Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola

The downy mildew disease caused by the oomycete Plasmopara viticola is a
serious threat for grapevine and can cause enormous yield losses in viticulture.
The quantitative trait locus Rpv12, mediating resistance against P. viticola, was
originally found in Asian Vitis amurensis. This locus and its genes were analyzed
here in detail. A haplotype-separated genome sequence of the diploid Rpv12-
carrier Gf.99-03 was created and annotated. The defense response against P.
viticola was investigated in an infection time-course RNA-seq experiment,
revealing approximately 600 upregulated Vitis genes during host–pathogen
interaction. The Rpv12 regions of the resistance and the sensitivity encoding
Gf.99-03 haplotype were structurally and functionally compared with each
other. Two different clusters of resistance-related genes were identified within
the Rpv12 locus. One cluster carries a set of four differentially expressed genes
with three ACCELERATED CELL DEATH 6-like genes. The other cluster carries a
set of six resistance gene analogs related to qualitative pathogen resistance. The
Rpv12 locus and its candidate genes for P. viticola resistance provide a precious
genetic resource for P. viticola resistance breeding. Newly developed cosegregating
simple sequence repeat markers in close proximity to the R-genes
enable its improved applicability in marker-assisted grapevine breeding.