Skip to main content
SpringerLink
Log in

Gene Mapping in Tomato

  • Chapter
  • First Online:
The Tomato Genome

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

Abstract

Tomato is a model species for genetic analyses since a long time. Many mutations controlled by a single gene were discovered and the underlying genes were mapped first on the tomato genetic map. Most of these genes are involved in fruit colour and shape, in plant growth and architecture and in disease resistances. With the construction of high-density molecular genetic maps, many genes were located on the genome and subsequently several of them were fine-mapped and further identified by positional cloning. Today with the availability of the tomato genome sequence these genes are physically located on the genome and the identification of new ones is being considerably accelerated. The alignment of the physical and genetic maps allowed the identification of hot spots of recombination and of large regions where recombination is almost suppressed, whatever the progeny studied. The impact of this heterogeneity in recombination is discussed.

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

  • Adato A, Mandel T, Mintz-Oron S et al (2009) Fruit-surface flavonoid accumulation in tomato is controlled by a SlMYB12-regulated transcriptional network. PLoS Genet 5:e1000777

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Aflitos SA, Schijlen EGWM, de Jong JHSGM et al (2014) Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J 80:136–148

    Article  PubMed  Google Scholar 

  • Astua-Monge G, Minsavage GV, Stall RE et al (2000) Xv4-vrxv4: a new gene-for-gene interaction identified between Xanthomonas campestris pv. vesicatoria Race T3 and the wild tomato relative Lycopersicon pennellii. Mol Plant Microbe Interact 13:1346–1355

    Article  CAS  PubMed  Google Scholar 

  • Bai Y, van der Hulst R, Huang CC et al (2004) Mapping Ol-4, a gene conferring resistance to Oidium neolycopersici and originating from Lycopersicon peruvianum LA2172, requires muliallelic, single-locus markers. Theor Appl Genet 109:1215–1223

    Article  CAS  PubMed  Google Scholar 

  • Bai Y, van der Hulst R, Bonnema G et al (2005) Tomato defense to Oidium neolycopersici: dominant Ol genes confer isolate-dependent resistance via a different mechanism than recessive ol-2. Mol Plant Microbe Interact 18(4):354–362

    Article  CAS  PubMed  Google Scholar 

  • Bai Y, Pavan S, Zheng Z et al (2008) Naturally occurring broad-spectrum powdery mildew resistance in a Central American tomato accession is caused by loss of Mlo function. Mol Plant Microbe Interact 21(1):30–39

    Article  CAS  PubMed  Google Scholar 

  • Ballester AR, Molthoff J, de Vos R et al (2010) Biochemical and molecular analysis of pink tomatoes: deregulated expression of the gene encoding transcription factor SlMYB12 leads to pink tomato fruit color. Plant Phys 152:71–84

    Article  CAS  Google Scholar 

  • Ballvora A, Pierre M, van den Ackerveken G et al (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  CAS  PubMed  Google Scholar 

  • Barry CS, Giovannoni JJ (2006) Ripening in the tomato Green-ripe mutant is inhibited by ectopic expression of a protein that disrupts ethylene signaling. Proc Natl Acad Sci USA 103(20):7923–7928

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barry CS, McQuinn RP, Chung MY et al (2008) Amino acid substitutions in homologs of the STAY-GREEN protein are responsible for the green-flesh and chlorophyll retainer mutations of tomato and pepper. Plant Physiol 147(1):179–187

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barry CS, Aldridge GM, Herzog G et al (2012) Altered chloroplast development and delayed fruit ripening caused by mutations in a zinc metalloprotease at the lutescent2 locus of tomato. Plant Physiol 159(3):1086–1098

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bassel GW, Mullen RT, Bewley JD (2008) procera is a putative DELLA mutant in tomato (Solanum lycopersicum): effects on the seed and vegetative plant. J Exp Bot 59(3):585–593

    Article  CAS  PubMed  Google Scholar 

  • Behare J, Laterrot H, Sarfatti M et al (1991) Restriction fragment length polymorphisms mapping of the Stemphylium resistance gene in tomato. Mol Plant Microbe Interact 4:489–492

    Article  CAS  Google Scholar 

  • Berger Y, Harpaz-Saad S, Brand A, Melnik H, Sirding N, Alvarez JP, Zinder M, Samach A, Eshed Y, Ori N (2009) The NAC-domain transcription factor GOBLET specifies leaflet boundaries in compound tomato leaves. Development 136(5):823–832

    Article  CAS  PubMed  Google Scholar 

  • Bhattarai KK, Li Q, Liu Y, Dinesh-Kumar SP, Kaloshian I (2007) The Mi-1-mediated pest resistance requires Hsp90 and Sgt1. Plant Physiol 144(1):312–323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bishop GJ, Harrison K, Jones JD (1996) The tomato Dwarf gene isolated by heterologous transposon tagging encodes the first member of a new cytochrome P450 family. Plant Cell 8(6):959–969

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brommonschenkel SH, Frary A, Tanksley SD (2000) The broadspectrum tospovirus resistance gene Sw-5 of tomato is a homolog of the root-knot nematode resistance gene Mi. Mol Plant Microbe Interact 13:1130–1138

    Article  CAS  PubMed  Google Scholar 

  • Budiman MA, Chang S-B, Lee S et al (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  CAS  PubMed  Google Scholar 

  • Burbidge A, Grieve TM, Jackson A et al (1999) Characterization of the ABA-deficient tomato mutant notabilis and its relationship with maize Vp14. Plant J 17(4):427–431

    Article  CAS  PubMed  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(10):3595–3609

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Butler L (1952) The linkage map of the tomato. J Heredity 43:25–35

    Google Scholar 

  • Causse M, Desplat N, Pascual L, Le Paslier MC, Sauvage C, Bauchet G et al (2013) Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genom 14:791

    Article  CAS  Google Scholar 

  • Chetelat RT (2005) Revised list of monogenic stocks. Rep Tomato Genet Coop 55:48–69

    Google Scholar 

  • Chunwongse J, Bunn TB, Crossman C et al (1994) Chromosomal localization and molecular-marker tagging of the powdery mildew resistance gene (Lv) in tomato. Theor Appl Genet 89:76–79

    Article  CAS  PubMed  Google Scholar 

  • Chunwongse S, Doganlar C, Crossman JJ et al (1997) High-resolution genetic map of the Lv resistance locus in tomato. Theor Appl Genet 95:220–223

    Article  CAS  Google Scholar 

  • David-Schwartz R, Koenig D, Sinha N (2009) LYRATE is a key regulator of leaflet initiation and lamina outgrowth in tomato. Plant Cell 21:3093–3104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • De Giovanni C, Dell’Orco P, Bruno A et al (2004) Identification of PCR-based markers (RAPD, AFLP) linked to a novel powdery mildew resistance gene (ol-2) in tomato. Plant Sci 166:41–48

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Dixon MS, Hatzixanthis K, Jones DA, Harrison K, Jones JD (1998) The tomato Cf-5 disease resistance gene and six homologs show pronounced allelic variation in leucine-rich repeat copy number. Plant Cell 10(11):1915–1925

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Doganlar S, Dodson J, Gabor B et al (1998) Molecular mapping of the py-1 gene for resistance to corky root rot (Pyrenochaeta lycopersici) in tomato. Theor Appl Genet 97:784–788

    Article  CAS  Google Scholar 

  • Ellis J, Dodds P, Pryor T (2000) Structure, function and evolution of plant disease resistance genes. Curr Opin Plant Biol 3:278–284

    Article  CAS  PubMed  Google Scholar 

  • Ernst K, Kumar A, Kriseleit D et al (2002) The broad-spectrum potato cyst nematode resistance gene (Hero) from tomato is the only member of a large gene family of NBS-LRR genes with an unusual amino acid repeat in the LRR region. Plant J 31(2):127–136

    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 

  • Fray RG, Grierson D (1993) Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequencing, complementation and co-suppression. Plant Mol Biol 22(4):589–602

    Article  CAS  PubMed  Google Scholar 

  • Fulton TM, van der Hoeven R, Eanetta NT et al (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14:1457–1467

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Galpaz N, Ronen G, Khalfa Z, Zamir D et al (2006) A chromoplast-specific carotenoid biosynthesis pathway is revealed by cloning of the tomato white-flower locus. Plant Cell 18(8):1947–1960

    Article  CAS  PubMed  PubMed Central  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  PubMed  Google Scholar 

  • Haanstra JPW, Wye C, Verbakel H et al (1999) An integrated high-density RFLP-AFLP map of tomato based on two Lycopersicon esculentum × L. pennellii F2 populations. Theor Appl Genet 99:254–271. doi:10.1007/s001220051231

    Article  CAS  Google Scholar 

  • Haanstra JPW, Meijer-Dekens F, Laugé R et al (2000) Mapping strategy for resistance genes against Cladosporium fulvum on the short arm of chromosome 1 of tomato: Cf-ECP5 near the Hcr9 milky way cluster. Theor Appl Genet 101:661–668

    Article  CAS  Google Scholar 

  • He C, Poysa V, Yu K (2002) Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars. Theor Appl Genet 106:363–373

    Article  PubMed  CAS  Google Scholar 

  • Hemming MN, Basuki S, McGrath DJ et al (2004) Fine mapping of the tomato I-3 gene for fusarium wilt resistance and elimination of a co-segregating resistance gene analogue as a candidate for I-3. Theor Appl Genet 109(2):409–418

    Article  CAS  PubMed  Google Scholar 

  • Hirschberg J (2001) Carotenoid biosynthesis in flowering plants. Curr Opin Plant Biol 4:210–218

    Article  CAS  PubMed  Google Scholar 

  • Hovav R, Chehanovsky N, Moy M et al (2007) The identification of a gene (Cwp1), silenced during Solanum evolution, which causes cuticle microfissuring and dehydration when expressed in tomato fruit. Plant J 52(4):627–639

    Article  CAS  PubMed  Google Scholar 

  • Huang CC, Cui YY, Weng CR et al (2000a) Development of diagnostic PCR markers closely linked to the tomato powdery mildew resistance gene Ol-1 on chromosome 6 of tomato. Theor Appl Genet 101:918–924

    Article  CAS  Google Scholar 

  • Huang CC, Hoefs-Van De Putte PM, Haanstra-Van Der Meer JG et al (2000b) Characterization and mapping of resistance to Oidium lycopersicum in two Lycopersicon hirsutum accessions: evidence for close linkage of two Ol-genes on chromosome 6 of tomato. Heredity 85:511–520

    Article  CAS  PubMed  Google Scholar 

  • Isaacson T, Ronen G, Zamir D et al (2002) Cloning of tangerine from tomato reveals a carotenoid isomerase essential for the production of beta-carotene and xanthophylls in plants. Plant Cell 14(2):333–342

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ishibashi K, Masuda K, Naito S et al (2007) An inhibitor of viral RNA replication is encoded by a plant resistance gene. Proc Natl Acad Sci USA 104:13833–13838

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jablonska B, Ammiraju JSS, Bhattarai KK et al (2007) The Mi-9 gene from Solanum arcanum conferring heat-stable resistance to root-knot nematodes is a homolog of Mi-1. Plant Physiol 143:1044–1054

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jones DA, Dickinson MJ, Balint-Kurti PJ et al (1993) Two complex resistance loci revealed in tomato by classical and RFLP mapping of the Cf-2, Cf-4, Cf-5, and Cf-9 genes for resistance to Cladosporium fulvum. Mol Plant Microbe Interact 6:348–357

    Article  CAS  Google Scholar 

  • Jones DA, Thomas CM, Hammond-Kosack KE et al (1994) Isolation of the tomato Cf-9 gene for resistance to Cladosporium fulvum by transposon tagging. Science 266:789–793

    Article  CAS  PubMed  Google Scholar 

  • Josse EM, Simkin AJ, Gaffé J et al (2000) A plastid terminal oxidase associated with carotenoid desaturation during chromoplast differentiation. Plant Physiol 123(4):1427–1436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kaloshian I, Yaghoobi J, Liharska T et al (1998) Genetic and physical localization of the root-knot nematode resistance locus Mi in tomato. Mol Gen Genet 257(3):376–385

    Article  CAS  PubMed  Google Scholar 

  • Katsir L, Schilmiller AL, Staswick PE et al (2008) COI1 is a critical component of a receptor for jasmonate and the bacterial virulence factor coronatine. Proc Natl Acad Sci USA 105(19):7100–7105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kawchuk LM, Hachey J, Lynch DR et al (2001) Tomato Ve disease resistance genes encode cell surface-like receptors. Proc Natl Acad Sci USA 98(11):6511–6515

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Kondo K, Yamamoto M, Matton DPY et al (2002) Cultivated tomato has defects in both S-RNase and HT genes required for stylar function of self-incompatibility. Plant J 29(5):627–636

    Article  CAS  PubMed  Google Scholar 

  • Labate JA, Baldo AM (2005) Tomato SNP discovery by EST mining and resequencing. Mol Breed 16:343–349

    Article  CAS  Google Scholar 

  • Labate JA, Grandillo S, Fulton T et al (2007) Tomato. In: Kole C (ed) Genome mapping and molecular breeding in plants, vol 5, Vegetables. Springer, Berlin, pp 11–135

    Google Scholar 

  • Lanfermeijer FC, Dijkhuis J, Sturre MJ et al (2003) Cloning and characterization of the durable tomato mosaic virus resistance gene Tm-2(2) from Lycopersicon esculentum. Plant Mol Biol 52(5):1037–1049

    Article  CAS  PubMed  Google Scholar 

  • Laterrot H (1996) Stock List. Rep Tom Genet Coop 46:34

    Google Scholar 

  • Lieberman M, Segev O, Gilboa N et al (2004) The tomato homolog of the gene encoding UV-damaged DNA binding protein 1 (DDB1) underlined as the gene that causes the high pigment-1 mutant phenotype. Theor Appl Genet 108(8):1574–1581

    Article  CAS  PubMed  Google Scholar 

  • Lim GT, Wang GP, Hemming MN et al (2008) High resolution genetic and physical mapping of the I-3 region of tomato chromosome 7 reveals almost continuous microsynteny with grape chromosome 12 but interspersed microsynteny with duplications on Arabidopsis chromosomes 1, 2 and 3. Theor Appl Genet 118(1):57–75

    Article  CAS  PubMed  Google Scholar 

  • Lin T, Zhu G, Zhang J et al (2014) Genomic analyses provide insights into the history of tomato breeding. Nat Genet 46:1220–1226

    Article  CAS  PubMed  Google Scholar 

  • Ling HQ, Koch G, Bäumlein H et al (1999) Map-based cloning of chloronerva, a gene involved in iron uptake of higher plants encoding nicotianamine synthase. Proc Natl Acad Sci USA 96(12):7098–7103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ling HQ, Bauer P, Bereczky Z et al (2002) The tomato fer gene encoding a bHLH protein controls iron-uptake responses in roots. Proc Natl Acad Sci USA 99(21):13938–13943

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lippman ZB, Cohen O, Alvarez JP et al (2008) The making of a compound inflorescence in tomato and related nightshades. PLoS Biol 11:e288

    Article  CAS  Google Scholar 

  • Liu Y, Roof S, Ye Z et al (2004) Manipulation of light signal transduction as a means of modifying fruit nutritional quality in tomato. Proc Nat Acad Sci USA 101:9897–9902

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Y, Chen H, Wei Y et al (2005) Construction of a genetic map and localization of QTLs for yield traits in tomato by SSR markers. Prog Nat Sci 15:793–797

    Article  CAS  Google Scholar 

  • Manning K, Tör M, Poole M et al (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38(8):948–952

    Article  CAS  PubMed  Google Scholar 

  • Mao L, Begum D, Chuang HW et al (2000) JOINTLESS is a MADS-box gene controlling tomato flower abscission zone development. Nature 406(6798):910–913

    Article  CAS  PubMed  Google Scholar 

  • Martin GB, Brommonschenkel S, Chunwongse J et al (1993) Map-based cloning of a protein-kinase gene conferring disease resistance in tomato. Science 262:1432–1436

    Article  CAS  PubMed  Google Scholar 

  • Martin GB, Frary A, Wu T et al (1994) A member of the tomato Pto gene family confers sensitivity to fenthion resulting in rapid cell death. Plant Cell 6(11):1543–1552

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martín-Trillo M, Grandío EG, Serra F et al (2011) Role of tomato BRANCHED1-like genes in the control of shoot branching. Plant J 67(4):701–714

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Mesbah LA, Kneppers TJ, Takken FL et al (1999) Genetic and physical analysis of a YAC contig spanning the fungal disease resistance locus Asc of tomato (Lycopersicon esculentum). Mol Gen Genet 261(1):50–57

    Article  CAS  PubMed  Google Scholar 

  • Molinero-Rosales N, Jamilena M, Zurita S et al (1999) FALSIFLORA, the tomato orthologue of FLORICAULA and LEAFY, controls flowering time and floral meristem identity. Plant J 20(6):685–693

    Article  CAS  PubMed  Google Scholar 

  • Molinero-Rosales N, Latorre A, Jamilena M et al (2004) SINGLE FLOWER TRUSS regulates the transition and maintenance of flowering in tomato. Planta 218(3):427–434

    Article  CAS  PubMed  Google Scholar 

  • Montoya T, Nomura T, Farrar K et al (2002) Cloning the tomato curl3 gene highlights the putative dual role of the leucine-rich repeat receptor kinase tBRI1/SR160 in plant steroid hormone and peptide hormone signaling. Plant Cell 14(12):3163–3176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moore S, Vrebalov J, Payton P et al (2002) Use of genomics tools to isolate key ripening genes and analyse fruit maturation in tomato. J Exp Bot 53(377):2023–2030

    Article  CAS  PubMed  Google Scholar 

  • Moreau P, Thoquet P, Olivier J et al (1998) Genetic Mapping of Ph-2, a single locus controlling partial resistance to Phytophthora infestans in tomato. Mol Plant Microbe Interact 11(4):259–269

    Article  CAS  Google Scholar 

  • Muramoto T, Kami C, Kataoka H et al (2005) The tomato photomorphogenetic mutant, aurea, is deficient in phytochromobilin synthase for phytochrome chromophore biosynthesis. Plant Cell Physiol 46(4):661–665

    Article  CAS  PubMed  Google Scholar 

  • Mustilli AC, Fenzi F, Ciliento R et al (1999) Phenotype of the tomato high pigment-2 mutant is caused by a mutation in the tomato homolog of DEETIOLATED1. Plant Cell 11:145–157

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nashilevitz S, Melamed-Bessudo C, Aharoni A et al (2009) The legwd mutant uncovers the role of starch phosphorylation in pollen development and germination in tomato. Plant J 57(1):1–13

    Article  CAS  PubMed  Google Scholar 

  • Okabe Y, Asamizu E, Saito T et al (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(11):1994–2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ori N, Eshed Y, Paran I et al (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(4):521–532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ori N, Cohen AR, Etzioni A et al (2007) Regulation of LANCEOLATE by miR319 is required for compound-leaf development in tomato. Nat Genet 39(6):787–791

    Article  CAS  PubMed  Google Scholar 

  • Park SJ, Jiang K, Tal L et al (2014) Optimization of crop productivity in tomato using induced mutations in the florigen pathway. Nat Genet 46(12):1337–1342

    Article  CAS  PubMed  Google Scholar 

  • Parnis A, Cohen O, Gutfinger T et al (1997) The dominant developmental mutants of tomato, Mouse-ear and Curl, are associated with distinct modes of abnormal transcriptional regulation of a Knotted gene. Plant Cell 9(12):2143–2158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parrella G, Ruffel S, Moretti A et al (2002a) Recessive resistance genes against potyviruses are localized in colinear genomic regions of the tomato (Lycopersicon spp.) and pepper (Capsicum spp.) genomes. Theor Appl Genet 105(6-7):855–861

    Article  CAS  PubMed  Google Scholar 

  • Parrella G, Ruffel S, Moretti A et al (2002b) Recessive resistance genes against potyviruses are localized in colinear genomic regions of the tomato (Lycopersicon spp.) and pepper (Capsicum spp.) genomes. Theor Appl Genet 105(6-7):855–861

    Article  CAS  PubMed  Google Scholar 

  • Parrella G, Moretti A, Gognalons P et al (2004) The Am gene controlling resistance to Alfalfa mosaic virus in tomato is located in the cluster of dominant resistance genes on chromosome 6. Phytopathology 94:345–350

    Article  CAS  PubMed  Google Scholar 

  • Piron F, Nicolaï M, Minoïa S et al (2010) An induced mutation in tomato eIF4E leads to immunity to two potyviruses. PLoS ONE 5(6):e11313

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pnueli L, Carmel-Goren L, Hareven D et al (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

    CAS  PubMed  Google Scholar 

  • Powell AL, Nguyen CV, Hill T et al (2012) Uniform ripening encodes a Golden 2-like transcription factor regulating tomato fruit chloroplast development. Science 336(6089):1711–1715

    Article  CAS  PubMed  Google Scholar 

  • Rivers BA, Bernatzky R, Robinson SJ et al (1993) Molecular diversity at the self-incompatibility locus is a salient feature in natural populations of wild tomato (Lycopersicon peruvianum). Mol Gen Genet 238(3):419–427

    Article  CAS  PubMed  Google Scholar 

  • Ronen GL, Cohen M, Zamir D et al (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  CAS  PubMed  Google Scholar 

  • Ronen G, Carmel-Goren L, Zamir D et al (2000) An alternative pathway to β-carotene formation in plant chromoplasts discovered by map-based cloning of Beta and old-gold color mutations in tomato. Proc Nat Acad Sci USA 97:11102–11107

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ruffel S, Gallois JL, Lesage ML et al (2005) The recessive potyvirus resistance gene pot-1 is the tomato orthologue of the pepper pvr2-eIF4E gene. Mol Gen Genomics 274:346–353

    Article  CAS  Google Scholar 

  • Sagi M, Scazzocchio C, Fluhr R (2002) The absence of molybdenum cofactor sulfuration is the primary cause of the flacca phenotype in tomato plants. Plant J 31(3):305–317

    Article  CAS  PubMed  Google Scholar 

  • Saliba-Colombani V, Causse M, Gervais L et al (2000) Efficiency of RFLP, RAPD, and AFLP markers for the construction of an intraspecific map of the tomato genome. Genome 43:29–40

    Article  CAS  PubMed  Google Scholar 

  • Salmeron J, Oldroyd G, Rommens C et al (1996) Tomato Prf is a member of the leucine-rich repeat class of plant disease resistance genes and lies embedded within the Pto kinase gene cluster. Cell 86:123–133

    Article  CAS  PubMed  Google Scholar 

  • Sarfatti M, Abu-Abied M, Katan J et al (1991) RFLP mapping of I1, a new locus in tomato conferring resistance against Fusarium oxysporum f. sp. lycopersici race 1. Theor Appl Genet 82:22–26

    Article  CAS  PubMed  Google Scholar 

  • Sato T, Iwatsubo T, Takahashi M et al (1993) Intercellular localization of acid invertase in tomato fruit and molecular cloning of a cDNA for the enzyme. Plant Cell Physiol 34(2):263–269

    CAS  PubMed  Google Scholar 

  • Schmitz G, Tillmann E, Carriero F et al (2002) The tomato Blind gene encodes a MYB transcription factor that controls the formation of lateral meristems. Proc Natl Acad Sci USA 99(2):1064–1069

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schornack S, Ballvora A, Gürlebeck D et al (2004) The tomato resistance protein Bs4 is a predicted non-nuclear TIR-NB-LRR protein that mediates defense responses to severely truncated derivatives of AvrBs4 and overexpressed AvrBs3. Plant J 37(1):46–60 Erratum in: Plant J 37(5):787

    Article  CAS  PubMed  Google Scholar 

  • Schumacher K, Schmitt T, Rossberg M et al (1999) The Lateral suppressor (Ls) gene of tomato encodes a new member of the VHIID protein family. Proc Natl Acad Sci USA 96(1):290–295

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Scott JW, Agrama HA, Jones JP (2004) RFLP-based analysis of recombination among resistance genes to Fusarium wilt races 1, 2, and 3 in tomato. J Am Soc Hortic Sci 129:394–400

    CAS  Google Scholar 

  • Sela-Buurlage MB, Budai-Hadrian O, Pan Q, Zamir D, Fluhr R (2001) Genome-wide dissection of Fusarium resistance in tomato reveals multiple complex loci. Mol Gen Genet 265:1104–1111

    Article  CAS  Google Scholar 

  • Shirasawa K, Isobe S, Hirakawa H et al (2010) SNP discovery and linkage map construction in cultivated tomato. DNA Res 17(6):381–391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sim SC, Robbins MD, Chilcott C et al (2009) Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding. BMC Genom 10:466

    Article  CAS  Google Scholar 

  • Sim S-C, Durstewitz G, Plieske J et al (2012) Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS ONE 7(7):e40563

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Soumpourou E, Iakovidis M, Chartrain L et al (2007) The Solanum pimpinellifolium Cf-ECP1 and Cf-ECP4 genes for resistance to Cladosporium fulvum are located at the Milky Way locus on the short arm of chromosome 1. Theor Appl Genet 115:1127–1136

    Article  CAS  PubMed  Google Scholar 

  • Stamova BS, Chetelat RT (2000) Inheritance and genetic mapping of cucumber mosaic virus resistance introgressed from Lycopersicon chilense into tomato. Theor Appl Genet 101:527–537

    Article  CAS  Google Scholar 

  • Tanksley SD, Loaiza-Figueroa F (1985) Gametophytic self-incompatibility is controlled by a single major locus on chromosome 1 in Lycopersicon peruvianum. Genetics 82:5093–5096

    CAS  Google Scholar 

  • Tanksley SD, Ganal MW, Prince JP et al (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160

    CAS  PubMed  PubMed Central  Google Scholar 

  • Terry MJ, Kendrick RE (1996) The aurea and yellow-green-2 mutants of tomato are deficient in phytochrome chromophore synthesis. J Biol Chem 271(35):21681–21686

    Article  CAS  PubMed  Google Scholar 

  • Thomas CM, Jones DA, Parniske M et al (1997) Characterization of the tomato Cf-4 gene for resistance to Cladosporium fulvum identifies sequences that determine recognitional specificity in Cf-4 and Cf-9. Plant Cell 9:2209–2224

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thompson AJ, Jackson AC, Parker RA et al (2000) Abscisic acid biosynthesis in tomato: regulation of zeaxanthin epoxidase and 9-cis-epoxycarotenoid dioxygenase mRNAs by light/dark cycles, water stress and abscisic acid. Plant Mol Biol 42(6):833–845

    Article  CAS  PubMed  Google Scholar 

  • Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485(7400):635–641

    Article  CAS  Google Scholar 

  • Vakalounakis DJ, Laterrot H, Moretti A et al (1997) Linkage between Frl (Fusarium oxysporum f.sp. radicis-lycopersici resistance) and Tm-2 (tobacco mosaic virus resistance-2) loci in tomato (Lycopersicon esculentum). Ann Appl Biol 130:319–323

    Article  Google Scholar 

  • van der Biezen EA, Brandwagt BF, van Leeuwen W et al (1996) Identification and isolation of the FEEBLY gene from tomato by transposon tagging. Mol Gen Genet 251(3):267–280

    PubMed  Google Scholar 

  • Verlaan MG, Hutton SF, Ibrahem RM et al (2013) The tomato yellow leaf curl virus resistance genes Ty-1 and Ty-3 are allelic and code for DFDGD-Class RNA–dependent RNA polymerases. PLoS Genet 9(3):e1003399

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Víquez-Zamora M, Vosman B, van de Geest H et al (2013) Tomato breeding in the genomics era: insights from a SNP array. BMC Genom 14:354

    Article  CAS  Google Scholar 

  • Viquez-Zamora AM, Caro Rios CM, Finkers R et al (2014) Mapping in the era of sequencing: high density genotyping and its application for mapping TYLCV resistance in Solanum pimpinellifolium. BMC Genom 15:1152. doi:10.1186/1471-2164-15-1152

    Article  CAS  Google Scholar 

  • Vrebalov J, Ruezinsky D, Padmanabhan V et al (2002) A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296(5566):343–346

    Article  CAS  PubMed  Google Scholar 

  • Weller JL, Perrotta G, Schreuder ME et al (2001) Genetic dissection of blue-light sensing in tomato using mutants deficient in cryptochrome 1 and phytochromes A, B1 and B2. Plant J 25(4):427–440

    Article  CAS  PubMed  Google Scholar 

  • Wilkinson JQ, Lanahan MB, Yen HC et al (1995) An ethylene-inducible component of signal transduction encoded by never-ripe. Science 270(5243):1807–1809

    Article  CAS  PubMed  Google Scholar 

  • Yaghoobi J, Kaloshian I, Wen Y et al (1995) Mapping a new nematode resistance locus in Lycopersicon peruvianum. Theor Appl Genet 91:457–464

    Article  CAS  PubMed  Google Scholar 

  • Yang C, Li H, Zhang J et al (2011) A regulatory gene induces trichome formation and embryo lethality in tomato. Proc Natl Acad Sci USA 108(29):11836–11841

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu ZH, Wang JF, Stall RE et al (1995) Genomic localization of tomato genes that control a hypersensitive reaction to Xanthomonas campestris pv. vesicatoria (Doidge) dye. Genetics 141(2):675–682

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yuan YN, Haanstra J, Lindhout P et al (2002) The Cladopsorium fulvum resistance gene Cf-ECP3 is part of the Orion cluster on the short arm of chromosome 1. Mol Breed 10:45–50

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Zhang C, Liu L, Wang X et al (2014) The Ph-3 gene from Solanum pimpinellifolium encodes CC-NBS-LRR protein conferring resistance to Phytophthora infestans. Theor Appl Genet 127(6):1353–1364

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang C, Liu L, Zheng Z et al (2013) Fine mapping of the Ph-3 gene conferring resistance to late blight (Phytophthora infestans) in tomato. Theor Appl Genet 126(10):2643–2653

    Article  CAS  PubMed  Google Scholar 

  • Zhang J, Chen R, Xiao J et al (2007) A single-base deletion mutation in SlIAA9 gene causes tomato (Solanum lycopersicum) entire mutant. J Plant Res 120(6):671–678

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. UR 1052 Génétique et Amélioration des Fruits et Légumes, INRA, CS60094, 84250, Montfavet, France

    Mathilde Causse

  2. Research Division Portici, Italian National Research Council, Institute of Bioscience and BioResources (CNR-IBBR), Via Università 133, 80055, Portici, Napoli, Italy

    Silvana Grandillo

Authors
  1. Mathilde Causse
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Silvana Grandillo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mathilde Causse .

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

Causse, M., Grandillo, S. (2016). Gene Mapping in Tomato. 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_3

Download citation

Publish with us

Policies and ethics

Search

Navigation