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Retrotransposon molecular markers resolve cocoyam (Xanthosoma sagittifolium) and taro (Colocasia esculenta) by type and variety

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Abstract

Retrotransposon-based molecular markers were applied for the first time within the genera Xanthosoma and Colocasia to assess intraspecific variability among 27 accessions of cocoyam (Xanthosoma sagittifolium) and taro (Colocasia esulenta). Retrotransposons were isolated and sequenced; long terminal repeat (LTR) primers were designed to obtain inter-retrotransposon amplified polymorphism (IRAP) fingerprints. A set of six chosen LTR primers yielded 433 reproducible bands across 20 X. sagittifolium samples. Out of the 433 bands, 400 fragments (92 %) were polymorphic. In seven C. esculenta accessions, the six primers amplified a total of 354 reproducible, informative data points, of which 285 (80.5 %) were polymorphic. Cluster analysis placed all the accessions in two groups according to their species. The accessions of X. sagittifolium were further divided into two subgroups corresponding to their ploidy level. Moreover, the genetic variability accessed by IRAP markers allowed separation of X. sagittifolium and C. esculenta accessions according to their type and botanical variety respectively. The results suggest that retrotransposon activity continued after Xanthosoma speciation. The data and approach provides a basis for better germplasm management, future systematic studies and genetic improvement, as well as for exploration of the role of retrotransposons in cocoyam and taro polyploid formation and genome dynamics.

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Abbreviations

IRAP:

Inter-retrotransposon amplified polymorphism

TEs:

Transposable elements

LTR:

Long terminal repeat

PBS:

Primer-binding site

CRRD:

Cocoyam root rot disease

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Acknowledgments

Anne-Mari Narvanto and Ursula Lönnqvist are thanked for their valuable technical assistance. D.O. was supported by an 8 month-mobility fellowship (Decision TM-09-6259) and a travel grant issued by the Finnish Centre for International Mobility (CIMO) and the Kirkhouse Trust respectively. R.K. was supported by a grant from the Academy of Finland (Decision 134079).

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Authors and Affiliations

  1. Jay P. Johnson Biotechnology Laboratory, IRAD Ekona Regional Research Centre, PMB 25, Buea, Cameroon

    Oumar Doungous & Amayana Adiobo

  2. LUKE/BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P.O. Box 65, 00014, Helsinki, Finland

    Ruslan Kalendar & Alan H. Schulman

  3. Green Technology, Luke Natural Resources Institute Finland, Viikinkaari 4, 00790, Helsinki, Finland

    Alan H. Schulman

Authors
  1. Oumar Doungous
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  2. Ruslan Kalendar
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  3. Amayana Adiobo
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  4. Alan H. Schulman
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Correspondence to Alan H. Schulman.

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The authors declare that they have no conflicts of interest. The experiments comply with the current laws of the countries in which they were performed.

Additional information

Data deposition The sequences reported here have been deposited in the GenBank database (accession nos.GU810535, KF813039–KF813057).

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Doungous, O., Kalendar, R., Adiobo, A. et al. Retrotransposon molecular markers resolve cocoyam (Xanthosoma sagittifolium) and taro (Colocasia esculenta) by type and variety. Euphytica 206, 541–554 (2015). https://doi.org/10.1007/s10681-015-1537-6

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