Genotype-associated transcriptional differences among grapevine lines carrying single and pyramided Rpv resistance loci

Abstract

Downy mildew caused by Plasmopara viticola is a major threat to grapevine production, yet the molecular organization of multilocus resistance remains poorly understood. We generated 36 time-resolved transcriptomes from grapevine genotypes carrying single (Rpv12), double (Rpv12+1), or triple (Rpv12+1+3) resistance loci together with a susceptible control and integrated co-transcriptional network analysis with systematic AlphaFold2-Multimer screening to identify candidate immune receptor complexes. A SOBIR1-associated receptor network emerged as a candidate interaction hub, with seven predicted partners enriched for leucine-rich repeat receptor-like proteins and kinases. Five partner genes showed coordinated transcript upregulation at inoculation (0 hpi) specifically in Rpv12 genotypes, whereas this signature was absent in multilocus backgrounds, suggesting genotype-specific regulatory restructuring rather than additive immune activation. Four of the seven partners were also predicted to interact with a grapevine EIX1 homolog, which itself was predicted to associate with SOBIR1 (ipTM = 0.81), consistent with the established tomato LeEIX-SOBIR1 co-receptor architecture. We additionally identified predicted structurally conserved EDS1-SAG101 candidate complexes despite substantial sequence divergence from Arabidopsis orthologs. Multilocus genotypes displayed distinct temporal transcriptional trajectories and altered co-transcriptional network organization, indicating that resistance stacking reshapes immune regulatory architecture. However, whether these transcriptional differences correspond to enhanced, equivalent, or reduced resistance requires quantitative phenotypic validation. Together, these results provide a structural and transcriptomic framework for investigating immune receptor organization in grapevine and generate testable hypotheses for functional dissection of multilocus resistance.