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Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques

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Abstract

The Sequence-Specific Amplification Polymorphism (S-SAP) method, and the related molecular marker techniques IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism), are based on retrotransposon activity, and are increasingly widely used. However, there have been no systematic analyses of the parameters of these methods or of the utility of different retrotransposon families in producing polymorphic, scorable fingerprints. We have generated S-SAP, IRAP, and REMAP data for three barley ( Hordeum vulgare L.) varieties using primers based on sequences from six retrotransposon families ( BARE -1, BAGY-1, BAGY-2, Sabrina, Nikita and Sukkula). The effect of the number of selective bases on the S-SAP profiles has been examined and the profiles obtained with eight MseI+3 selective primers compared for all the elements. Polymorphisms detected in the insertion pattern of all the families show that each can be used for S-SAP. The uniqueness of each transposition event and differences in the historic activity of each family suggest that the use of multiple retrotransposon families for genetic analysis will find applications in mapping, fingerprinting, and marker-assisted selection and evolutionary studies, not only in barley and other Hordeum species and related taxa, but also more generally.

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Acknowledgements

This work was funded by the European Union FP5 initiative projects QLRT-1999-PL1499 and QLK5-CT-2000-01502. DNA was kindly provided by Keygene NV (Wageningen, The Netherlands). The authors wish to thank the two anonymous referees and the Communicating Editor for helpful comments on the manuscript

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Correspondence to A. H. Schulman.

Additional information

Communicated by M.-A. Grandbastien

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Leigh, F., Kalendar, R., Lea, V. et al. Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques. Mol Gen Genomics 269, 464–474 (2003). https://doi.org/10.1007/s00438-003-0850-2

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Keywords

  • Barley DNA fingerprinting
  • Inter-retrotransposon amplified polymorphism (IRAP)
  • Retrotransposon-microsatellite amplified polymorphism (REMAP)
  • Retrotransposon insertional polymorphism
  • Sequence-specific amplified polymorphism (S-SAP) markers