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Background  Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian  Populus  species. However, there is also the need for high-density genetic linkage maps for the European aspen ( P. tremula ) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the  Populus  species native to Europe.    Results  We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits. We performed RADseq of 122 F1 progenies and two parents yielding 15,732 high-quality SNPs that were successfully identified using the reference genome of  P. trichocarpa . 2055 SNPs were employed for the construction of maternal and paternal linkage maps. The maternal linkage map was assembled with 1000 SNPs, containing 19 linkage groups and spanning 3054.9 cM of the genome, with an average distance of 3.05 cM between adjacent markers. The paternal map consisted of 1055 SNPs and the same number of linkage groups with a total length of 3090.56 cM and average interval distance of 2.93 cM. The linkage maps were employed for QTL mapping of one-year-old seedlings height variation. The most significant QTL (LOD = 5.73) was localized to LG5 (96.94 cM) of the male linkage map, explaining 18% of the phenotypic variation.    Conclusions  The set of 15,732 SNPs polymorphic in aspen and high-density genetic linkage maps constructed for the  P. tremula  intra-specific cross will provide a valuable source for QTL mapping and identification of candidate genes facilitating marker-assisted selection in European aspen.    Electronic supplementary material  The online version of this article (10.1186/s12870-017-1127-y) contains supplementary material, which is available to authorized users.

Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology