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Background  Transcriptomic analyses were performed to compare the molecular responses of two potato varieties previously shown to differ in the severity of disease symptoms due to infection by “ Candidatus  Liberibacter solanacearum” (Lso), the causative agent of Zebra Chip in potato. A factorial design utilizing the two varieties and psyllids either harboring Lso or without bacteria was used to discriminate varietal responses to pathogen infection versus psyllid feeding. Plant response was determined from leaf samples 3 weeks after infection.    Results  In response to Lso infection, 397 genes were differentially expressed in the variety Atlantic (most susceptible) as compared to 1027 genes in Waneta. Over 80% of the transcriptionally-changed genes were down-regulated in both varieties, including genes involved in photosynthesis or primary and secondary metabolism. Many of the Lso-responsive genes involved in stress responses or hormonal pathways were regulated differently in the two potato varieties.    Conclusions  This study focused on the time point just prior to the onset of symptom development and provides valuable insight into the mechanisms of  Liberibacter  pathogenicity, especially the widespread suppression of plant gene expression, including genes involved in plant defenses.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4313-2) contains supplementary material, which is available to authorized users.

Global gene expression in two potato cultivars in response to ‘Candidatus Liberibacter solanacearum’ infection