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Background  The vigour and precocity of trees highly influences their efficiency in commercial production. In apple, dwarfing rootstocks allow high-density plantings while their precocious flowering enables earlier fruit production. Currently, there is a lack of pear ( Pyrus communis  L.) rootstocks that are equivalent to the high yielding apple rootstock ‘M9’. For the efficient breeding of new  Pyrus  rootstocks it is crucial to understand the genetic determinants of vigour control and precocity. In this study we used quantitative trait loci (QTLs) analysis to identify genetic loci associated with the desired traits, using a segregating population of 405 F1  P. communis  seedlings from a cross between ‘Old Home’ and ‘Louise Bonne de Jersey’ (OHxLBJ). The seedlings were grafted as rootstocks with ‘Doyenne du Comice’ scions and comprehensively phenotyped over four growing seasons for traits related to tree architecture and flowering, in order to describe the growth of the scions.    Results  A high density single nucleotide polymorphism (SNP)-based genetic map comprising 597 polymorphic pear and 113 apple markers enabled the detection of QTLs influencing expression of scion vigour and precocity located on linkage groups (LG)5 and LG6 of ‘Old Home’. The LG5 QTL maps to a position that is syntenic to the apple ‘Malling 9’ (‘M9’)  Dw1  locus at the upper end of LG5. An allele of a simple sequence repeat (SSR) associated with apple  Dw1  segregated with dwarfing and precocity in pear and was identified in other pear germplasm accessions. The orthology of the vigour-controlling LG5 QTL between apple and pear raises the possibility that the dwarfing locus  Dw1  arose before the divergence of apple and pear, and might therefore be present in other Rosaceae species.    Conclusion  We report the first QTLs associated with vigour control and flowering traits in pear rootstocks. Orthologous loci were found to control scion growth and precocity in apple and pear rootstocks. The application of our results may assist in the breeding process of a pear rootstock that confers both vigour control and precocity to the grafted scion cultivar.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-015-0620-4) contains supplementary material, which is available to authorized users.

Genetic control of pear rootstock-induced dwarfing and precocity is linked to a chromosomal region syntenic to the apple Dw1 loci