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Characterization and comparative analysis of sequence-specific amplified polymorphisms based on two subfamilies of IRRE retrotransposons in Iris missouriensis (Iridaceae)

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Abstract

DNA markers based on transposable-element polymorphisms are potentially useful alternatives to anonymous fragment-length polymorphisms (AFLPs). We developed the retrotransposon sequence-specific amplified polymorphism (retrotransposon SSAP) technique for the angiosperm Iris missouriensis (Iridaceae) in order to evaluate its use in generating population-genetic markers. Our cloning strategy identified two groups of long-terminal repeat retrotransposons of the IRRE family. Primers homologous to conserved regions of these elements generated repeatable and polymorphic markers. In comparison, the AFLP protocol failed to produce useful markers in our hands in this species. To investigate the distribution and evolutionary tempo of the two retrotransposons, we developed a phylogeny of representative species of subgenus Limniris based on chloroplast sequence. Sequences of both groups of retrotransposons were widespread in Limniris, but we also found evidence of substantial sequence and copy-number evolution since the divergence of I. missouriensis from other Limniris species. We corroborated these results with quantitative real-time PCR estimates of relative copy number. Importantly, the geographic structure of retrotransposon SSAP was strikingly different for the two groups of retrotransposons, indicating that different mutational dynamics and/or selective pressures govern their distribution. Although these primers should be useful for population-genetic studies of Iris missouriensis and other Limniris species, our findings reinforce the need for caution in evaluating transposable-element markers used to analyze the relatedness of populations or cultivars, as very different conclusions may be reached depending on the sequence amplified.

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Abbreviations

AFLP:

Amplified fragment-length polymorphism

AMOVA:

Analysis of molecular variance

IMRE1:

An Iris missouriensis IRRE retroelement of undetermined subcategory identified in this study

IRRE:

Family of gypsy-type retrotransposons in Iris

IRRE-SSAP:

Sequence-specific amplified polymorphism using IRRE sequences as targets

LTR:

Long terminal repeat

RFU:

Relative fluorescence units

SSAP:

Sequence-specific amplified polymorphism

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Acknowledgments

We gratefully acknowledge technical advice or assistance from E. Basenko, E. Kentner, M. McEachern, M. Osterlund, D. Tolligan, R. Peeler, and J. Willis. This work was supported by a grant from the American Iris Society (R.S.C.), by National Science Foundation Training Grant DBI 9602223 (R.S.C.), and by National Science Foundation Grant DEB-0345123 (M.L.A.). R.S.C. was also supported by a University of Georgia Presidential Fellowship.

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Authors and Affiliations

  1. Department of Genetics, University of Georgia, Athens, GA, 30602, USA

    R. Scott Cornman & Michael L. Arnold

  2. Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA

    R. Scott Cornman

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  1. R. Scott Cornman
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  2. Michael L. Arnold
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Correspondence to R. Scott Cornman.

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Cornman, R.S., Arnold, M.L. Characterization and comparative analysis of sequence-specific amplified polymorphisms based on two subfamilies of IRRE retrotransposons in Iris missouriensis (Iridaceae). Genetica 135, 25–38 (2009). https://doi.org/10.1007/s10709-008-9248-8

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  • DOI: https://doi.org/10.1007/s10709-008-9248-8

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