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Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR

Abstract

The retrotransposon-based sequence-specific amplification polymorphism (SSAP) marker system was used to assess the genetic diversities of collections of tomato and pepper industrial lines. The utility of SSAP markers was compared to that of amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. On the basis of our results, SSAP is most informative of the three systems for studying genetic diversity in tomato and pepper, with a significant correlation of genetic relationships between different SSAP datasets and between SSAP, AFLP and SSR markers. SSAP showed about four- to ninefold more diversity than AFLP and had the highest number of polymorphic bands per assay ratio and the highest marker index. For tomato, SSAP is more suitable for inferring overall genetic variation and relationships, while SSR has the ability to detect specific genetic relationships. All three marker results for pepper showed general agreement with pepper types. Additionally, retrotransposon sequences isolated from one species can be used in related Solanaceae genera. These results suggest that different marker systems are suited for studying genetic diversity in different contexts depending on the group studied, where discordance between different marker systems can be very informative for understanding genetic relationships within the study group.

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Acknowledgements

We wish to thank Q.H. Le, A. Charcosset, M. Tenaillon, V. Lefebvre, D. Higuet and E. Bonnivard for their useful comments and suggestions. This work was funded by the FW6 EC TEGERM project EC-QLRT-1999-31502.

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Correspondence to Marie-Angèle Grandbastien.

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Communicated by I. Paran

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Tam, S.M., Mhiri, C., Vogelaar, A. et al. Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theor Appl Genet 110, 819–831 (2005). https://doi.org/10.1007/s00122-004-1837-z

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Keywords

  • Amplify Fragment Length Polymorphism
  • Long Terminal Repeat
  • Marker System
  • Bell Pepper
  • Long Terminal Repeat Sequence