Haplotype-phased 'Ottawa 3' genome unravels differential reaction of apple rootstock roots to mixed viral infection

Authors: COSTA, LARISSA CARVALH - Animal And Plant Health Inspection Service (APHIS); Gottschalk, Christopher; UPCHURCH, DAVIS - Cornell University; HURTADO-GONZALES, OSCAR - Animal And Plant Health Inspection Service (APHIS); MANSFIELD, BEN - University Of Washington; YOCCA, ALAN - Bayer Crop Science; WHITT, LAUREN - Former ARS Employee; Vann, Cheryl; Fazio, Gennaro

Submitted to: The Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/17/2026
Publication Date: 4/15/2026
Citation: Costa, L.O., Gottschalk, C.C., Upchurch, D., Hurtado-Gonzales, O., Mansfield, B., Yocca, A., Whitt, L., Vann, C.D., Fazio, G. 2026. Haplotype-phased 'Ottawa 3' genome unravels differential reaction of apple rootstock roots to mixed viral infection. The Plant Journal. 126(1). https://doi.org/10.1111/tpj.70849.
DOI: https://doi.org/10.1111/tpj.70849

Interpretive Summary: Viral diseases pose a significant threat to global apple production. Most commercial apple trees are grafted onto rootstocks which provide nutrients and impart increased productivity to the trees. Selecting appropriate rootstocks is a crucial strategy to mitigate viral infections, however, the underlying mechanisms governing rootstock tolerance or sensitivity to viral infection at the root level remain under explored. We conducted an aeroponic experiment analyzing gene expression in the roots to document changes in two important, related commercial apple rootstocks with contrasting virus sensitivity, G.890 (virus-tolerant) and G.935 (virus-sensitive). To understand the contrasting sensitivity, each rootstock variety was grafted with virus-infected and non-infected scions. In addition, we assembled the genome of one of the parents of these rootstocks, 'Ottawa 3', which is the source of sensitivity. Our results revealed distinct root-level responses to viral infection, with the sensitive G.935 exhibiting reduced root length and increased disease symptoms. Gene expression analysis identified both common and parental-genome specific differentially expressed genes. Both rootstocks shared a common set of gene expression responses to viral infection, including genes involved in general stress and RNA processing pathways. The expression profile of G.935 was found to be broader stress/metabolic responses, whereas G.890, being more tolerant, activated more specific and targeted antiviral pathways signaling a stronger immune response compared to G.935. These findings reveal specific gene expression patterns within host immune system defense pathways critical for viral tolerance, thereby providing valuable insights for the development of future virus-resistant apple rootstocks.

Technical Abstract: Viral diseases pose a significant threat to global apple 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 under explored. We conducted an aeroponic experiment analyzing root transcriptome changes in two full-sibling commercial apple rootstocks, G.890 (Tolerant) and G.935 (Sensitive), after grafting with mixed virus-infected and non-infected scions. To provide a robust genetic framework, we assembled the haplotyped-phased genome of one of the parents, 'Ottawa 3', which is the source of sensitivity. Our results revealed distinct root-level responses to viral infection, with G.935 showing reduced root length and increased disease index. Transcriptome analysis identified both common and haplotype-specific differentially expressed genes. While G.935 and G.890 rootstocks shared a core set of common transcriptional responses to viral infection, including general stress and RNA processing pathways, the expression profile of G.935 exhibited broader stress/metabolic responses, whereas G.890, being more tolerant, activated more specific and targeted antiviral RNA silencing pathways. These findings reveal allele-specific gene expression within host defense pathways critical for viral tolerance, thereby providing valuable insights for developing future virus-resistant apple rootstocks.