Functional dissection of grapevine resistance loci against Plasmopara viticola (Rpv) using a comparative multi-omics approach

Abstract

Grapevine resistance breeding relies on a limited number of major resistance loci (Rpv) to control Plasmopara viticola. Although previous findings suggest locus-specific resistance patterns, we currently lack comparative multi-omics data conducted within a uniform, genetic background and standardized laboratory conditions.

In this work, we analysed the resistance conferred by Rpv1, Rpv3.1 and Rpv10 in a dedicated biparental population, using a single pathogen strain and standardized infection conditions. By integrating transcriptomic analyses across several early infection time points with metabolomics, we characterized the temporal dynamics of the defence responses deployed by each locus.

Before 1 day post inoculation (dpi), a small core of common infection-responsive genes was identified, although most transcriptional changes differed between Rpv backgrounds. Indeed, the three loci exhibited distinct gene expression patterns and temporal dynamics, indicating that Rpv-mediated resistance is not controlled by a single common programme but instead reflects locus-specific regulatory strategies. At the metabolic level, significant changes associated with the Rpv responses emerged after 1 dpi in terms of the time and amplitude of compound accumulation. However, many grapevine-associated resistance metabolites were common to all three Rpv loci, whereas some changes were shared by only two loci or were locus-specific.

In conclusion, our results show that major Rpv loci differ not only in resistance level but also in the regulatory mechanisms underlying the temporal evolution of resistance responses. This comparative multi-omics approach improves our functional understanding of grapevine responses to P. viticola and supports breeding strategies aimed at combining loci to achieve effective and durable resistance.