Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
권호 표지
DOI QR코드

DOI QR Code

Current status on expression profiling using rice microarray

벼 microarray를 이용한 유전자발현 profiling 연구동향

  • Yoon, Ung-Han (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Kim, Yeon-Ki (Bioscience and Bioinformatics Division, MyongJi University) ;
  • Kim, Chang-Kug (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Hahn, Jang-Ho (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Kim, Dong-Hern (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Lee, Tae-Ho (Bioscience and Bioinformatics Division, MyongJi University) ;
  • Lee, Gang-Seob (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Park, Soo-Chul (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Nahm, Baek-Hie (Bioscience and Bioinformatics Division, MyongJi University)
  • Received : 2010.04.05
  • Accepted : 2010.04.14
  • Published : 2010.06.30
Download PDF
⟨ Previous Next ⟩

Abstract

As the International Rice Genome Sequencing Project (IRGSP) was completed in 2005 and opened to the public, many countries are making a lot of investments in researches on the utilization of sequence information along with system development. Also, the necessity of the functional genomics researches using microarray is increased currently to secure unique genes related with major agricultural traits and analyze metabolic pathways. Microrarray enables efficient analysis of large scale gene expression and related transcription regulation. This review aims to introduce available microarrays made based on rice genome information and current status of gene expression analysis using these microarrays integrated with the databases available to the public. Also, we introduce the researches on the large scale functional analysis of genes related with useful traits and genetic networks. Understanding of the mechanism related with mutual interaction between proteins with co-expression among rice genes can be utilized in the researches for improving major agricultural traits. The direct and indirect interactions of various genes would provide new functionality of rice. The recent results of the various expression profiling analysis in rice will promote functional genomic researches in plants including rice and provide the scientists involved in applications researches with wide variety of expression informations.

Keywords

References

  1. Aoki K, Ogata Y, Shibata D (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol 48:381-390 https://doi.org/10.1093/pcp/pcm013
  2. Arora R, Agarwal P, Ray S, Singh AK, Singh VP, Tyagi AK, Kapoor S. (2007) MADS-box gene family in rice: genomewide identification, organization and expression profiling during reproductive development and stress. BMC Genomics 8:242 https://doi.org/10.1186/1471-2164-8-242
  3. Berri S, Abbruscato P, Faivre-Rampant O, Brasileiro AC, Fumasoni I, Satoh K, Kikuchi S, Mizzi L, Morandini P, Pè ME, Piffanelli P. (2009) Characterization of WRKY co-regulatory networks in rice and Arabidopsis. BMC Plant Biol 9:120 https://doi.org/10.1186/1471-2229-9-120
  4. Briggs SP, Singer T. (2005) Genetic networks. Plant Physiol 138:542-4 https://doi.org/10.1104/pp.104.900147
  5. Caldana C, Scheible WR, Mueller-Roeber B, Ruzicic S. (2007) A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors. Plant Methods 3:7 https://doi.org/10.1186/1746-4811-3-7
  6. Chou HH, Hsia AP, Mooney DL, Schnable PS. (2004) Picky: oligo microarray design for large genomes. Bioinformatics 20:2893-902 https://doi.org/10.1093/bioinformatics/bth347
  7. Cooper B, Clarke JD, Budworth P, Kreps J, Hutchison D, Park S, Guimil S, Dunn M, Luginbühl P, Ellero C, Goff SA, Glazebrook J. (2003) A network of rice genes associated with stress response and seed development. Proc Natl Acad Sci U S A 100:4945-50 https://doi.org/10.1073/pnas.0737574100
  8. Coulibaly I, Page GP. (2008) Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data II: Analysis Beyond Single Gene. Int J Plant Genomics 2008:893-941
  9. Degenkolbe T, Do PT, Zuther E, Repsilber D, Walther D, Hincha DK, Kohl KI. (2009) Expression profiling of rice cultivars differing in their tolerance to long-term drought stress. Plant Mol Biol 69:133-53 https://doi.org/10.1007/s11103-008-9412-7
  10. Frei M, Tanaka JP, Chen CP, Wissuwa M. (2010) Mechanisms of ozone tolerance in rice: characterization of two QTLs affecting leaf bronzing by gene expression profiling and biochemical analyses. J Exp Bot 2010
  11. Furutani I, Sukegawa S, Kyozuka J. (2006) Genome-wide analysis of spatial and temporal gene expression in rice panicle development. Plant J 46:503-11 https://doi.org/10.1111/j.1365-313X.2006.02703.x
  12. International Rice Genome Sequencing Project. (2005) The map-based sequence of the rice genome. Nature 436:793-800 https://doi.org/10.1038/nature03895
  13. Jain M, Tyagi AK, Khurana JP. (2008) Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice. FEBS J 275:2845-61 https://doi.org/10.1111/j.1742-4658.2008.06424.x
  14. Jain M, Khurana JP. (2009) Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS J 276:3148-62 https://doi.org/10.1111/j.1742-4658.2009.07033.x
  15. Jung KH, An G, Ronald PC. (2008a) Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nat Rev Genet 9:91-101
  16. Jung KH, Lee J, Dardick C, Seo YS, Cao P, Canlas P, Phetsom J, Xu X, Ouyang S, An K, Cho YJ, Lee GC, Lee Y, An G, Ronald PC. (2008b) Identification and functional analysis of lightresponsive unique genes and gene family members in rice. PLoS Genet 4:e1000164 https://doi.org/10.1371/journal.pgen.1000164
  17. Jupiter D, Chen H, VanBuren V. (2009) STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data. BMC Bioinformatics 10:332 https://doi.org/10.1186/1471-2105-10-332
  18. Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, Galbraith D, Bohnert HJ. (2001) Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13:889-905 https://doi.org/10.1105/tpc.13.4.889
  19. Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Yasunishi A. (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301:376-9 https://doi.org/10.1126/science.1081288
  20. Lee TH, Kim YK, Pham TT, Song SI, Kim JK, Kang KY, An G, Jung KH, Galbraith DW, Kim M, Yoon UH, Nahm BH. (2009) RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice. Plant Physiol 151:16-33 https://doi.org/10.1104/pp.109.139030
  21. Lim SD, Yim WC, Moon JC, Kim DS, Lee BM, Jang CS. (2010) A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes. Plant Mol Biol 72:369-80 https://doi.org/10.1007/s11103-009-9576-9
  22. Lu T, Huang X, Zhu C, Huang T, Zhao Q, Xie K, Xiong L, Zhang Q, Han B. (2008) RICD: a rice indica cDNA database resource for rice functional genomics. BMC Plant Biol 8:118 https://doi.org/10.1186/1471-2229-8-118
  23. Lu XC, Gong HQ, Huang ML, Bai SL, He YB, Mao X, Geng Z, Li SG, Wei L, Yuwen JS, Xu ZH, Bai SN. (2006) Molecular analysis of early rice stamen development using organ-specific gene expression profiling. Plant Mol Biol 61:845-61 https://doi.org/10.1007/s11103-006-0054-3
  24. Ludwikow A, Sadowski J. (2008) Gene networks in plant ozone stress response and tolerance. J Integr Plant Biol 50:1256-67 https://doi.org/10.1111/j.1744-7909.2008.00738.x
  25. Nakamura H, Hakata M, Amano K, Miyao A, Toki N, Kajikawa M, Pang J, Higashi N, Ando S, Toki S, Fujita M, Enju A, Seki M, Nakazawa M, Ichikawa T, Shinozaki K, Matsui M, Nagamura Y, Hirochika H, Ichikawa H. (2007) A genome-wide gain-of function analysis of rice genes using the FOX-hunting system. Plant Mol Biol 65:357-71 https://doi.org/10.1007/s11103-007-9243-y
  26. Narsai R, Howell KA, Carroll A, Ivanova A, Millar AH, Whelan J. (2009) Defining core metabolic and transcriptomic responses to oxygen availability in rice embryos and young seedlings. Plant Physiol 151:306-22 https://doi.org/10.1104/pp.109.142026
  27. Nijhawan A, Jain M, Tyagi AK, Khurana JP. (2008) Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice. Plant Physiol 146:333-50 https://doi.org/10.1104/pp.107.112821
  28. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35(Database issue):D883-7 https://doi.org/10.1093/nar/gkl976
  29. Park DS, Park SK, Han AI, Wang HJ, Jun NS, Manigbas NL, Woo YM, Ahn BO, Yun DW, Yoon UH, Kim YW, Lee MC, Kim DH, Nam MH, Han CD, Kang HW, Yi G. (2009) Genetic variation through Dissociation(Ds) insertional mutagenesis system for rice in Korea : progress and current ststus. Molecular Breeding 24:1-15 https://doi.org/10.1007/s11032-009-9300-0
  30. Perez-Rodríguez P, Riano-Pachon DM, Correa LG, Rensing SA, Kersten B, Mueller-Roeber B. (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res 38(Database issue):D822-7 https://doi.org/10.1093/nar/gkp805
  31. Rensink WA, Buell CR. (2005) Microarray expression profiling resources for plant genomics. Trends Plant Sci 10:603-9 https://doi.org/10.1016/j.tplants.2005.10.003
  32. Rice Annotation Project. (2008) The Rice Annotation Project Database (RAP-DB). Nucleic Acids Res 36(Database issue): D1028-33 https://doi.org/10.1093/nar/gkm978
  33. Sarkar NK, Kim YK, Grover A. (2009) Rice sHsp genes: genomic organization and expression profiling under stress and development. BMC Genomics 10:393 https://doi.org/10.1186/1471-2164-10-393
  34. 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:e1235 https://doi.org/10.1371/journal.pone.0001235
  35. Shinozaki K, Yamaguchi-Shinozaki K. (2007) Gene networks involved in drought stress response and tolerance. J Exp Bot 58:221-7 https://doi.org/10.1093/jxb/erl164
  36. Yamakawa H, Hirose T, Kuroda M, Yamaguchi T. (2007) Comprehensive expression profiling of rice grain filling-related genes under high temperature using DNA microarray. Plant Physiol 144:258-77 https://doi.org/10.1104/pp.107.098665
  37. Yamaguchi-Shinozaki K, Shinozaki K. (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses.. Annu Rev Plant Biol 57:781-803 https://doi.org/10.1146/annurev.arplant.57.032905.105444
  38. Yanhui C, Xiaoyuan Y, Kun H, Meihua L, Jigang L, Zhaofeng G, Zhiqiang L, Yunfei Z, Xiaoxiao W, Xiaoming Q, Yunping S, Li Z, Xiaohui D, Jingchu L, Xing-Wang D, Zhangliang C, Hongya G, Li-Jia Q. (2006) The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Mol Biol 60:107-24 https://doi.org/10.1007/s11103-005-2910-y
  39. Yazaki J, Kishimoto N, Nakamura K, Fujii F, Shimbo K, Otsuka Y, Wu J, Yamamoto K, Sakata K, Sasaki T, Kikuchi S. (2000) Embarking on rice functional genomics via cDNA microarray: use of 3' UTR probes for specific gene expression analysis. DNA Res 7:367-70 https://doi.org/10.1093/dnares/7.6.367
  40. Ye H, Du H, Tang N, Li X, Xiong L. (2009) Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice. Plant Mol Biol. 71:291-305 https://doi.org/10.1007/s11103-009-9524-8
  41. Yoon UH, Lee GS, Lee JS, Hahn JH, Kim CK, Kikuchi S, Satoh K, Kim JA, Lee JH, Lee TH, Kim YH. (2009) Structural Analysis of Seed Developmental Stage ESTs in Oryza sativa L. Korean J of Plant Biotechnology 36:130-136 https://doi.org/10.5010/JPB.2009.36.2.130
  42. Zhou J, Wang X, Jiao Y, Qin Y, Liu X, He K, Chen C, Ma L, Wang J, Xiong L, Zhang Q, Fan L, Deng XW. (2007) Global genome expression analysis of rice in response to drought and highsalinity stresses in shoot, flag leaf, and panicle. Plant Mol Biol. 63:591-608 https://doi.org/10.1007/s11103-006-9111-1
  43. Zhu T. (2003) Global analysis of gene expression using GeneChip microarrays. Curr Opin Plant Biol. 6:418-25 https://doi.org/10.1016/S1369-5266(03)00083-9

Cited by

  1. Structural and expression analysis of glutelin genes in Oryza sativa L. vol.38, pp.2, 2011, https://doi.org/10.5010/JPB.2011.38.2.176