title: Development of a microarray for two rice subspecies: characterization and validation of gene expression in rice tissues.
abstract: BACKGROUND
  Rice is one of the major crop species in the world helping to sustain approximately half of the global population's diet especially in Asia. However, due to the impact of extreme climate change and global warming, rice crop production and yields may be adversely affected resulting in a world food crisis. Researchers have been keen to understand the effects of drought, temperature and other environmental stress factors on rice plant growth and development. Gene expression microarray technology represents a key strategy for the identification of genes and their associated expression patterns in response to stress. Here, we report on the development of the rice OneArray® microarray platform which is suitable for two major rice subspecies, japonica and indica.
  
  
  RESULTS
  The rice OneArray® 60-mer, oligonucleotide microarray consists of a total of 21,179 probes covering 20,806 genes of japonica and 13,683 genes of indica. Through a validation study, total RNA isolated from rice shoots and roots were used for comparison of gene expression profiles via microarray examination. The results were submitted to NCBI's Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE50844 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50844). A list of significantly differentially expressed genes was generated; 438 shoot-specific genes were identified among 3,138 up-regulated genes, and 463 root-specific genes were found among 3,845 down-regulated genes. GO enrichment analysis demonstrates these results are in agreement with the known physiological processes of the different organs/tissues. Furthermore, qRT-PCR validation was performed on 66 genes, and found to significantly correlate with the microarray results (R = 0.95, p < 0.001***).
  
  
  CONCLUSIONS
  The rice OneArray® 22 K microarray, the first rice microarray, covering both japonica and indica subspecies was designed and validated in a comprehensive study of gene expression in rice tissues. The rice OneArray® microarray platform revealed high specificity and sensitivity. Additional information for the rice OneArray® microarray can be found at http://www.phalanx.com.tw/index.php.
authors.forename: Jia-Shing
authors.initials: JS
authors.lastname: Chen
authors.forename: Shang-Chi
authors.initials: SC
authors.lastname: Lin
authors.forename: Chia-Ying
authors.initials: CY
authors.lastname: Chen
authors.forename: Yen-Ting
authors.initials: YT
authors.lastname: Hsieh
authors.forename: Ping-Hui
authors.initials: PH
authors.lastname: Pai
authors.forename: Long-Kung
authors.initials: LK
authors.lastname: Chen
authors.affiliation: Phalanx Biotech Group, 6F, No,6, Technology Road 5, Hsinchu Science Park, Hsinchu 30078, Taiwan, Republic of China. swlee@phalanxbiotech.com.
authors.forename: Shengwan
authors.initials: S
authors.lastname: Lee
mesh_terms: D001483:Base Sequence; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity; D012275:Oryza / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D018384:Oxidative Stress / Q000235:genetics; D010940:Plant Proteins / Q000096:biosynthesis / Q000235:genetics; D018517:Plant Roots / Q000737:chemistry; D018520:Plant Shoots / Q000737:chemistry; D011786:Quality Control; D018749:RNA, Plant / Q000032:analysis / Q000235:genetics*; D015203:Reproducibility of Results; D013045:Species Specificity
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant