Grapevine Red Blotch Virus Induces Haplotype-specific Genetic and Epigenetic Responses

Haplotype-resolved genomes provide a powerful framework for uncovering allele-specific regulatory mechanisms obscured in collapsed diploid references. Despite growing evidence of cultivar- and clone-dependent variation in disease severity caused by Grapevine Red Blotch Virus (GRBV), the contribution of haplotype-specific transcriptional and epigenetic regulation to host-virus interactions remains poorly understood. Here, we integrate a haplotype-resolved grapevine genome with time-resolved transcriptomic and whole-genome bisulfite sequencing to dissect allele-specific regulatory responses to GRBV infection. Allele-aware RNA-seq analysis revealed extensive haplotype-dependent transcriptional remodeling, with both shared and divergent temporal expression programs across infection stages. Soft clustering and weighted gene co-expression network analysis (WGCNA) identified haplotype-specific co-expression modules and regulatory hubs, uncovering asymmetric network organization and distinct antiviral strategies between parental haplotypes. Notably, chloroplast-associated defense networks emerged as conserved but highly infection-sensitive modules, exhibiting haplotype-dependent recovery or sustained disruption during infection. Methylome profiling demonstrated that GRBV infection induces pronounced haplotype-specific epigenetic reprogramming, with differential DNA methylation concentrated in promoter-proximal and transposable element-associated regions. Together, our results demonstrate that haplotype-resolved, multi-omic analyses reveal regulatory complexity and divergent antiviral strategies that are hidden by collapsed-genome approaches. This work provides new mechanistic insight into grapevine-virus interactions and lays a foundation for leveraging allelic variation to improve disease resilience in clonally propagated crops.