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Phased grapevine genome sequence assembly of an Rpv12 carrier for exploration of Rpv12 associated positional and functional Plasmopara viticola resistance genes

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 the Asian Vitis amurensis species. Here, we present a detailed analysis of this locus and its genes. The Rpv12-carrying breeding line Gf.99-03 was long-read sequenced and a high-quality haplotype separated genome sequence assembly including gene annotation was worked out. The defense response against P. viticola was investigated through an infection time-course experiment. Differential gene expression analysis revealed approximately 600 up-regulated genes during infection. The Rpv12 region of both haplotypes of Gf.99-03, one conferring resistance and the other one sensitivity, were structurally and functionally compared to each other as well as to the corresponding alleles of the susceptible grapevine model cultivar PN40024 and revealed great structural differences. Two diverse clusters with important resistance related genes were identified that clearly characterize the Rpv12 resistance locus. One cluster carries a set of four differentially expressed genes with three ACCELERATED CELL DEATH 6 related genes. The other cluster carries a set of six resistance gene analogues for potential qualitative pathogen resistance. Co-segregating simple sequence repeat markers for Rpv12 are located in close proximity to the R-genes. The Rpv12 locus and its candidate genes for P. viticola resistance provide a precious genetic resource for P. viticola resistance breeding. Significance statement The detailed characterization of the Rpv12 locus for P. viticola resistance revealed important candidate resistance genes. As the downy mildew disease caused by P. viticola is one of the major grapevine diseases, these findings are a cornerstone for further P. viticola resistance research and of major impact for breeding of resistant grapevine varieties for more sustainable viticulture.