Summary of study ST000007

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000006. The data can be accessed directly via it's Project DOI: 10.21228/M8CC7R This work is supported by NIH grant, U2C- DK119886.


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Study IDST000007
Study TitleRice Infection Study
Study TypeMS analysis
Study SummaryBacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), gives rise to devastating crop losses in rice. Disease resistant rice cultivars are the most economical way to combat the disease. The TP309 cultivar is susceptible to infection by Xoo strain PXO99. A transgenic variety, TP309_Xa21, expresses the pattern recognition receptor Xa21, and is resistant. PXO99?raxST, a strain lacking the raxST gene, is able to overcome Xa21-mediated immunity. We used a single extraction solvent to demonstrate comprehensive metabolomics and transcriptomics profiling under sample limited conditions, and analyze the molecular responses of two rice lines challenged with either PXO99 or PXO99?raxST. LCTOF raw data file filtering resulted in better within group reproducibility of replicate samples for statistical analyses. Accurate mass match compound identification with molecular formula generation (MFG) ranking of 355 masses was achieved with the METLIN database. GCTOF analysis yielded an additional 441 compounds after BinBase database processing, of which 154 were structurally identified by retention index/MS library matching. Multivariate statistics revealed that the susceptible and resistant genotypes possess distinct profiles. Although few mRNA and metabolite differences were detected in PXO99 challenged TP309 compared to mock, many differential changes occurred in the Xa21-mediated response to PXO99 and PXO99?raxST. Acetophenone, xanthophylls, fatty acids, alkaloids, glutathione, carbohydrate and lipid biosynthetic pathways were affected. Significant transcriptional induction of several pathogenesis related genes in Xa21 challenged strains, as well as differential changes to GAD, PAL, ICL1 and Glutathione-S-transferase transcripts indicated limited correlation with metabolite changes under single time point global profiling conditions.
University of California, Davis
DepartmentDavis Genome Center
Last NameKind
First NameTobias
Address451 E. Health Sci. Drive, Davis, California 95616, USA
Submit Date2013-02-22
Num Groups7
Total Subjects60
Raw Data AvailableNo
Analysis Type DetailGC-MS
Release Date2013-03-24
Release Version1
Tobias Kind Tobias Kind application/zip

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Project ID:PR000006
Project DOI:doi: 10.21228/M8CC7R
Project Title:Rice Infection Project
Project Type:Metabolomic and transcriptomic analysis
Project Summary:Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae
Institute:University of California, Davis
Department:Davis Genome Center
Last Name:Fiehn
First Name:Oliver
Address:451 E. Health Sci. Drive, Davis, California 95616, USA