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Transcriptome versus Genomic Microsatellite Markers: Highly Informative Multiplexes for Genotyping Abies alba Mill. and Congeneric Species

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Abstract

The availability of high-resolution, cost-effective polymorphic genetic markers displaying Mendelian inheritance is a prerequisite for fine-scale population genetic analyses as well as informed conservation and sustainable management. Silver fir (Abies alba Mill.) is a widespread European species of economic and ecological importance for which genetic markers are needed but difficult to develop, as in most conifer species. In this work, we introduce two sets of new multiplexed transcriptome-derived expressed sequence tag microsatellites (EST-simple sequence repeats (SSRs)) which we compare to a set of multiplexed genomic microsatellites (gSSRs). For both marker types, transferability was tested in 17 congeneric taxa. A total of 16 new EST-SSRs and two new gSSRs were developed. The EST-SSR multiplexes produced easily scorable amplification patterns that allow rapid and cost-effective genotyping at low-error rates, and include loci that display very low null allele frequencies. Generally, EST-SSRs displayed lower polymorphism and frequency of null alleles, but higher genetic differentiation among populations than gSSRs. Preliminary tests revealed that the EST-SSR markers are highly transferable and polymorphic across Abies species. This study also confirmed that SSRs can be successfully developed using next-generation sequencing technology also in large genome species such as conifers.

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Acknowledgments

This study was financed by the Italian MIUR project “Biodiversitaly” (RBAP10A2T4) and by the ERA-Net BiodivERsA LinkTree project (EUI2008-03713). We thank Dr. Popescu Flaviu, Daniel Pitar, Ovidiu Iordan and Daniel Suciu (Forest Research and Management Institute, Romania) and Prof. Peter Zhelev (University of Forestry, Sofia, Bulgaria) for their help with the sampling in the Romanian Carpathians and in the Pirin Mountains.

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Authors and Affiliations

  1. Scuola Superiore Sant’Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy

    Dragos Postolache

  2. Plant Genetics Institute, National Research Council (CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino (Firenze), Italy

    Dragos Postolache, Andrea Piotti, Ilaria Spanu & Giovanni Giuseppe Vendramin

  3. Department of Biosciences, University of Parma, Viale Usberti 11/A, 43124, Parma, Italy

    Cristina Leonarduzzi & Andrea Piotti

  4. INRA, UR629 Ecologie des Forêts Méditerranéennes (URFM), 84914, Avignon, France

    Anne Roig & Bruno Fady

  5. Faculty of Biology, Conservation Biology, University of Marburg, Karl-von-Frisch-Strasse, 35032, Marburg, Germany

    Anna Roschanski & Sascha Liepelt

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  1. Dragos Postolache
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  2. Cristina Leonarduzzi
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  3. Andrea Piotti
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  4. Ilaria Spanu
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  5. Anne Roig
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  6. Bruno Fady
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  7. Anna Roschanski
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  8. Sascha Liepelt
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  9. Giovanni Giuseppe Vendramin
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Correspondence to Giovanni Giuseppe Vendramin.

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Dragos Postolache and Cristina Leonarduzzi contributed to this study equally.

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Postolache, D., Leonarduzzi, C., Piotti, A. et al. Transcriptome versus Genomic Microsatellite Markers: Highly Informative Multiplexes for Genotyping Abies alba Mill. and Congeneric Species. Plant Mol Biol Rep 32, 750–760 (2014). https://doi.org/10.1007/s11105-013-0688-7

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