Theoretical and Applied Genetics

, Volume 121, Issue 7, pp 1199–1207 | Cite as

Discovery of intron polymorphisms in cultivated tomato using both tomato and Arabidopsis genomic information

  • Yuanyuan Wang
  • Jia Chen
  • David M. Francis
  • Huolin Shen
  • Tingting Wu
  • Wencai Yang
Original Paper

Abstract

A low level of genetic variation has limited the application of molecular markers for characterizing important traits in cultivated tomato. To detect polymorphisms in tomato conserved ortholog sets (COS), expressed sequence tags (ESTs) were searched against tomato and Arabidopsis genomic sequences to define the positions of introns. Introns were amplified from 12 different accessions of tomato by polymerase chain reaction and nucleotide sequences were determined by sequencing. Results indicated that there was a possibility of 71% to amplify introns from tomato genomic DNA through this approach. A total of 201 introns were sequenced from 86 COS unigenes. The intron positions and numbers were conserved between tomato and Arabidopsis, but average intron length was three times longer in tomato than in Arabidopsis. A total of 307 single nucleotide polymorphisms (SNPs) and 75 indels were detected in introns of 57 COS unigenes among 12 tomato lines. Within cultivated tomato germplasm 172 SNPs and 47 indels were detected in introns of 33 COS unigenes. In addition, 41 SNPs were identified in the exons of 27 COS unigenes. The frequency of SNPs was 2.4 times higher in introns than in exons in the 22 COS unigenes having both intronic and exonic polymorphisms. These results indicate that intronic regions may contain sufficient variation to develop sufficient marker resources for genome-wide analysis in cultivated tomato.

Supplementary material

122_2010_1381_MOESM1_ESM.xls (356 kb)
Supplementary material 1 (XLS 355 kb)

References

  1. Archak S, Karihaloo JL, Jain A (2002) RAPD markers reveal narrowing genetic base of Indian tomato cultivars. Curr Sci 82:1139–1143Google Scholar
  2. Bernatzky R, Tanksley SD (1986) Toward a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genetics 112:887–898PubMedGoogle Scholar
  3. Bierne N, Lehnert SA, Bédier E, Bonhomme F, Moore SS (2000) Screening for intron-length polymorphism in penaeid shrimps using exon-primed intron-crossing (EPIC)-PCR. Mol Ecol 9:233–235CrossRefPubMedGoogle Scholar
  4. Chen J, Shen HL, Yang WC (2007) Development of tomato molecular markers. Mol Plant Breed 5(6S):130–138Google Scholar
  5. Chen J, Wang H, Shen HL, Chai M, Li JS, Qi MF, Yang WC (2009) Genetic variation in tomato populations from four breeding programs revealed by single nucleotide polymorphism and simple sequence repeat markers. Sci Hortic 122:6–16CrossRefGoogle Scholar
  6. Daguin C, Borsa P (1999) Genetic characterization of Mytilus galloprovincialis Lmk. in North West Africa using nuclear DNA markers. J Exp Mar Biol Ecol 235:55–65CrossRefGoogle Scholar
  7. Foolad MR (2007) Genome mapping and molecular breeding of tomato. Int J Plant Genomics. doi:10.1155/2007/64358
  8. Fulton TM, Van der Hoeven R, Eannetta NT, Tanksley SD (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14:1457–1467CrossRefPubMedGoogle Scholar
  9. Garcia-Martinez S, Andreani L, Garcia-Gusano M, Geuna F, Ruiz JJ (2005) Evolution of amplified length polymorphism and simple sequence repeats for tomato germplasm fingerprinting: utility for grouping closely related traditional cultivars. Genome 49:648–656CrossRefGoogle Scholar
  10. Hassan M, Lemaire C, Fauvelot C, Bonhomme F (2003) Seventeen New EPIC-PCR amplifiable introns in fish. Mol Ecol 2:334–340Google Scholar
  11. Jiménez-Gómez JM, Maloof JN (2009) Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol 9:85CrossRefPubMedGoogle Scholar
  12. Kabelka E, Franchino B, Francis DM (2002) Two loci from Lycopersicon hirsutum LA407 confer resistance to strains of Clavibacter michiganensis subsp. michiganensis. Phytopathology 92:504–510CrossRefPubMedGoogle Scholar
  13. Labate JA, Baldo AM (2005) Tomato SNP discovery by EST mining and resequencing. Mol Breed 16:343–349CrossRefGoogle Scholar
  14. Labate JA, Robertson LD, Baldo AM (2009) Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.). Heredity 103:257–267CrossRefPubMedGoogle Scholar
  15. Lessa EP (1992) Rapid survey of DNA sequence variation in natural populations. Mol Biol Evol 9:323–330PubMedGoogle Scholar
  16. Miller JC, Tanksley SD (1990) RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor Appl Genet 80:437–448Google Scholar
  17. Mueller LA, Lankhorst RK, Tanksley SD et al (2009) A snapshot of the emerging tomato genome sequence. Plant Genome 2:78–92CrossRefGoogle Scholar
  18. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
  19. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273CrossRefPubMedGoogle Scholar
  20. Nesbitt TC, Tanksley SD (2002) Comparative sequencing in the genus Lycopersicon: implications for the evolution of fruit size in the domestication of cultivated tomatoes. Genetics 162:365–379PubMedGoogle Scholar
  21. Park YH, West MAL, St. Clair DA (2004) Evaluation of AFLPs for germplasm fingerprinting and assessment of genetic diversity in cultivars of tomato (Lycopersicon esculentum L.). Genome 47:510–518CrossRefPubMedGoogle Scholar
  22. Rick CM, Fobes JF (1974) Association of an allozyme with nematode resistance. Rpt Tomato Genet Coop 24:25Google Scholar
  23. Rozas J, Rozas R (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174–175CrossRefPubMedGoogle Scholar
  24. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386PubMedGoogle Scholar
  25. Scott JW, Harbaugh BK (1989) Micro-Tom—a miniature dwarf tomato, Circular S-370, Florida Agricultural Experiment Station, pp 1–6Google Scholar
  26. Scott JW, Francis DM, Miller SA, Somodi GC, Jones JB (2003) Tomato bacterial spot resistance derived from PI 114490; inheritance to race T2 and relationship across three pathogen races. J Am Soc Hortic Sci 128:698–703Google Scholar
  27. Sim SC, Robbins MD, Chilcott C, Zhu T, Francis DM (2009) Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding. BMC Genomics 10:466CrossRefPubMedGoogle Scholar
  28. Tajima F (1993) Statistical analysis of DNA polymorphism. Jpn J Genet 68:567–595CrossRefPubMedGoogle Scholar
  29. Tam SM, Mhiri C, Vogelaar A, Kerkveld M, Pearce SR, Grandbastien MA (2005) Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theor Appl Genet 110:819–831CrossRefPubMedGoogle Scholar
  30. Temesgen B, Brown GR, Harry DE, Kinlaw CS, Sewell MM, Neale DB (2001) Genetic mapping of expressed sequence tag polymorphism (ESTP) markers in loblolly pine (Pinus taeda L.). Theor Appl Genet 102:664–675CrossRefGoogle Scholar
  31. Van der Hoeven R, Ronning C, Giovannoni J, Martin G, Tanksley S (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 14:1441–1456CrossRefPubMedGoogle Scholar
  32. Van Deynze A, Stoffel K, Buell CR, Kozik A, Liu J, van der Knapp E, Francis D (2007) Diversity in conserved genes in tomato. BMC Genomics 8:465CrossRefPubMedGoogle Scholar
  33. Watterson GA (1975) On the number of segregating sites in geneticalmodels without recombination. Theor Popul Biol 7:256–276CrossRefPubMedGoogle Scholar
  34. Wei H, Fu Y, Arora R (2005) Intron-flanking EST–PCR markers: from genetic marker development to gene structure analysis in Rhododendron. Theor Appl Genet 111:1347–1356CrossRefPubMedGoogle Scholar
  35. Williams CE, St Clair DA (1993) Phenetic relationships and levels of variability detected by restriction fragment length polymorphism and random amplified polymorphic DNA analysis of cultivated and wild accessions of Lycopersicon esculentum. Genome 36:619–630CrossRefPubMedGoogle Scholar
  36. Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD (2006) Combining bioinformatics and phylogenetics to identify large sets of single copy, orthologous genes (COSII) for comparative, evolutionary and systematics studies: a test case in the Euasterid plant clade. Genetics 174:1407–1420CrossRefPubMedGoogle Scholar
  37. Yamamoto N, Tsugane T, Watanabe M, Yano K, Maeda F, Kuwata C, Torki M, Ban Y, Nishimura S, Shibata D (2005) Expressed sequence tags from the laboratory-grown miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom and mining for single nucleotide polymorphisms and insertions/deletions in tomato cultivars. Gene 356:127–134CrossRefPubMedGoogle Scholar
  38. Yang W, Bai X, Kabelka E, Eaton C, Kamoun S, van der Knaap E, Francis D (2004) Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags. Mol Breed 14:21–34CrossRefGoogle Scholar
  39. Yang W, Miller SA, Scott JW, Jones JB, Francis DM (2005) Mining tomato genome sequence databases for molecular markers: application to bacterial resistance and marker assisted selection. Acta Hortic 695:241–250Google Scholar
  40. Yang L, Jin GL, Zhao XQ, Zheng Y, Xu ZH, Wu WR (2007) PIP: a database of potential intron polymorphism markers. Bioinformatics 23:2174–2177CrossRefPubMedGoogle Scholar
  41. Yuan DJ, Chen J, Shen HL, Yang WC (2008) Genetics of flesh color and nucleotide sequence analysis of phytoene synthase gene 1 in a yellow-fruited tomato accession PI114490. Sci Hortic 118:20–24CrossRefGoogle Scholar
  42. Zhao XQ, Wu WR (2008) Construction of a genetic map based on ILP markers in rice. Hereditas (Beijing) 30(2):225–230CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Yuanyuan Wang
    • 1
  • Jia Chen
    • 1
  • David M. Francis
    • 2
  • Huolin Shen
    • 1
  • Tingting Wu
    • 1
  • Wencai Yang
    • 1
  1. 1.Department of Vegetable Science, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
  2. 2.Department of Horticulture and Crop ScienceThe Ohio State University/OARDCWoosterUSA

Personalised recommendations