Haplotype‐phased ‘Ottawa 3’ genome unravels differential reaction of apple rootstock roots to mixed viral infection

SUMMARY Viral diseases pose a significant threat to global apple ( Malus spp.) production. While selecting appropriate rootstocks is a crucial strategy to mitigate their effects, the underlying mechanisms governing rootstock tolerance or sensitivity to viral infection at the root level remain underexplored. We conducted an aeroponic experiment to analyze the root transcriptome changes of two full‐sibling commercial apple rootstocks, G.890 (Tolerant) and G.935 (Sensitive), after grafting with scions from mixed virus‐infected and virus‐treated trees. To provide a robust genetic framework for this study, we assembled the haplotyped‐phased genome of one of their parents, ‘Ottawa 3’, which is the source of viral sensitivity. Our results revealed distinct root‐level responses to viral infection, with G.935 showing relatively reduced root length and an increased disease index. Transcriptome analysis identified a subtle yet meaningful set of differentially expressed genes within key host defense pathways, with some haplotype‐specific expression. Although G.935 and G.890 rootstocks shared a robust core set of transcriptional responses to viral infection, including general stress response and RNA processing pathways, our analysis revealed significant differences in their responsiveness. While G.935's unique expression profile had broader stress/metabolic changes, G.890, being more tolerant, exhibited a more dynamic reprogramming in targeted antiviral RNA silencing pathways and membrane‐mediated defense. These findings provide valuable insights and key molecular targets for developing future virus‐tolerant apple rootstocks. The newly assembled ‘Ottawa 3’ genome also provides the plant science community with a foundational genomic resource for future apple research.