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A multi-omics approach thus adds new layers of information such as identifying metabolites with antimicrobial properties, elucidating metabolomic profiles of infected and non-infected plants, and reveals pathogenic requirements for infection and colonisation. In this study, two oat cultivars (Dunnart and SWK001) were inoculated with <jats:italic>Pseudomonas syringae<\/jats:italic> pathovars, pathogenic and non-pathogenic on oat. Following inoculation, metabolites were extracted with methanol from leaf tissues at 2, 4 and 6\u00a0days post-infection and analysed by multiple reaction monitoring (MRM) on a triple quadrupole mass spectrometer system. Relatedly, mRNA was isolated at the same time points, and the cDNA analysed by quantitative PCR (RT-qPCR) for expression levels of selected gene transcripts associated with avenanthramide (Avn) biosynthesis. The targeted amino acids, hydroxycinnamic acids and Avns were successfully quantified. Distinct cultivar-specific differences in the metabolite responses were observed in response to pathogenic and non-pathogenic strains. Trends in aromatic amino acids and hydroxycinnamic acids seem to indicate stronger activation and flux through these pathways in Dunnart as compared to SWK001. A positive correlation between hydroxycinnamoyl-CoA:hydroxyanthranilate <jats:italic>N<\/jats:italic>-hydroxycinnamoyl transferase (<jats:italic>HHT<\/jats:italic>) gene expression and the abundance of Avn A in both cultivars was documented. However, transcript profiling of selected genes involved in Avn synthesis did not reveal a clear pattern to distinguish between the tolerant and susceptible cultivars.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Graphical abstract<\/jats:title>\n                \n              <\/jats:sec>","DOI":"10.1007\/s00425-024-04435-w","type":"journal-article","created":{"date-parts":[[2024,5,24]],"date-time":"2024-05-24T17:02:08Z","timestamp":1716570128000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Integration of targeted metabolome and transcript profiling of Pseudomonas syringae-triggered changes in defence-related phytochemicals in oat plants"],"prefix":"10.1007","volume":"260","author":[{"given":"Chanel J.","family":"Pretorius","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9079-4769","authenticated-orcid":false,"given":"Ian A.","family":"Dubery","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,5,24]]},"reference":[{"key":"4435_CR1","doi-asserted-by":"publisher","first-page":"1117","DOI":"10.1104\/pp.114.253120","volume":"167","author":"JA Asselin","year":"2015","unstructured":"Asselin JA, Lin J, Perez-Quintero AL, Gentzel I, Majerczak D, Opiyo SO, Zhao W, Paek SM, Kim MG, Coplin DL, Blakeslee JJ (2015) Perturbation of maize phenylpropanoid metabolism by an AvrE family type III effector from Pantoea stewartii. 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