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Background  Genomic analysis technologies can promote efficient fruit tree breeding. Genotyping by sequencing (GBS) enables generating efficient data for high-quality genetic map construction and QTL analysis in a relatively accessible way. Furthermore, High-resolution genetic map construction and accurate QTL detection can significantly narrow down the putative candidate genes associated with important plant traits.    Results  We genotyped 162 offspring in the F1 ‘Spadona’ x ‘Harrow Sweet’ pear population using GBS. An additional 21 pear accessions, including the F1 population’s parents, from our germplasm collection were subjected to GBS to examine diverse genetic backgrounds that are associated to agriculturally relevant traits and to enhance the power of SNP calling. A standard SNP calling pipeline identified 206,971 SNPs with Asian pear (‘Suli’) as the reference genome and 148,622 SNPs with the European genome (‘Bartlett’). These results enabled constructing a genetic map, after further stringent SNP filtering, consisting of 2036 markers on 17 linkage groups with a length of 1433 cM and an average marker interval of 0.7 cM. We aligned 1030 scaffolds covering a total size of 165.5 Mbp (29%) of the European pear genome to the 17 linkage groups. For high-resolution QTL analysis covering the whole genome, we used phenotyping for vegetative budbreak time in the F1 population. New QTLs associated to vegetative budbreak time were detected on linkage groups 5, 13 and 15. A major QTL on linkage group 8 and an additional QTL on linkage group 9 were confirmed. Due to the significant genotype-by-environment (GxE) effect, we were able to identify novel interaction QTLs on linkage groups 5, 8, 9 and 17. Phenotype–genotype association analysis in the pear accessions for main genotype effect was conducted to support the QTLs detected in the F1 population. Significant markers were detected on every linkage group to which main genotype effect QTLs were mapped.    Conclusions  This is the first vegetative budbreak study of European pear that makes use of high-resolution genetic mapping. These results provide tools for marker-assisted selection and accurate QTL analysis in pear, and specifically at vegetative budbreak, considering the significant GxE and phenotype-plasticity effects.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1386-2) contains supplementary material, which is available to authorized users.

High-resolution genetic linkage map of European pear (Pyrus communis) and QTL fine-mapping of vegetative budbreak time