The epigenetic response of a resistant and a susceptible variety of Vitis vinifera to downy mildew

Abstract

Plant-pathogen interactions can trigger extensive epigenetic modifications in the host genome. These include local changes to DNAmethylation that may mediate host defence responses by altering the expression of key genes involved in disease resistance or susceptibility. This study characterises and compares the epigenetic response of a resistant and a susceptible grapevine variety to Plasmopara viticola infections, with the aim of identifying new candidate genes for resistance breeding.

The experimental designed included two Vitis vinifera varieties, one susceptible (Pinot noir) and one resistant (Mgaloblishvili) to downy mildew. Plants were artificially inoculated with a sporangia suspension of P. viticola (I) or water as a non-inoculated control (NI). Three biological replicas were used per treatment. Disease incidence was scored at 7 days post inoculation (dpi). Genomic DNAwas extracted from I and NI leaves at 12, 24, 48 and 72 hours post inoculation (hpi) and sequenced on a Oxford Nanopore Technologies PromethION, followed by whole-genome methylation analysis. Local and genome-wide epigenetic differences were evaluated in the three methylation contexts: CG, CHG and CHH (where H can be either an A, C or T). Genetic and phenotypic data were also compared.

Phenotypic analysis confirmed Mgaloblishvili’s resistance to downy mildew. At a genome-wide level, the two varieties contrasting methylation profiles at 12 hpi: global CHH methylation increased significantly in Pinot noir following inoculation, whereas in Mgaloblishvili it decreased. Local differentially methylated regions associated with infection will be discussed for 12, 24 and 48 hpi in both varieties.

Overall, this study provides insights into the temporal dynamics of epigenetic responses in grapevine to P. viticola infections. The comparison of a susceptible and a resistant variety, demonstrates epigenetic features associated with different responses to disease infection. It also supports the identification of novel candidate genes for susceptibility and resistance to downy mildew, that may be applied in future grapevine breeding programs.