Transcriptomics and metabolomics of age-related resistance to Phytophthora capsici in cucumber
For this project, we performed RNA sequencing (RNAseq) and metabolomic analysis on cucumber peels to identify genes of interest associated with age-related resistance (ARR) to P. capsici. Age-related resistance has been studied in many pathosystems, however the molecular mechanism controlling these types of resistance are poorly understood. The complexity and appeal of studying this trait stem from it being both a developmental biology and disease resistance question. These studies, furthering our understanding of ARR have implications for both developmental biology and disease resistance.
As part of this project we also re-annotated the GO-term database for the entire cucumber genome using in-house R scripts. To further assist the cucumber and cucurbit scientific community, this database will be published and made available as supplementary material alongside the manuscript covering this research.
The RNAseq experiments revealed developmental differential expression of specialized metabolism genes, as well as other genes potentially involved in resistance. To further understand the metabolomic changes associated with ARR, and with assistance from the RTSF Metabolomics Core, we established a rapid protocol for untargeted metabolomic analyses of cucumber peel extracts using HPLC-QToF-MS. To improve on the available statistical analysis software available at RTSF, we developed a Principal Component Analysis based multivariate approach to identify compounds associated with ARR, with guidance from the MSU Center for Statistical Training and Consulting. To identify the classes of compounds we observed in our analyses, we utilized a recently published, novel filtering approach developed by Dr. Dan Jones (MSU, Biochemistry). We identified putative terpenoid glycosides in the peels of 16-day old cucumber fruit. Prior knowledge of this class of compounds in cucumber is extremely limited.
Though ARR to P. capsici is expressed in cucumber fruit that are past harvest age, understanding the regulation of this trait may help us develop resistance that manifests in earlier stages of fruit development, thus benefitting farmers.