title: Defining reference genes in Oryza sativa using organ, development, biotic and abiotic transcriptome datasets.
abstract: BACKGROUND
  Reference genes are widely used to normalise transcript abundance data determined by quantitative RT-PCR and microarrays. However, the approaches taken to define reference genes can be variable. Although Oryza sativa (rice) is a widely used model plant and important crop specie, there has been no comprehensive analysis carried out to define superior reference genes.
  
  
  RESULTS
  Analysis of 136 Affymetrix transcriptome datasets comprising of 373 genome microarrays from studies in rice that encompass tissue, developmental, abiotic, biotic and hormonal transcriptome datasets identified 151 genes whose expression was considered relatively stable under all conditions. A sub-set of 12 of these genes were validated by quantitative RT-PCR and were seen to be stable under a number of conditions. All except one gene that has been previously proposed as a stably expressed gene for rice, were observed to change significantly under some treatment.
  
  
  CONCLUSIONS
  A new set of reference genes that are stable across tissue, development, stress and hormonal treatments have been identified in rice. This provides a superior set of reference genes for future studies in rice. It confirms the approach of mining large scale datasets as a robust method to define reference genes, but cautions against using gene orthology or counterparts of reference genes in other plant species as a means of defining reference genes.
authors.affiliation: ARC Centre of Excellence in Plant Energy Biology, MCS Building M316 University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
authors.forename: Reena
authors.initials: R
authors.lastname: Narsai
authors.forename: Aneta
authors.initials: A
authors.lastname: Ivanova
authors.forename: Sophia
authors.initials: S
authors.lastname: Ng
authors.forename: James
authors.initials: J
authors.lastname: Whelan
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity / Q000235:genetics*; D012275:Oryza / Q000235:genetics*; D012015:Reference Standards; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000592:standards; D013312:Stress, Physiological / Q000235:genetics