Transcriptome Profiling Analysis Using Rice Oligonucleotide Microarrays

  • Ki-Hong Jung
  • Pamela C. RonaldEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 956)


Transcriptome analysis using oligonucleotide microarrays is a powerful tool for detecting changes in genome-wide transcripts under a given biological condition. Although the rice genome sequence is available, the number of functionally characterized genes in rice is still very limited. Genome-wide transcriptome analysis is a useful tool for elucidating the functions of rice genes that have not yet been determined. Currently, more than 3,000 arrays are publicly available. Here, we introduce methods for genome-wide transcriptome analysis in rice.

Key words

Rice Microarray GEO aRNA Hybridization 


  1. 1.
    Bowtell DD (1999) Options available–from start to finish–for obtaining expression data by microarray. Nat Genet 21:25–32PubMedCrossRefGoogle Scholar
  2. 2.
    Yazaki J, Shimatani Z, Hashimoto A, Nagata Y, Fujii F, Kojima K, Suzuki K, Taya T, Tonouchi M, Nelson C, Nakagawa A, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S (2004) Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis. Physiol Genomics 17:87–100PubMedCrossRefGoogle Scholar
  3. 3.
    Yazaki J, Kojima K, Suzuki K, Kishimoto N, Kikuchi S (2004) The rice PIPELINE: a unification tool for plant functional genomics. Nucleic Acids Res 32:D383–D387PubMedCrossRefGoogle Scholar
  4. 4.
    Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J, Xu J, Cui X, Close TJ (2005) Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol 139:822–835PubMedCrossRefGoogle Scholar
  5. 5.
    Jung KH, An G, Ronald PC (2008) Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nat Rev Genet 9:91–101PubMedGoogle Scholar
  6. 6.
    Jung KH, Dardick C, Bartley LE, Cao P, Phetsom J, Canlas P, Seo YS, Shultz M, Ouyang S, Yuan Q, Frank BC, Ly E, Zheng L, Jia Y, Hsia AP, An K, Chou HH, Rocke D, Lee GC, Schnable PS, An G, Buell CR, Ronald PC (2008) Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PLoS One 3:e3337PubMedCrossRefGoogle Scholar
  7. 7.
    Ma L, Chen C, Liu X, Jiao Y, Su N, Li L, Wang X, Cao M, Sun N, Zhang X, Bao J, Li J, Pedersen S, Bolund L, Zhao H, Yuan L, Wong GK, Wang J, Deng XW (2005) A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res 15:1274–1283PubMedCrossRefGoogle Scholar
  8. 8.
    Satoh K, Doi K, Nagata T, Kishimoto N, Suzuki K, Otomo Y, Kawai J, Nakamura M, Hirozane-Kishikawa T, Kanagawa S, Arakawa T, Takahashi-Iida J, Murata M, Ninomiya N, Sasaki D, Fukuda S, Tagami M, Yamagata H, Kurita K, Kamiya K, Yamamoto M, Kikuta A, Bito T, Fujitsuka N, Ito K, Kanamori H, Choi IR, Nagamura Y, Matsumoto T, Murakami K, Matsubara K, Carninci P, Hayashizaki Y, Kikuchi S (2007) Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PLoS One 2:e1235PubMedCrossRefGoogle Scholar
  9. 9.
    Suwabe K, Suzuki G, Takahashi H, Shiono K, Endo M, Yano K, Fujita M, Masuko H, Saito H, Fujioka T, Kaneko F, Kazama T, Mizuta Y, Kawagishi-Kobayashi M, Tsutsumi N, Kurata N, Nakazono M, Watanabe M (2008) Separated transcriptomes of male gametophyte and tapetum in rice: validity of a laser microdissection (LM) microarray. Plant Cell Physiol 49:1407–1416PubMedCrossRefGoogle Scholar
  10. 10.
    Chou HH, Hsia AP, Mooney DL, Schnable PS (2004) Picky: oligo microarray design for large genomes. Bioinformatics 20:2893–2902PubMedCrossRefGoogle Scholar
  11. 11.
    Jung KH, Bartley LE, Cao P, Canlas PE, Ronald PC (2009) Analysis of alternatively spliced rice transcripts using microarray data. Rice 2:44–55CrossRefGoogle Scholar
  12. 12.
    Jain M, Nijhawan A, Tyagi AK, Khurana JP (2006) Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem Biophys Res Commun 345:646–651PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Department of Plant PathologyUniversity of CaliforniaDavisUSA
  2. 2.Department of Plant Molecular Systems Biotechnology, Crop Biotech InstituteKyung Hee UniversityYonginRepublic of Korea

Personalised recommendations