Abstract The phylloxera resistant rootstock cultivar ‘Börner’ is an interspecific hybrid derived from Vitis riparia and V. cinerea and a valuable resource for Vitis disease resistances. We created a fully phased, high-quality ‘Börner’ genome sequence named BoeRC using long PacBio reads. Comprehensive gene annotation of both ‘Börner’ haplotypes, designated BoeRip and BoeCin, was applied to describe the phylloxera resistance locus Rdv1 . Using a mapping population derived from a susceptible V. vinifera breeding line and ‘Börner’, the Rdv1 locus was further delimited. Rdv1 , which is derived from V. cinerea and included in the haplotype BoeCin, was compared with sequences of phylloxera-susceptible and phylloxera-tolerant cultivars. Between flanking regions that display high synteny, we detected and precisely characterized a diverse sequence region that covers between 202 to 403 kbp in different haplotypes. In BoeCin, five putative disease resistance genes were identified that represent likely candidates for conferring resistance to phylloxera.

A fully phased interspecific grapevine rootstock genome sequence representingV. ripariaandV. cinereaand allele-aware annotation of the phylloxera resistance locusRdv1