Differentiation of Populus species by chloroplast SNP markers for barcoding and breeding approaches

doi:10.3832/ifor1326-007

About 30 species within the genus Populus are classified in six sections. Several species belonging to different sections are cross-compatible, resulting in a high number of naturally occurring interspecies hybrids. Additionally, an even higher number of hybrids has been produced in huge breeding programs during the last 100 years. Hence, determination of poplar species used for production of “multi-species-hybrids” is often difficult and, therefore, a challenge in developing molecular markers for species identification. Fourteen out of the 30 poplar species known are used more or less regularly for production of artificial hybrids and clones. In this study, we focused on over 20 chloroplast regions, and we tested 23 primer combinations already established for “Barcoding” approaches and seventeen new primer combinations designed earlier for the applicability to differentiate fourteen poplar species. In contrast to the self-designed primer combinations with a much higher amplification success, only about half of the established barcoding primer combinations yielded amplification products. In total, for eleven of the fourteen used poplar species we found species-specific SNPs or Indels. Most of the variation was found in intergenic spacers. In order to design an inexpensive and fast method of species identification, we developed PCR-RFLPs applicable for seven of the species-specific SNPs. Altogether there is high variation in chloroplast intergenic spacers within the genus Populus, illustrated by the fact that four primer combinations are needed to differentiate eleven species. Thus, we support the suggestion of using multi-locus combinations in barcoding analyses.

Keywords

Chloroplast Genome, SNPs, Indel, Barcoding, Intergenic Spacer

Authors’ address

(1)

Thünen Institute of Forest Genetics, Sieker Landstrasse 2, D-22927 Grosshansdorf (Germany)

Corresponding author

Hilke Schroeder
hilke.schroeder@ti.bund.de

Citation

Schroeder H, Fladung M (2014). Differentiation of Populus species by chloroplast SNP markers for barcoding and breeding approaches. iForest 8: 544-546. - doi: 10.3832/ifor1326-007

Academic Editor

Elena Paoletti

Paper history

Received: Apr 28, 2014
Accepted: Sep 16, 2014

First online: Nov 13, 2014
Publication Date: Aug 02, 2015
Publication Time: 1.93 months

Open Access

This article is distributed under the terms of the Creative Commons Attribution-Non Commercial 4.0 International (https://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

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