title: Transcriptomic dissection of the rice-Burkholderia glumae interaction.
abstract: BACKGROUND
  Bacterial panicle blight caused by the bacterium Burkholderia glumae is an emerging disease of rice in the United States. Not much is known about this disease, the disease cycle or any source of disease resistance. To understand the interaction between rice and Burkholderia glumae, we used transcriptomics via next-generation sequencing (RNA-Seq) and bioinformatics to identify differentially expressed transcripts between resistant and susceptible interactions and formulate a model for rice resistance to the disease.
  
  
  RESULTS
  Using inoculated young seedlings as sample tissues, we identified unique transcripts involved with resistance to bacterial panicle blight, including a PIF-like ORF1 and verified differential expression of some selected genes using qRT-PCR. These transcripts, which include resistance genes of the NBS-LRR type, kinases, transcription factors, transporters and expressed proteins with functions that are not known, have not been reported in other pathosystems including rice blast or bacterial blight. Further, functional annotation analysis reveals enrichment of defense response and programmed cell death (biological processes); ATP and protein binding (molecular functions); and mitochondrion-related (cell component) transcripts in the resistant interaction.
  
  
  CONCLUSIONS
  Taken together, we formulated a model for rice resistance to bacterial panicle blight that involves an activation of previously unknown resistance genes and their activation partners upon challenge with B. glumae. Other interesting findings are that 1) though these resistance transcripts were up-regulated upon inoculation in the resistant interaction, some of them were already expressed in the water-inoculated control from the resistant genotype, but not in the water- and bacterium-inoculated samples from the susceptible genotype; 2) rice may have co-opted an ORF that was previously a part of a transposable element to aid in the resistance mechanism; and 3) resistance may have existed immediately prior to rice domestication.
authors.affiliation: Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762, USA. zvm2@pss.msstate.edu.
authors.forename: Zenaida V
authors.initials: ZV
authors.lastname: Magbanua
authors.forename: Mark
authors.initials: M
authors.lastname: Arick
authors.forename: Teresia
authors.initials: T
authors.lastname: Buza
authors.forename: Chuan-Yu
authors.initials: CY
authors.lastname: Hsu
authors.forename: Kurt C
authors.initials: KC
authors.lastname: Showmaker
authors.forename: Philippe
authors.initials: P
authors.lastname: Chouvarine
authors.forename: Peng
authors.initials: P
authors.lastname: Deng
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Peterson
authors.forename: Shien
authors.initials: S
authors.lastname: Lu
mesh_terms: D019117:Burkholderia; D002874:Chromosome Mapping; D019295:Computational Biology; D060467:Disease Resistance / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D020022:Genetic Predisposition to Disease; D054884:Host-Pathogen Interactions / Q000235:genetics*; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000235:genetics* / Q000382:microbiology*; D010641:Phenotype; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology*; D015203:Reproducibility of Results; D059467:Transcriptome