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

Bianca Frommer; Sophia Müllner; Daniela Holtgräwe; Prisca Viehöver; Bruno Huettel; Reinhard Töpfer; Bernd Weisshaar; Eva Zyprian

doi:10.3389/fpls.2023.1180982

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

Front Plant Sci. 2023 May 8:14:1180982. doi: 10.3389/fpls.2023.1180982. eCollection 2023.

Authors

Bianca Frommer^{1

2}, Sophia Müllner³, Daniela Holtgräwe¹, Prisca Viehöver¹, Bruno Huettel⁴, Reinhard Töpfer³, Bernd Weisshaar¹, Eva Zyprian³

Affiliations

¹ Genetics and Genomics of Plants, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
² Computational Biology, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
³ Institute for Grapevine Breeding Geilweilerhof, Julius Kühn-Institute, Siebeldingen, Germany.
⁴ Max Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany.

Abstract

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 co-segregating simple sequence repeat markers in close proximity to the R-genes enable its improved applicability in marker-assisted grapevine breeding.

Keywords: QTL; Vitis spec.; fully-phased genome assembly; plant defense; resistance genes; time course infection experiment; trio binning.

Grants and funding

This work was funded by the European INTERREG V Upper Rhine Program (“Vitifutur”) and the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG Zy11/11-1). This work was supported by the BMBF-funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI).