Molecular Breeding

, Volume 14, Issue 1, pp 21–34

Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags

  • Wencai Yang
  • Xiaodong Bai
  • Eileen Kabelka
  • Christina Eaton
  • Sophien Kamoun
  • Esther van der Knaap
  • David Francis


Single nucleotide polymorphisms (SNPs) are useful for characterizing allelic variation, for genome-wide mapping, and as a tool for marker-assisted selection. Discovery of SNPs through de novo sequencing is inefficient within cultivated tomato (Lycopersicon esculentum Mill.) because the polymorphism rate is more than ten-fold lower than the sequencing error rate. The availability of expressed sequence tag (EST) data has made it feasible to discover putative SNPs “in silico” prior to experimental verification. By exploiting redundancy among EST data available for different varieties among 148,373 tomato ESTs, we have identified candidate SNPs for use within cultivated germplasm pools. 1,245 contigs having three EST sequences of Rio Grande and three EST sequences of TA496 were used for SNP discovery. We detected 1 SNP for every 8,500 bases analyzed, with 101 candidate SNPs in 44 genes identified. Sixty-six SNPs could be recognized by restriction enzymes, and subsequent experimental verification using restriction digestion or CEL I digestion confirmed 83% of the putative polymorphisms tested. SNPs between TA496 and Rio Grande have a high probability (53%) of detecting polymorphisms between other L. esculentum varieties. Twenty-six SNPs in 18 unigenes were mapped to specific chromosomes. Two SNPs, LEOH23 and LEOH37, were shown to be linked to quantitative trait loci contributing to fruit color within elite breeding populations. These results suggest that the growing databases of DNA sequence will yield information that facilitates improvement within the germplasm pools that have contributed to productive modern varieties.

Fruit color Lycopersicon esculentum Mapping QTL Single nucleotide polymorphisms (SNP) 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Aerts J., Wetzels Y., Cohen N. and Aerssens J. 2002. Data mining of public SNP databases for the selection of intragenic SNPs. Human Mutation 20: pp162–173.CrossRefGoogle Scholar
  2. Balasubramanian S., Harrison P., Hegyi H., Bertone P., Luscombe N., Echols N., McGarvey P., Zhang Z. and Gerstein M. 2002. SNPs on human chromosomes 21 and 22-analysis in terms of protein features and pseudogenes Pharmacogenomics 3(3): 393–402.Google Scholar
  3. Bartley G.E. and Scolnik P.A. 1993. cDNA cloning, expression during development, and genome mapping of PSY2, a second tomato gene encoding phytoene synthase. J. Biol. Chem. 268(34): 25718–25721.PubMedGoogle Scholar
  4. Berger-Schunn A. 1994. Practical color measurement: A primer for the beginner, a reminder for the expert. Wiley, New York, New York, USA.Google Scholar
  5. Bonnema G., Berg P. and Lindhout P. 2002. AFLPs mark different genomic regions compared with RFLPs: a case study in tomato. Genome 45: 217–221.CrossRefPubMedGoogle Scholar
  6. Bredemeijer G.M.M., Cooke R.J., Ganal M.W., Peeters R., Isaac P., Noordijk Y., Rendell S., Jackson J., Röder M.S., Wendehake K., Dijcks M., Amelaine M., Wickaert V., Bertrand L. and Vosman B. 2002. Construction and testing of a microsatellite database containing more than 500 tomato varieties. Theor. Appl. Genet. 105: 1019–1026.CrossRefPubMedGoogle Scholar
  7. Chen L.Y.Y., Lu S.H., Shih E.S.C. and Hwang M.J. 2002. Single nucleotide polymorphism mapping using genome-wide unique sequences. Genome Research 12: 1106–1111.PubMedGoogle Scholar
  8. Ching A., Caldwell K.S., Jung M., Dolan M., Smith O.S., Tingey S., Morgante M. and Rafalski A.J. 2002. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet. 3(1):19.CrossRefPubMedGoogle Scholar
  9. Eshed Y. and 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.PubMedGoogle Scholar
  10. Giordano M., Oefner P.J., Underhill P.A., Cavalli Sforza L.L., Tosi R. and Momigliano Richiardi P. 1999. Identification by denaturing high-performance liquid chromatography of numerous polymorphisms in a candidate region for multiple sclerosis susceptibility. Genomics 56: 247–253.CrossRefPubMedGoogle Scholar
  11. Giritch A., Ganal M., Stephan U.W. and Baumlein H. 1998. Structure, expression and chromosomal localisation of the metallothionein-like gene family of tomato. Plant Molecular Biology 37: 701–714.CrossRefPubMedGoogle Scholar
  12. Goff S.A., Ricke D., Lan T.H. et al. 2002. A draft sequence of the rice genome Oryza sativa L. ssp japonica. Science 296: 92–100.CrossRefPubMedGoogle Scholar
  13. Gupta P.K., Roy J.K. and Prasad M. 2002. Single nucleotide polymorphisms: A new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Current Science 80: 524–535.Google Scholar
  14. Hardin C.L. 1990. Why color? Perceiving, Measuring, and Using Color. Soc. Photo-Optical Instrumentation Engineers, 1250: 293–300.Google Scholar
  15. International SNP Map Working Group. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409: 928–933.CrossRefPubMedGoogle Scholar
  16. Kabelka E. 2001. Discovery and introgression of beneficial loci from Lycopersicon hirsutum, LA407, a wild species of tomato. PhD dissertation, Horticulture and Crop Science, The Ohio State University, Ohio, USA.Google Scholar
  17. Kabelka E., Franchino B. and Francis D.M. 2002. Two loci from Lycopercosin hirstum LA407 confer resistance to strains of Clavibacter michiganensis subsp michiganensis. Phytopathology 92: 504–510.Google Scholar
  18. Kanazin V., Talbert H., See D., DeCamp P., Nevo E. and Blake T. 2002. Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare). Plant Molecular Biology 48: 529–537.CrossRefPubMedGoogle Scholar
  19. Lander E.S., Green P., Abrahamson J., Barlow A., Daly M.J., Lincoln S.E. and Newburg L. 1987. MAPMAKER APMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174–181.PubMedGoogle Scholar
  20. Margiotti K., Kim E., Pearce C.L., Spera E., Novelli G. and Reichardt J.KV. 2002. Association of the G289S Single Nucleotide Polymorphism in the HSD17B3 Gene With Prostate Cancer in Italian Men. The Prostate 53: 65–68.CrossRefPubMedGoogle Scholar
  21. Oleykowski C.A., Mullins C.R.B., Godwin A.K., and Yeung A.T. 1998. Mutation detection using a novel plant endonuclease. Nucleic Acids Research 26: 4597–4602.CrossRefPubMedGoogle Scholar
  22. Precheur R.J. 2000. Ohio vegetable production guide. The Ohio State University Cooperative Extension, Bulletin 672.Google Scholar
  23. Rozen S. and Skaletsky H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Molecular Biology 132: 365–386.Google Scholar
  24. Sacks E.J. and Francis D.M. 2001. Genetic and environmental variation for tomato flesh color in a population of modern breeding lines. J. Am. Soc. Hortic. Sci. 126: 221–226.Google Scholar
  25. Smulders M.J.M, Bredemeijer G., Rus-Kortekaas W., Arens P. and Vosman B. 1997. Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theor. Appl. Genet. 94: 264–272.CrossRefGoogle Scholar
  26. Sugimoto Y., Kuzushita N., Takehara T., Kanto T., Tatsumi T., Miyagi T., Jinushi M., Ohkawa K., Horimoto M., Kasahara A., Hori M., Sasaki Y. and Hayashi N. 2002. A single nucleotide polymorphism of the low molecular mass polypeptide 7 gene influences the interferon response in patients with chronic hepatitis C. Journal of Viral Hepatitis 9: 377–384.CrossRefPubMedGoogle Scholar
  27. Suliman-Pollatschek S., Kashkush K., Shats H., Hillel J. and Lavi U. 2002. Generation and mapping of AFLP, SSRs and SNPs in Lycopersicon esculentum. Cellular and Molecular Biology Letters 7: 583–597.PubMedGoogle Scholar
  28. Tanksley S.D. and Jones R.A. 1981. Effects of O2 stress on tomato alcohol dehydrogenase activity: description of a second ADH coding genes. Biochem. Genet. 19(3-4): 397–409.PubMedGoogle Scholar
  29. Van der Hoeven R., Ronning C., Giovannoni J., Martin G. and Tanksley S.D. 2002. Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell 14: 1441–1456.CrossRefPubMedGoogle Scholar
  30. Van der Knaap E. and Tanksley S.D. 2001. Identification and characterization of a novel locus controlling early fruit development in tomato. Theor. Appl. Genet. 103: 353–358.CrossRefGoogle Scholar
  31. Van Tuinen A., Cordonnier-Pratt M.M., Pratt L.H., Verkerk R., Zabel P. and Koornneef M. 1997. The mapping of phytochrome genes and photomorphogenic mutants of tomato. Theor. Appl. Genet. 94: 115–122.CrossRefGoogle Scholar
  32. Verhage B.A.J., van Houwelingen K., Ruijter T.E.G., Kiemeney L.A. and Schalken J.A. 2002. Single-nucleotidepolymorphisminthee-cadherin gene promoter modifies the risk of prostate cancer. Int. J. Cancer 100: 683–685.CrossRefPubMedGoogle Scholar
  33. Yang B., Wen X., Kodali N.S., Oleykowdki C.A., Miller C.G., Kulinski J., Besack D., Yeung J.A., Kowalski D. and Yeung A.T. 2000. Purification, cloning, and characterization of the CEL I nuclease. Biochemistry 39: 3533–3541.CrossRefPubMedGoogle Scholar
  34. Yu J., Hu S.N., Wang J., et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 296: 79–92.CrossRefPubMedGoogle Scholar
  35. Zhu Y.L., Hyatt S., Quigley C., Song Q.J., Grimm D., Young N. and Cregan P. 2001. Single nucleotide polymorphisms (snps) in soybean genes, cdnas, and random genomic sequence, in Plant & Animal Genome IX Conference, January 13-17, 2001. San Diego, California, USA.Google Scholar

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Wencai Yang
    • 1
  • Xiaodong Bai
    • 2
  • Eileen Kabelka
    • 1
  • Christina Eaton
    • 1
  • Sophien Kamoun
    • 3
  • Esther van der Knaap
    • 1
  • David Francis
    • 1
  1. 1.Department of Horticulture and Crop ScienceUSA
  2. 2.USA
  3. 3.Department of Plant Pathology, The Ohio State UniversityOhio Agricultural Research and Development CenterWoosterUSA

Personalised recommendations