Original Article


, Volume 6, Issue 3, pp 451-465

First online:

Open Access This content is freely available online to anyone, anywhere at any time.

Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae

  • Theodore R. SanaAffiliated withMetabolomics Laboratory, Agilent Technologies Life Sciences Group Email author 
  • , Steve FischerAffiliated withMetabolomics Laboratory, Agilent Technologies Life Sciences Group
  • , Gert WohlgemuthAffiliated withUniversity of California Davis Genome Center
  • , Anjali KatrekarAffiliated withMetabolomics Laboratory, Agilent Technologies Life Sciences Group
  • , Ki-hong JungAffiliated withDepartment of Plant Pathology, University of California Davis
  • , Pam C. RonaldAffiliated withDepartment of Plant Pathology, University of California Davis
  • , Oliver FiehnAffiliated withUniversity of California Davis Genome Center Email author 


Bacterial 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. LC–TOF 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. GC–TOF 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.


Metabolomics LC/MS GC/MS Microarray Rice Bacterial leaf blight Pathogen Pattern recognition receptor Pathogen associated molecular pattern