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Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats

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Abstract

Molecular markers based on retrotransposon insertions are widely used for various applications including phylogenetic analysis. Multiple cases were described where retrotransposon-based markers, namely sequence-specific amplification polymorphism (SSAP), were superior to other marker types in resolving the phylogenetic relationships due to their higher variability and informativeness. However, the patterns of evolutionary relationships revealed by SSAP may be dependent on the underlying retrotransposon activity in different periods of time. Hence, the proper choice of retrotransposon family is essential for obtaining significant results. We compared the phylogenetic trees for a diverse set of diploid A-genome wheat species (Triticum boeoticum, T. urartu and T. monococcum) based on two unrelated retrotransposon families, BARE-1 and Jeli. BARE-1 belongs to Copia class and has a uniform distribution between common wheat (T. aestivum) genomes of different origin (A, B and D), indicating similar activity in the respective diploid genome donors. Gypsy-class family Jeli was found by us to be an A-genome retrotransposon with >70% copies residing in A genome of hexaploid common wheat, suggesting a burst of transposition in the history of A-genome progenitors. The results indicate that a higher Jeli transpositional activity was associated with T. urartu versus T. boeoticum speciation, while BARE-1 produced more polymorphic insertions during subsequent intraspecific diversification; as an outcome, each retrotransposon provides more informative markers at the corresponding level of phylogenetic relationships. We conclude that multiple retroelement families should be analyzed for an image of evolutionary relationships to be solid and comprehensive.

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Acknowledgments

The authors are grateful to Drs. O.P. Mitrofanova and O.A. Lyapunova (Vavilov Institute of Plant Industry, St. Petersburg, Russia), Dr. H. Bockelman (the National Small Grains Collection, Aberdeen, USA), Dr. T. Kawahara (Graduate School of Agriculture of Kyoto University, Kyoto, Japan), Dr. J. Valkoun (ICARDA, Aleppo, Syria) for providing the seed material used in the study. We would like to thank Dr. Elena Khlestkina (Institute of Cytology and Genetics of SB RAS, Novosibirsk, Russia) for providing DNA of common wheat cv. Chinese Spring aneuploid lines, and Dr. Ekaterina Badaeva (Vavilov Institute of General Genetics, Moscow, Russia) for helpful discussions. The work was supported by the subprogram “Gene Pools and Genetic Diversity” of the program “Biodiversity” of Russian Academy of Sciences, by a Young Scientist Support grant from Russian Academy of Sciences (F.K.) and by state contract no. 02.740.11.0281 from the Russian government.

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The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Vavilov Institute of General Genetics (VIGG RAS), GSP-1, Gubkina 3, Moscow, 119991, Russia

    Fedor A. Konovalov, Svetlana Goryunova, Aleksandra Shaturova, Tatyana Proshlyakova & Alexander Kudryavtsev

  2. Institute of Cytology and Genetics, Novosibirsk, Russia

    Nikolay P. Goncharov

  3. Moscow State University, Moscow, Russia

    Aleksandra Shaturova & Tatyana Proshlyakova

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  1. Fedor A. Konovalov
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  2. Nikolay P. Goncharov
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  3. Svetlana Goryunova
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  5. Tatyana Proshlyakova
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  6. Alexander Kudryavtsev
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Correspondence to Fedor A. Konovalov.

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Communicated by M.-A. Grandbastien.

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Konovalov, F.A., Goncharov, N.P., Goryunova, S. et al. Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats. Mol Genet Genomics 283, 551–563 (2010). https://doi.org/10.1007/s00438-010-0539-2

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