PCR-based detection of single sequence variants from a natural collection of the non-model tree species European Aspen Populus tremula (L.)

In the present study we present and discuss the identification of species-specific SNPs to rule out any experimental influence of species-specific primer design (Populus tremula vs. the closely related model-species Populus trichocarpa) on the detectability of SNPs. Applying a species-optimized method, partial sequences of 14 genes involved in xylem cell development, xylogenesis, pectin formation, and drought stress reaction were analyzed at the genomic level. About 3 Mb of sequence information were generated by Sanger sequencing technology and 258 sequence variants were identified. 15 out of these represent insertions /deletions located exclusively in non-coding regions and the remaining 243 are SNPs found in coding and non-coding regions of candidate genes.

The introduction of a species-specific SNP detection pipeline will help to detect nucleotide variants in P. tremula and to conduct association mapping in natural P. tremula populations.