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Prediction and screening of candidate resistance genes of Ocimum basilicum in response to the basil downy mildew pathogen Peronospora belbahrii

Kelly Allen: Plant Biology Graduate Program, University of Massachusetts Amherst

<div>Basil downy mildew, caused by the biotrophic oomycete <em>Peronospora belbahrii</em>, is a destructive disease of sweet basil (<em>Ocimum basilicum</em>) that results in high yield losses worldwide. Chemical and cultural control options have offered insufficient control for growers, and breeding has been a slow process due to the lack of annotated genetic resources and the necessity for retaining plant morphological and chemical characteristics for marketability. Following phenotypic screening for disease resistance, RNA-seq was used to compare the host-pathogen interactions of a downy mildew resistant sweet basil cultivar ‘Mirihani’ to a susceptible sweet basil line Rutgers SB22 during the inoculation and infection process. Following a previously-reported <em>de novo</em>-assembly based data analysis pipeline, this data has been used to predict candidate resistant genes uniquely present in the resistant cultivar ‘Mirihani’. Both nucleotide-binding leucine rich repeat proteins and receptor-like kinases are represented in the candidate genes. These protein classes are known to act upstream or alongside defense triggering pathways, including plant hormone responses. Analysis of hormone pathways shows that unlike ‘Mirihani’, SB22 does not accumulate some mRNAs associated with salicylic acid signaling and biosynthesis while both the jasmonic acid and ethylene pathways are consistent between cultivars. The predicted resistance gene sequences were used for primer design and expression profiles observed in the data were validated using qRT-PCR. This research presents the analytical approach for prediction of these candidate resistance genes, as well as the validation of the analysis using gene expression data.</div>