Transcriptional Profiling of Rough Lemon and Sweet Orange Reveals Critical Involvement of Reprogramming of Signaling Pathways in Early Response and Strong Quantitative Nature of Defense to ‘Candidatus Liberibacter asiaticus’

Commercial citrus varieties have little resistance to Huanglongbing (HLB), a disease presumably caused by Candidatus Liberibacter asiaticus (CLas). As HLB has become widespread in Florida over ten years, we have observed very substantial variation in the speed of spread and the severity of symptoms in field trials. Understanding the underlying mechanisms of apparent tolerance is critical to the development of CLas tolerant citrus varieties to combat HLB. Transcriptome profiling using RNA-seq data collected from CLas- and mock-inoculated tolerant rough lemon and susceptible sweet orange reveals critical involvement of reprogramming of signaling pathways in early responses to infection. A Subnetwork Enrichment Analysis further revealed different regulation patterns among functional categories, suggesting differentially expressed genes with different functions were subjected to distinct regulation programming. Time series analysis reveals the strong quantitative nature of defense signaling in rough lemon compared with sweet orange. Overall, our studies indicated that HLB tolerance is complex trait controlled by many genes, and could be exploited by using advanced breeding tools to deliver HLB-tolerant cultivars.