title: A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement.
abstract: BACKGROUND
  The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant.
  
  
  RESULTS
  We used an integrated approach to compare the transcriptome, proteome and metabolome of the rhizome to other tissues of red rice. 116 Gb of transcriptome sequence was obtained from various tissues and used to identify rhizome-specific and preferentially expressed genes, including transcription factors and hormone metabolism and stress response-related genes. Proteomics and metabolomics approaches identified 41 proteins and more than 100 primary metabolites and plant hormones with rhizome preferential accumulation. Of particular interest was the identification of a large number of gene transcripts from Magnaportha oryzae, the fungus that causes rice blast disease in cultivated rice, even though the red rice plants showed no sign of disease.
  
  
  CONCLUSIONS
  A significant set of genes, proteins and metabolites appear to be specifically or preferentially expressed in the rhizome of O. longistaminata. The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease.
authors: Ruifeng
authors: R
authors: He
authors: Fernanda
authors: F
authors: Salvato
authors: Jeong-Jin
authors: JJ
authors: Park
authors: Min-Jeong
authors: MJ
authors: Kim
authors: William
authors: W
authors: Nelson
authors: Tiago S
authors: TS
authors: Balbuena
authors: Mark
authors: M
authors: Willer
authors: John A
authors: JA
authors: Crow
authors: Greg D
authors: GD
authors: May
authors: Carol A
authors: CA
authors: Soderlund
authors: Jay J
authors: JJ
authors: Thelen
authors: Institute of Biological Chemistry, Washington State University, PO Box 646340, Pullman, WA 99164, USA. gangd@wsu.edu.
authors: David R
authors: DR
authors: Gang
mesh_terms: D060467:Disease Resistance / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D012275:Oryza / Q000235:genetics / Q000378:metabolism* / Q000502:physiology; D027343:Rhizome / Q000235:genetics / Q000378:metabolism* / Q000502:physiology; D059467:Transcriptome / Q000235:genetics