title: Biomarker metabolites capturing the metabolite variance present in a rice plant developmental period.
abstract: BACKGROUND
  This study analyzes metabolomic data from a rice tillering (branching) developmental profile to define a set of biomarker metabolites that reliably captures the metabolite variance of this plant developmental event, and which has potential as a basis for rapid comparative screening of metabolite profiles in relation to change in development, environment, or genotype. Changes in metabolism, and in metabolite profile, occur as a part of, and in response to, developmental events. These changes are influenced by the developmental program, as well as external factors impinging on it. Many samples are needed, however, to characterize quantitative aspects of developmental variation. A biomarker metabolite set could benefit screening of quantitative plant developmental variation by providing some of the advantages of both comprehensive metabolomic studies and focused studies of particular metabolites or pathways.
  
  
  RESULTS
  An appropriate set of biomarker metabolites to represent the plant developmental period including the initiation and early growth of rice tillering (branching) was obtained by: (1) determining principal components of the comprehensive metabolomic profile, then (2) identifying clusters of metabolites representing variation in loading on the first three principal components, and finally (3) selecting individual metabolites from these clusters that were known to be common among diverse organisms. The resultant set of 21 biomarker metabolites was reliable (P = 0.001) in capturing 83% of the metabolite variation in development. Furthermore, a subset of the biomarker metabolites was successful (P = 0.05) in correctly predicting metabolite change in response to environment as determined in another rice metabolomics study.
  
  
  CONCLUSIONS
  The ability to define a set of biomarker metabolites that reliably captures the metabolite variance of a plant developmental event was established. The biomarker metabolites are all commonly present in diverse organisms, so studies of their quantitative relationships can provide comparative information concerning metabolite profiles in relation to change in plant development, environment, or genotype.
authors.affiliation: Texas A&M Agricultural Research and Extension Center, 1509 Aggie Dr, Beaumont, Texas 77713, USA. ltarpley@tamu.edu
authors.forename: Lee
authors.initials: L
authors.lastname: Tarpley
authors.forename: Anthony L
authors.initials: AL
authors.lastname: Duran
authors.forename: Tesfamichael H
authors.initials: TH
authors.lastname: Kebrom
authors.forename: Lloyd W
authors.initials: LW
authors.lastname: Sumner
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D015415:Biomarkers / Q000378:metabolism*; D050260:Carbohydrate Metabolism; D002254:Carbonates / Q000378:metabolism; D002264:Carboxylic Acids / Q000378:metabolism; D018556:Crops, Agricultural / Q000033:anatomy & histology / Q000254:growth & development* / Q000378:metabolism; D004777:Environment; D014644:Genetic Variation; D005838:Genotype; D006573:Heterocyclic Compounds, 1-Ring / Q000378:metabolism; D012275:Oryza / Q000033:anatomy & histology / Q000254:growth & development* / Q000378:metabolism
chemical_list: D000596:Amino Acids; D015415:Biomarkers; D002254:Carbonates; D002264:Carboxylic Acids; D006573:Heterocyclic Compounds, 1-Ring