Genomic analysis of the phylloxera resistance locus Rdv1 of the rootstock variety ‘Börner’

Abstract

Resistance to phylloxera (Daktulosphaira vitifoliae) is the most important trait in grapevine rootstock breeding. Up to now, there are eight quantitative trait loci (QTL) described mediating resistance on roots or leaves. In order to understand the genetic basis of one of these genetic loci, the genome of the resistance donor ‘Börner’ was sequenced and the genomic region of the Rdv1 locus analyzed.

A biparental basic population of Vitis vinifera 𝑥 ‘Börner’ (V. riparia 𝑥 V. cinerea) was used to genetically map the resistance to phylloxera (absence of nodosities on roots). Molecular markers were developed to screen the extended population for recombinants followed by a phenotypic resistance test. PacBio long reads and Illumina short reads were generated and used to assemble a haplotype-separated genome sequence. Gene models were predicted and functionally annotated with a focus on resistance gene analogs (RGAs). Simple sequence repeat marker and skim sequencing were applied to determine recombination sites.

The genome sequence of ‘Börner’ was assembled and two separated haplophases were obtained. Based on the resistant phase derived from V. cinerea, the Rdv1 locus could be limited to a size of less than 300 kb. The center of the Rdv1 locus shows a clear deviating synteny and repetitive sequence structures compared to the second phase from V. riparia and the PN40024 reference. Among the annotated genes within this locus, a cluster with several putative RGAs was identified. Since RGAs are known to confer resistance to other pests and diseases, they represent candidate genes for the phylloxera resistance of ‘Börner’.