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

Abstract

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