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

RNA-Seq based transcriptome profiling were performed on these samples with a minimum of 20 million reads per sample; read mapping, transcript discovery and differentially expressed gene (DEG) identification were carried out using CLC Genomics Workbench software suit, followed by Gene Ontology and pathway analyses. The highest defense response occurred at 48 hpi based on the number of the identified DEGs along the infection process. Transcriptomic changes related to oxido-reduction balance, trans-membrane trafficking and metabolic activities indicated the re-direction of cellular activities to combat P. ultimum infection. DEGs functioning in hormone signaling including ethylene, jasmonate, gibberellin, cytokinin and auxin, and those encoding NAC, WRKY, MYB and ERF transcription factors were identified from 24-48 hpi; DEGs encoding enzymes in several biosynthesis pathways of secondary metabolisms and cell wall modification proteins are among the consistently up-regulated in the later stages. DEGs encoding defense and stress related protein such as wall-associated receptor kinase (WAK), endochitinase (PR4), thaumatin (PR5)-like protein, laccase, mandelonitrile lyase and cyanogenic beta-glucosidase were also highly induced. Overall design: root tissues of apple seedlings inoculated with Pythium ultimum, were sampled at 0, 1, 4, 8, 24, 48, 72 and 96 hour post inoculation (hpi) along with mock inoculated tissue at each time point.