Transcriptome changes specifically associated with apple (Malus domestica) root defense response during Pythium ultimum infection

•The defense response of apple root to P. ultimum infection was studied using RNA-seq.•Specific re-direction of cellular activities was identified by bioinformatic analysis.•Pathogen detection, defense hormones and antimicrobial metabolites are key components.•Cytokinin and the release of potent toxic HCN may play a unique role in root defense.

RNA-seq technology was applied to identify the transcriptomic changes associated with apple root defense response to Pythium ultimum infection. Genes encoding homolog proteins with functions of pathogen detection such as chitin elicitor receptor kinase (CERK) and wall-associated receptor kinase (WAK) were among the differentially expressed apple genes. The biosynthesis and signaling of several plant hormones including ethylene, jasmonate and cytokinin were specifically induced in response to P. ultimum inoculation. Genes encoding enzymes of secondary metabolisms, cell wall fortification and pathogenesis related (PR) protein, laccase, mandelonitrile lyase and cyanogenic beta-glucosidase were consistently up-regulated in the later stages of infection.