Gene Expression Profiling of Resistance and Susceptibility to Beet Curly Top Virus in Sugarbeet

Resistance to Beet curly top virus (BCTV) is a required trait for variety approval in the western USA. There is sparse public knowledge of genes regulating resistance. This research focused on gene expression profiling of resistance to the three BCTV strains:  Cal/Logan (Cal), Worland (Wor), and severe.  Differential gene expression was studied via RNA-sequencing of a highly resistant doubled haploid line (KDH13-PI663862) compared to a highly susceptible line (K19-19). KDH13 was subjected to 7 treatments: infested with non-infectious leafhoppers, infected with leafhoppers population carrying a single, two, or three strains, and control leaf, in addition to K19-19 infected with the three strains.  Leaf samples were sequenced in a HiSeq2500 and data was analyzed using TopHat and Cufflinks software. All sequences were aligned to the RefBeet-1.2. Based on 28 pair-wise comparisons, differentially expressed genes were determined with an adjusted false-discovery-rate (q-value) lower than 0.05. For example, DND1 gene, that is involved in innate immune response to pathogens (6.8kb located on chromosome1), was found down regulated (q = 0.01), in KDH13 when infected with the three strains compared to infestation with non-infections leafhoppers, but no response of DND1 was observed in K19-19. Additionally, transcripts of IDH1 gene were undetectable in K19-19 infected with the three strains. There was a pattern of some defense genes, such as ATL6 subunits that were evidence to strain-specific and strain interaction gene expression. This research is the first to reveal gene transcriptional profiles associated with resistance and susceptibility to BCTV.