Plant Molecular Biology Reporter

, Volume 32, Issue 3, pp 750–760

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

Authors

  • Dragos Postolache
    • Scuola Superiore Sant’Anna
    • Plant Genetics InstituteNational Research Council (CNR)
  • Cristina Leonarduzzi
    • Department of BiosciencesUniversity of Parma
  • Andrea Piotti
    • Plant Genetics InstituteNational Research Council (CNR)
    • Department of BiosciencesUniversity of Parma
  • Ilaria Spanu
    • Plant Genetics InstituteNational Research Council (CNR)
  • Anne Roig
    • INRA, UR629 Ecologie des Forêts Méditerranéennes (URFM)
  • Bruno Fady
    • INRA, UR629 Ecologie des Forêts Méditerranéennes (URFM)
  • Anna Roschanski
    • Faculty of Biology, Conservation BiologyUniversity of Marburg
  • Sascha Liepelt
    • Faculty of Biology, Conservation BiologyUniversity of Marburg
    • Plant Genetics InstituteNational Research Council (CNR)
Original Paper

DOI: 10.1007/s11105-013-0688-7

Cite this article as:
Postolache, D., Leonarduzzi, C., Piotti, A. et al. Plant Mol Biol Rep (2014) 32: 750. doi:10.1007/s11105-013-0688-7

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.

Keywords

EST-SSRs Genomic SSRs Multiplex PCR Diversity Silver fir

Supplementary material

11105_2013_688_MOESM1_ESM.doc (54 kb)
Table S1 (DOC 54 kb)

Copyright information

© Springer Science+Business Media New York 2013