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Molecular characterization of Fagaceae species using inter-primer binding site (iPBS) markers

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Abstract

Retrotransposons (RTNs) contribute for genome evolution, influencing its size and structure. We investigated the utility of the RTN-based markers inter-primer binding site (iPBS) for the molecular characterization of 25 Fagaceae species from genera Castanea, Fagus and Quercus. The assessment of genetic diversity, relationships and structure, as well as taxonomic classification of Fagaceae based on molecular data is important for definition of conservation, forestry management strategies and discrimination among natural hybrids and their parents since natural hybridization may increase with the climate changes. Here, iPBS primers designed by other authors were tested alone and combined. Some of them were discriminative, revealed polymorphism within and among taxa allowing the production of a total of 150 iPBS markers. In addition, several monomorphic iPBS markers were also amplified in each taxon. The UPGMA dendrogram based on the pooled iPBS data revealed 27% of genetic similarity among species. The individuals were clustered per genus and most of the oaks per infrageneric group corroborating the adopted taxonomy. Globally, the iPBS markers demonstrated suitability for DNA fingerprinting, determination of phylogenies and taxonomic discrimination in Fagaceae, and could constitute a useful and alternative tool for germplasm characterization, and for definition of conservation strategies and forestry management. Moreover, these markers would be useful for fingerprinting natural hybrids that share morphological similarities with their parents. Since iPBS markers could also enable insights about RTNs evolution, an eventual correlation among iPBS polymorphism, variability of RTN insertions and/or genome size in Fagaceae is discussed.

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Acknowledgements

The author João Coutinho acknowledges to the “Fundação para a Ciência e a Tecnologia” (FCT) for his Ph.D. grant SFRH/BD/42837/2008, co-financed by the “Fundo Social Europeu” (FSE) under the “Programa Operacional Potencial Humano” (POPH)—“Quadro de Referência Estratégico Nacional 2007–2013” (QREN). The authors thank the botanical gardens that kindly provided the seeds used in this work.

Funding

The “Fundação para a Ciência e a Tecnologia” (FCT) attributed to the author João Coutinho the Ph.D. grant SFRH/BD/42837/2008, co-financed by the “Fundo Social Europeu” (FSE) under the “Programa Operacional Potencial Humano” (POPH)—“Quadro de Referência Estratégico Nacional 2007–2013” (QREN).

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Authors and Affiliations

  1. BioISI – Biosystems & Integrative Sciences Institute, University of Tras-os-Montes and Alto Douro (BioISI-UTAD), Quinta de Prados, 5000-801, Vila Real, Portugal

    João Paulo Coutinho, Ana Carvalho & José Lima-Brito

  2. CSIC – Consejo Superior de Investigaciones Científicas, Alameda del Obispo, 4084, 14080, Córdoba, Spain

    Antonio Martín

  3. Department of Genetics and Biotechnology, University of Tras-os-Montes and Alto Douro, 5001-801, Vila Real, Portugal

    José Lima-Brito

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  1. João Paulo Coutinho
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Correspondence to José Lima-Brito.

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Coutinho, J.P., Carvalho, A., Martín, A. et al. Molecular characterization of Fagaceae species using inter-primer binding site (iPBS) markers. Mol Biol Rep 45, 133–142 (2018). https://doi.org/10.1007/s11033-018-4146-3

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