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Assigning biological functions to rice genes by genome annotation, expression analysis and mutagenesis

Abstract

Rice is the first cereal genome to be completely sequenced. Since the completion of its genome sequencing, considerable progress has been made in multiple areas including the whole genome annotation, gene expression profiling, mutant collection, etc. Here, we summarize the current status of rice genome annotation and review the methodology of assigning biological functions to hundreds of thousands of rice genes as well as discuss the major limitations and the future perspective in rice functional genomics. Available data analysis shows that the rice genome encodes around 32,000 protein-coding genes. Expression analysis revealed at least 31,000 genes with expression evidence from full-length cDNA/EST collection or other transcript profiling. In addition, we have summarized various strategies to generate mutant population including natural, physical, chemical, T-DNA, transposon/retrotransposon or gene silencing based mutagenesis. Currently, more than 1 million of mutants have been generated and 27,551 of them have their flanking sequence tags. To assign biological functions to hundreds of thousands of rice genes, global co-operations are required, various genetic resources should be more easily accessible and diverse data from transcriptomics, proteomics, epigenetics, comparative genomics and bioinformatics should be integrated to better understand the functions of these genes and their regulatory mechanisms.

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References

  1. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218

    CAS  Article  Google Scholar 

  2. Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745

    CAS  Article  PubMed  Google Scholar 

  3. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R (2007) NCBI GEO: mining tens of millions of expression profiles. Database and tools update. Nucleic Acids Res 35:D760–D765

    CAS  Article  PubMed  Google Scholar 

  4. Barry GR (2001) The use of the Monsanto draft rice genome sequence in research. Plant Physiol 125:1164–1165

    CAS  Article  PubMed  Google Scholar 

  5. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268:78–94

    CAS  Article  PubMed  Google Scholar 

  6. Chern CG, Fan MJ, Yu SM et al (2007) A rice phenomics study-phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population. Plant Mol Biol 65:427–438

    CAS  Article  PubMed  Google Scholar 

  7. Chin HG, Choe MS, Lee SH et al (1999) Molecular analysis of rice plants harboring an Ac/Ds transposable element-mediated gene trapping system. Plant J 19:615–623

    CAS  Article  PubMed  Google Scholar 

  8. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641

    CAS  Article  PubMed  Google Scholar 

  9. Eckardt NA (2000) Sequencing the rice genome. Plant Cell 12:2011–2017

    CAS  Article  PubMed  Google Scholar 

  10. Goff SA, Ricke D, Lan TH et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. Japonica). Science 296:92–100

    CAS  Article  PubMed  Google Scholar 

  11. Greco R, Ouwerkerk PB, De Kam RJ, Sallaud C, Favalli C, Colombo L, Guiderdoni E, Meijer AH, Hoge Dagger JH, Pereira A (2003) Transpositional behaviour of an Ac/Ds system for reverse genetics in rice. Theor Appl Genet 108:10–24

    CAS  Article  PubMed  Google Scholar 

  12. Guo HS, Fei JF, Xie Q, Chua NH (2003) A chemical-regulated inducible RNAi system in plants. Plant J 34:383–392

    CAS  Article  PubMed  Google Scholar 

  13. Hiei Y, Ohta S, Komari T, Kumashiro T (1994) An efficient transformation of rice (Oryza sativa L.) mediated by Agrobaterium and sequence analysis of boundaries of the T-DNA. Plant J 6:271–282

    CAS  Article  PubMed  Google Scholar 

  14. Hirochika H (2001) Contribution of the Tos17 retrotransposon to rice functional genomics. Curr Opin Plant Biol 4:118–122

    CAS  Article  PubMed  Google Scholar 

  15. Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci USA 93:7783–7788

    CAS  Article  PubMed  Google Scholar 

  16. Huang X, Qian Q, Liu Z, Sun H, He S, Luo D, Xia G, Chu C, Li J, Fu X (2009) Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet 41:494–497

    CAS  Article  PubMed  Google Scholar 

  17. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Article  Google Scholar 

  18. Ito Y, Arikawa K, Antonio BA et al. (2005) Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics. Nucleic Acids Res 33(Database issue):D651–D655

    Google Scholar 

  19. Itoh T, Tanaka T, Barrero RA et al (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res 17:175–183

    Article  PubMed  Google Scholar 

  20. Jain M, Khurana JP (2009) Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS J 276:3148–3162

    CAS  Article  PubMed  Google Scholar 

  21. Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AK, Khurana JP (2007) F-box proteins in rice: genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143:1467–1483

    CAS  Article  PubMed  Google Scholar 

  22. Jeon JS, Lee S, Jung KH et al (2000) T-DNA insertional mutagenesis for functional genomics in rice. Plant J 22:561–570

    CAS  Article  PubMed  Google Scholar 

  23. Jiang SY, Ramachandran S (2010) Natural and artificial mutants as valuable resources for functional genomics and molecular breeding. Int J Biol Sci 6:228–251

    CAS  PubMed  Google Scholar 

  24. Jiang SY, Bachmann D, La H, Ma Z, Venkatesh PN, Ramamoorthy R, Ramachandran S (2007a) Ds insertion mutagenesis as an efficient tool to produce diverse variations for rice breeding. Plant Mol Biol 65:385–402

    CAS  Article  PubMed  Google Scholar 

  25. Jiang SY, Cai M, Ramachandran S (2007b) ORYZA SATIVA MYOSIN XI B controls pollen development by photoperiod-sensitive protein localizations. Dev Biol 304:579–592

    CAS  Article  PubMed  Google Scholar 

  26. Jiang SY, Christoffels A, Ramamoorthy R, Ramachandran S (2009) Expansion mechanisms and functional annotations of hypothetical genes in rice genome. Plant Physiol 150:1997–2008

    CAS  Article  PubMed  Google Scholar 

  27. 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 9:91–101

    CAS  PubMed  Google Scholar 

  28. Kikuchi S, Satoh K, Nagata T et al (2003) Collection, mapping, and annotation of over 28, 000 cDNA clones from japonica rice. Science 301:376–379

    Article  PubMed  Google Scholar 

  29. Kolesnik T, Szeverenyi I, Bachmann D, Kumar CS, Jiang SY, Ramamoorthy R, Cai M, Ma ZG, Sundaresan V, Ramachandran S (2004) Establishing an efficient Ac/Ds tagging system in rice: large-scale analysis of Ds flanking sequences. Plant J 37:301–314

    CAS  Article  PubMed  Google Scholar 

  30. Koorneef M, Dellaert LWM, Vab der Veen JH (1982) EMS- and radiation-induced mutation frequencies at individual loci in Arabidopsis thaliana (L.), Heynh. Mutation Res 93:109–123

    Google Scholar 

  31. Krishnan A, Guiderdoni E, An G et al (2009) Mutant resources in rice for functional genomics of the grasses. Plant Physiol 149:165–170

    CAS  Article  PubMed  Google Scholar 

  32. Krysan PJ, Young JC, Sussman MR (1999) T-DNA as an insertional mutagen in Arabidopsis. Plant Cell 11:2283–2290

    CAS  Article  PubMed  Google Scholar 

  33. Kumar CS, Wing RA, Sundaresan V (2005) Efficient insertional mutagenesis in rice using the maize En/Spm elements. Plant J 44:879–892

    CAS  Article  PubMed  Google Scholar 

  34. Kuromori T, Takahashi S, Kondou Y, Shinozaki K, Matsui M (2009) Phenome analysis in plant species using loss-of-function and gain-of-function mutants. Plant Cell Physiol 50:1215–1231

    CAS  Article  PubMed  Google Scholar 

  35. Larmande P, Gay C, Lorieux M et al. (2008) Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. Nucleic Acids Res 36 (Database issue):D1022–D1027

  36. Li X, Song Y, Century K, Straight S, Ronald P, Dong X, Lassner M, Zhang Y (2001) A fast neutron deletion mutagenesis-based reverse genetics system for plants. Plant J 27:235–242

    CAS  Article  PubMed  Google Scholar 

  37. Li X, Lassner M, Zhang Y (2002) Deleteagene: a fast neutron deletion mutagenesis-based knockout system for plants. Comp Funct Genomics 3:158–160

    CAS  Article  PubMed  Google Scholar 

  38. Li X, Qian Q, Fu Z et al (2003) Control of tillering in rice. Nature 422:618–621

    CAS  Article  PubMed  Google Scholar 

  39. Lister R, Gregory BD, Ecker JR (2009) Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr Opin Plant Biol 12:107–118

    CAS  Article  PubMed  Google Scholar 

  40. Liu X, Lu T, Yu S et al (2007) A collection of 10, 096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies. Plant Mol Biol 65:403–415

    CAS  Article  PubMed  Google Scholar 

  41. Lu T, Huang X, Zhu C, Huang T, Zhao Q, Xie K, Xiong L, Zhang Q, Han B (2008a) RICD: a rice indica cDNA database resource for rice functional genomics. BMC Plant Biol 8:118

    Article  PubMed  Google Scholar 

  42. Lu T, Yu S, Fan D, Mu J, Shangguan Y, Wang Z, Minobe Y, Lin Z, Han B (2008b) Collection and comparative analysis of 1888 full-length cDNAs from wild rice Oryza rufipogon Griff. W1943. DNA Res 15:285–295

    CAS  Article  PubMed  Google Scholar 

  43. Lukashin AV, Borodovsky M (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 26:1107–1115

    CAS  Article  PubMed  Google Scholar 

  44. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402

    CAS  Article  PubMed  Google Scholar 

  45. McCallum CM, Comai L, Greene EA, Henikoff S (2000a) Targeting induced local lessions in genomes (TILLING) for plant functional genomics. Plant Physiol 123:439–442

    CAS  Article  PubMed  Google Scholar 

  46. McCallum CM, Comai L, Greene EA, Henikoff S (2000b) Targeted screening for induced mutations. Nat Biotechnol 18:455–457

    CAS  Article  PubMed  Google Scholar 

  47. Miki D, Shimamoto K (2004) Simple RNAi vectors for stable and transient suppression of gene function in rice. Plant Cell Physiol 45:490–495

    CAS  Article  PubMed  Google Scholar 

  48. Miyao A, Tanaka K, Murata K, Sawaki H, Takeda S, Abe K, Shinozuka Y, Onosato K, Hirochika H (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15:1771–1780

    Article  PubMed  Google Scholar 

  49. Miyao A, Iwasaki Y, Kitano H, Itoh J, Maekawa M, Murata K, Yatou O, Nagato Y, Hirochika H (2007) A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes. Plant Mol Biol 63:625–635

    CAS  Article  PubMed  Google Scholar 

  50. Mochida K, Shinozaki K (2010) Genomics and bioinformatics resources for crop improvement. Plant Cell Physiol 51:497–523

    CAS  Article  PubMed  Google Scholar 

  51. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628

    CAS  Article  PubMed  Google Scholar 

  52. Nagy A, Hegyi H, Farkas K, Tordai H, Kozma E, Bányai L, Patthy L (2008) Identification and correction of abnormal, incomplete and mispredicted proteins in public databases. BMC Bioinformatics 9:353

    Article  PubMed  Google Scholar 

  53. Nobuta K, Venu RC, Lu C et al (2007) An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol 25:473–477

    CAS  Article  PubMed  Google Scholar 

  54. Ohyanagi H, Tanaka T, Sakai H et al. (2006) The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Res 34(Database issue):D741–D744

  55. Ouyang S, Zhu W, Hamilton J et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35(Database issue):D883–D887

    Google Scholar 

  56. Park SH, Jun NS, Kim CM et al (2007) Analysis of gene-trap Ds rice populations in Korea. Plant Mol Biol 65:373–384

    CAS  Article  PubMed  Google Scholar 

  57. Park DS, Park SK, Han SI et al (2009) Genetic variation through Dissociation (Ds) insertional mutagenesis system for rice in Korea: progress and current status. Mol Breed 24:1–15

    CAS  Article  Google Scholar 

  58. Pertea M, Lin X, Salzberg SL (2001) GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res 29:1185–1190

    CAS  Article  PubMed  Google Scholar 

  59. Piffanelli P, Droc G, Mieulet D et al (2007) Large-scale characterization of Tos17 insertion sites in a rice T-DNA mutant library. Plant Mol Biol 65:587–601

    CAS  Article  PubMed  Google Scholar 

  60. Sakata K, Nagasaki H, Idonuma A, Waki K, Kise M, Sasaki T (1999) A computer program for prediction of gene domain on rice genome sequence. In: The 2nd Georgia tech international conference on bioinformatics, Abstracts p 78

  61. Sakata K, Nagamura Y, Numa H et al (2002) RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Res 30:98–102

    CAS  Article  PubMed  Google Scholar 

  62. Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10:516–522

    CAS  Article  PubMed  Google Scholar 

  63. Satoh K, Doi K, Nagata T et al (2007) Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PLoS One 2:e1235

    Article  PubMed  Google Scholar 

  64. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470

    CAS  Article  PubMed  Google Scholar 

  65. Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023–1028

    CAS  Article  PubMed  Google Scholar 

  66. Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623–630

    CAS  Article  PubMed  Google Scholar 

  67. Souvorov A (2007) Gnomon? NCBI gene prediction tool for eukaryotic genomes. In: Plant & Animal Genomes XV Conference. January 13–17, Town & Country Convention Center, San Diego, CA

  68. Springer PS (2000) Gene traps: tools for plant development and genomics. Plant Cell 12:1007–1020

    CAS  Article  PubMed  Google Scholar 

  69. Tanaka T, Antonio BA, Kikuchi S et al (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res 36 (Database issue):D1028–D1033

  70. Upadhyaya NM, Zhou XR, Ramm K et al (2002) An iAc/Ds gene and enhancer trapping system for insertional mutagenesis in rice. Funct Plant Biol 29:547–559

    CAS  Article  Google Scholar 

  71. van Enckevort LJ, Droc G, Piffanelli P et al (2005) EU-OSTID: a collection of transposon insertional mutants for functional genomics in rice. Plant Mol Biol 59:99–110

    CAS  Article  PubMed  Google Scholar 

  72. Vaughan DA (1994) The wilde relatives of rice: a genetic resource handbook. International Rice Research Institute, Manila, Philippines

    Google Scholar 

  73. Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE Jr, Hieter P, Vogelstein B, Kinzler KW (1997) Characterization of the yeast transcriptome. Cell 88:243–251

    CAS  Article  PubMed  Google Scholar 

  74. Wang Z, Chen C, Xu Y, Jiang R, Xu Z, Chong K (2004) A Practical Vector for Efficient Knockdown of Gene Expression in Rice (Oryza sativa L.). Plant Mol Biol Rep 22:409–417

    CAS  Article  Google Scholar 

  75. Wesley SV, Helliwell CA, Smith NA et al (2001) Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J 27:581–590

    CAS  Article  PubMed  Google Scholar 

  76. Wu TD, Watanabe CK (2005) GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21:1859–1875

    CAS  Article  PubMed  Google Scholar 

  77. Wu JL, Wu C, Lei C et al (2005) Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics. Plant Mol Biol 59:85–97

    CAS  Article  PubMed  Google Scholar 

  78. Xue W, Xing Y, Weng X et al (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767

    CAS  Article  PubMed  Google Scholar 

  79. Yamazaki M, Tsugawa H, Miyao A, Yano M, Wu J, Yamamoto S, Matsumoto T, Sasaki T, Hirochika H (2001) The rice retrotransposon Tos17 prefers low copy sequences as integration targets. Mol Gen Genet 265:336–344

    CAS  Google Scholar 

  80. Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. Indica). Science 296:79–92

    CAS  Article  PubMed  Google Scholar 

  81. Yu J, Wang J, Lin W et al (2005) The Genomes of Oryza sativa: a history of duplications. PLoS Biol 3:e38

    Article  PubMed  Google Scholar 

  82. Yuan Q, Ouyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J, Buell CR (2003) The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res 31:229–233

    CAS  Article  PubMed  Google Scholar 

  83. Yuan Q, Ouyang S, Wang A et al (2005) The institute for genomic research Osa1 rice genome annotation database. Plant Physiol 138:18–26

    CAS  Article  PubMed  Google Scholar 

  84. Zhang Q (2007) Strategies for developing green super rice. Proc Natl Acad Sci USA 104:16402–16409

    CAS  Article  PubMed  Google Scholar 

  85. Zhang Q, Li J, Xue Y, Han B, Deng XW (2008) Rice 2020: a call for an international coordinated effort in rice functional genomics. Mol Plant 1:715–719

    CAS  Article  PubMed  Google Scholar 

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Acknowledgements

We thank Drs. Ildiko Szeverenyi, Tatiana Kolesnik and Doris Bachmann as well as Zhigang Ma and Hongfen Luan for their help in the generation and investigation of Ds insertion lines.

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Correspondence to Srinivasan Ramachandran.

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Jiang, SY., Ramachandran, S. Assigning biological functions to rice genes by genome annotation, expression analysis and mutagenesis. Biotechnol Lett 32, 1753–1763 (2010). https://doi.org/10.1007/s10529-010-0377-7

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Keywords

  • Database
  • Expression profiling
  • Functional genomics
  • Mutagenesis
  • Rice