iForest - Biogeosciences and Forestry


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

Hilke Schroeder   , Matthias Fladung

iForest - Biogeosciences and Forestry, Volume 8, Issue 4, Pages 544-546 (2014)
doi: https://doi.org/10.3832/ifor1326-007
Published: Nov 13, 2014 - Copyright © 2014 SISEF

Short Communications

Collection/Special Issue: COST Action FP0905
Biosafety of forest transgenic trees and EU policy directives
Guest Editors: Cristina Vettori, Matthias Fladung

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.


Chloroplast Genome, SNPs, Indel, Barcoding, Intergenic Spacer

Authors’ address

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

Corresponding author

Hilke Schroeder


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

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Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, Haidar N, Savolainen V (2005)
Land plants and DNA barcodes: short-term and long-term goals. Philosophical Transaction of the Royal Society of London Series B Biological Science 360: 1889-1895.
CrossRef | Gscholar
Dickman DI, Stuart K (1983)
The culture of poplars in Eastern North America. Department of Forestry, Michigan State University, East Lansing, MC, USA, pp. 168.
Dumolin S, Demesure B, Petit RJ (1995)
Inheritance of chloroplast and mitochondrial genomes in pedunculate oak investigated with an efficient PCR method. Theoretical and Applied Genetics 91: 1253-1256.
CrossRef | Gscholar
Hoenicka H, Fladung M (2006)
Biosafety in Populus spp. and other forest trees: from non-native species to taxa derived from traditional breeding and genetic engineering. Trees 20: 131-144.
CrossRef | Gscholar
Hollingsworth ML, Clark AA, Forrest LL, Richardson J, Pennington RT, Long DG, Cowan R, Chase MW, Gaudeul M, Hollingsworth PM (2009)
Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants. Molecular Ecology Resources 9: 439-457.
CrossRef | Gscholar
Kress WJ, Erickson DL (2008)
DNA barcodes: genes, genomics, and bioinformatics. Proceedings of the National Academy of Science USA 105 (8): 2761-2762.
CrossRef | Gscholar
Little DP, Stevenson DW (2007)
A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms. Cladistics 23: 1-21.
CrossRef | Gscholar
Sass C, Little DP, Stevenson DW, Specht CD (2007)
DNA barcoding in the Cycadales: testing the potential of proposed barcoding markers for species identification of cycads. PLoS ONE 2 (11): e1154.
CrossRef | Gscholar
Schroeder H, Fladung M (2010)
SSR and SNP markers for the identification of clones, hybrids and species within the genus Populus. Silvae Genetica 59 (6): 257-263.
Online | Gscholar
Schroeder H, Höltken AM, Fladung M (2011)
Chloroplast SNP-marker as powerful tool for differentiation of Populus species in reliable poplar breeding and barcoding approaches. BMC Proceedings 5 (Suppl 7): P56.
CrossRef | Gscholar
Schroeder H, Höltken AM, Fladung M (2012)
Differentiation of Populus species using chloroplast SNP-markers - essential for comprehensible and reliable poplar breeding. Plant Biology 14: 374-381.
CrossRef | Gscholar
Stettler R, Bradshaw T, Heilman P, Hinckley T (1996)
Biology of Populus and its implications for management and conservation. NRC Research Press. Montreal, Canada, pp. 542.
Tuskan GA, DiFazio S, Jansson S, Bohlmann J, et al. (2006)
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.
CrossRef | Gscholar
Walter C, Fladung M, Boerjan W (2010)
The 20-year environmental safety record of GM trees. Nature Biotechnology 28 (7): 656-658.
CrossRef | Gscholar

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