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


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.


Bacterial Artificial Chromosome Intron Position Tomato Line Intron Polymorphism Tomato Genomic Sequence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors thank the Tomato Genetic Resource Center at the University of California Davis (California, USA) for providing seeds of some tomato lines. We also thank Dr. David B. Weaver from Auburn University for his critical review on the manuscript. The work was supported by National Natural Science Foundation of China (30671425) and the Program for New Century Excellent Talents in University (NCET-08-0531).

Supplementary material

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


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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

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