthesis and systemic wound signaling in tomato. Plant Cell 17:971–986

    Article  PubMed  CAS  Google Scholar 

  • Ling HQ, Bauer P, Bereczky Z, Keller B, Ganal M (2002) The tomato fer gene encoding a bHLH protein controls iron-uptake responses in roots. Proc Natl Acad Sci USA 99:13938–13943

    Article  PubMed  CAS  Google Scholar 

  • Lippman ZB, Semel Y, Zamir D (2007) An integrated view of quantitative trait variation using tomato interspecific introgression lines. Curr Opin Genet Dev 17:545–552

    Article  PubMed  CAS  Google Scholar 

  • Liu YS, Gur A, Ronen G, Causse M, Damidaux R, Buret M, Hirschberg J, Zamir D (2003) There is more to tomato fruit colour than candidate carotenoid genes. Plant Biotechnol J 1:195–207

    Article  PubMed  CAS  Google Scholar 

  • Madishetty K, Bauer P, Sharada MS, Al-Hammadi ASA, Sharma R (2006) Genetic characterization of the polycotyledon locus in tomato. Theor Appl Genet 113:673–683

    Google Scholar 

  • Martin GB, Ganal MW, Tanksley SD (1992) Construction of a yeast artificial chromosome library of tomato and identification of cloned segments linked to 2 disease resistance loci. Mol Gen Genet 233:25–32

    Article  PubMed  CAS  Google Scholar 

  • Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, Spivey R, Wu T, Earle ED, Tanksley SD (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science 262:1432–1436

    Article  PubMed  CAS  Google Scholar 

  • Martin GB, Frary A, Wu T, Brommonschenkel S, Chunwongse J, Earle ED, Tanksley SD (1994) A member of the tomato Pto gene family confers sensitivity to fenthion resulting in rapid cell death. Plant Cell 6:1543–1552

    PubMed  CAS  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  PubMed  CAS  Google Scholar 

  • Matsukura C, Aoki K, Fukuda N, Mizoguchi T, Asamizu E, Saito T, Shibata D, Ezura H (2008) Comprehensive resources for tomato functional genomics based on the miniature model tomato micro-tom. Curr Genomics 9:436–443

    Article  PubMed  CAS  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  PubMed  CAS  Google Scholar 

  • Mesbah LA, Kneppers TJ, Takken FL, Laurent P, Hille J, Nijkamp HJ (1999) Genetic and physical analysis of a YAC contig spanning the fungal disease resistance locus Asc of tomato (Lycopersicon esculentum). Mol Gen Genet 261:50–57

    Article  PubMed  CAS  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  CAS  Google Scholar 

  • Monforte AJ, Tanksley SD (2000) Development of a set of near isogenic and backcross recombinant inbred lines containing most of the Lycopersicon hirsutum genome in a L. esculentum genetic background: a tool for gene mapping and gene discovery. Genome 43:803–813

    PubMed  CAS  Google Scholar 

  • Morgante M, Salamini F (2003) From plant genomics to breeding practice. Curr Opin Biotechnol 14:214–219

    Article  PubMed  CAS  Google Scholar 

  • Oh K, Hardeman K, Ivanchenko MG, Ellard-Ivey M, Nebenfuhr A, White TJ, Lomax TL (2002) Fine mapping in tomato using microsynteny with the Arabidopsis genome: the Diageotropica (Dgt) locus. Genome Biol 3:0049

    Article  Google Scholar 

  • Ori N, Eshed Y, Paran I, Presting G, Aviv D, Tanksley S, Zamir D, Fluhr R (1997) The I2C family from the wilt disease resistance locus I2 belongs to the nucleotide binding, leucine-rich repeat superfamily of plant resistance genes. Plant Cell 9:521–532

    PubMed  CAS  Google Scholar 

  • Otoni WC, Picoli EAT, Costa MGC, Nogueira FTS, Zerbini FM (2003) Transgenic tomato. In: Singh RP, Jaiwal PK (eds) Plant genetic engineering. Sci-Tech. Pub. Co., Houston, pp 41–131

    Google Scholar 

  • Pan Q, Liu YS, Budai-Hadrian O, Sela M, Carmel-Goren L, Zamir D, Fluhr R (2000) Comparative genetics of nucleotide binding site-leucine rich repeat resistance gene homologues in the genomes of two dicotyledons: tomato and Arabidopsis. Genetics 155:309–322

    Google Scholar 

  • Paran I, van der Knaap E (2007) Genetic and molecular regulation of fruit and plant domestication traits in tomato and pepper. J Exp Bot 58:3841–3852

    Article  PubMed  CAS  Google Scholar 

  • Paterson AH, DeVerna JW, Lanini B, Tanksley SD (1990) Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics 124:735–742

    PubMed  CAS  Google Scholar 

  • Pedley KF, Martin GB (2003) Molecular basis of Pto-mediated resistance to bacterial speck disease in tomato. Annu Rev Phytopathol 41:215–243

    Article  PubMed  CAS  Google Scholar 

  • Peterson DG, Stack SM, Price HJ, Johnston JS (1996) DNA content of heterochromatin and euchromatin in tomato (Lycopersicon esculentum) pachytene chromosomes. Genome 39:77–82

    Article  PubMed  CAS  Google Scholar 

  • Pillen K, Ganal MW, Tanksley SD (1996) Cinstruction of a high-resolution genetic map and YAC-contigs in the tomato Tm-2a region. Theor Appl Genet 93:228–233

    Article  CAS  Google Scholar 

  • Pnueli L, Carmel-Goren L, Hareven D, Gutfinger T, Alvarez J, Ganal M, Zamir D, Lifschitz E (1998) The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. Development 125:1979–1989

    PubMed  CAS  Google Scholar 

  • Rick CM, Laterrot H, Philouze J (1990) A revised key for the Lycopersicon species. Tomato Genet Coop Rep 40:31

    Google Scholar 

  • Rivas S, Thomas CM (2005) Molecular interactions between tomato and the leaf mold pathogen Cladosporium fulvum. Annu Rev Phytopathol 43:395–436

    Article  PubMed  CAS  Google Scholar 

  • Rodríguez GR, Moyseenko JB, Robbins MD, Huarachi MN, Francis DM, van der Knaap E (2010) Tomato Analyzer:a useful software application to collect accurate and detailed morphological and colorimetric data from two-dimensional objects. JoVE 37. http://www.jove.com/index/Details.stp?ID=1856. doi:10.3791/1856

  • Ron M, Avni A (2004) The receptor for the fungal elicitor ethylene-inducing xylanase is a member of a resistance-like gene family in tomato. Plant Cell 16:1604–1615

    Article  PubMed  CAS  Google Scholar 

  • Ronen G, Cohen M, Zamir D, Hirschberg J (1999) Regulation of carotenoid biosynthesis during tomato fruit development: expression of the gene for lycopene epsilon-cyclase is down-regulated during ripening and is elevated in the mutant Delta. Plant J 17:341–351

    Article  PubMed  CAS  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  PubMed  CAS  Google Scholar 

  • Schauer N, Semel Y, Roessner U, Gur A, Balbo I, Carrari F, Pleban T, Perez-Melis A, Bruedigam C, Kopka J, Willmitzer L, Zamir D, Fernie AR (2006) Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotechnol 24:447–454

    Article  PubMed  CAS  Google Scholar 

  • Schumacher K, Ganal M, Theres K (1995) Genetic and physical mapping of the lateral suppressor (ls) locus in tomato. Mol Gen Genet 246:761–766

    Article  PubMed  CAS  Google Scholar 

  • Sevenier R, van der Meer IM, Bino R, Koops AJ (2002) Increased production of nutriments by genetically engineered crops. J Am Coll Nutr 21(3 Suppl):199–204

    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  CAS  Google Scholar 

  • Stahl W, Heinrich U, Aust O, Tronnier H, Sies H (2006) Lycopene-rich products and dietary photoprotection. Photochem Photobiol Sci 5:238–242

    Article  PubMed  CAS  Google Scholar 

  • Tanksley SD (2004) The genetic, developmental, and molecular bases of fruit size and shape variation in tomato. Plant Cell 16(Suppl):181

    Google Scholar 

  • Tanksley SD, Ganal MW, Prince JP, de-Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160

    Google Scholar 

  • Tanksley SD, Ganal MW, Martin GB (1995) Chromosome landing: a paradigm for map-based gene cloning in plants with large genomes. Trends Genet 11:63–68

    Article  PubMed  CAS  Google Scholar 

  • The tomato core collection: mapping genetic diversity for breeding (2009). Eu-SOL Email newsletter no 5

    Google Scholar 

  • Thomas CM, Dixon MS, Parniske M, Golstein C, Jones JD (1998) Genetic and molecular analysis of tomato Cf genes for resistance to Cladosporium fulvum. Philos Trans R Soc Lond B Biol Sci 353:1413–1424

    Article  PubMed  CAS  Google Scholar 

  • van der Knaap E, Tanksley SD (2001) Identification and characterization of a novel locus controlling early fruit development in tomato. Theor Appl Genet 103:353–358

    Article  Google Scholar 

  • van der Knaap E, Sanyal A, Jackson SA, Tanksley SD (2004) High-resolution fine mapping and fluorescence in situ hybridization analysis of sun, a locus controlling tomato fruit shape, reveals a region of the tomato genome prone to DNA rearrangements. Genetics 168:2127–2140

    Article  PubMed  CAS  Google Scholar 

  • van Ooijen JW, Sandbrink JM, Vrielink M, Verkerk R, Zabel P, Lindhout P (1994) An RFLP linkage map of Lycopersicon peruvianum. Theor Appl Genet 89:1007–1013

    Google Scholar 

  • Vankadavath RN, Hussain AJ, Bodanapu R, Kharshiing E, Basha PO, Gupta S, Sreelakshmi Y, Sharma R (2009) Computer aided data acquisition tool for high-throughput phenotyping of plant populations. Plant Methods 5:18

    Article  PubMed  CAS  Google Scholar 

  • Wasternack C, Stenzel I, Hause B, Hause G, Kutter C, Maucher H, Neumerkel J, Feussner I, Miersch O (2006) The wound response in tomato - role of jasmonic acid. J Plant Physiol 163:297–306

    Article  PubMed  CAS  Google Scholar 

  • Willcox JK, Catignani GL, Lazarus S (2003) Tomatoes and cardiovascular health. Crit Rev Food Sci Nutr 43:1–18

    Article  PubMed  CAS  Google Scholar 

  • Yaghoobi J, Yates JL, Williamson VM (2005) Fine mapping of the nematode resistance gene Mi-3 in Solanum peruvianum and construction of a S. lycopersicum DNA contig spanning the locus. Mol Genet Genomics 274:60–69

    Article  PubMed  CAS  Google Scholar 

  • Yen HC, Shelton BA, Howard LR, Lee S, Vrebalov J, Giovannoni JJ (1997) The tomato high-pigment (hp) locus maps to chromosome 2 and influences plastome copy number and fruit quality. Theor Appl Genet 95:1069–1079

    Article  CAS  Google Scholar 

  • Zamir D (2001) Improving plant breeding with exotic genetic libraries. Nat Rev Genet 2:983–989

    PubMed  CAS  Google Scholar 

  • Zhang HB, Martin GB, Tanksley SD, Wing RA (1994) Map-based cloning in crop plants: tomato as a model system II. Isolation and characterization of a set of overlapping yeast artificial chromosomes encompassing the jointless locus. Mol Gen Genet 244:613–621

    Article  PubMed  CAS  Google Scholar 

  • Zhang HB, Budiman MA, Wing RA (2000) Genetic mapping of jointless-2, a locus controlling tomato pedicel abscission zone structure, using RAPD and RFLP analysis. Theor Appl Genet 100:1183–1189

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to P. Ananda Kumar .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this chapter

Cite this chapter

Solanke, A.U., Kumar, P.A. (2013). Phenotyping of Tomatoes. In: Panguluri, S., Kumar, A. (eds) Phenotyping for Plant Breeding. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8320-5_6

Download citation

Publish with us

Policies and ethics