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Molecular Breeding

, Volume 26, Issue 2, pp 257–273 | Cite as

Rice genomics moves ahead

  • Saurabh Raghuvanshi
  • Meenu Kapoor
  • Shashi Tyagi
  • Sanjay Kapoor
  • Paramjit Khurana
  • Jitendra Khurana
  • Akhilesh TyagiEmail author
Article

Abstract

Rice is one of the pillars of world-wide food security. Improvement in its yield is necessary to mitigate hunger of millions of people who depend on rice as a staple. Decoding rice genome sequence is expected to complement efforts being made to improve rice and its yield. The information about more than 32,000 genes, regulatory elements, repeat DNA, and DNA markers opens-up new horizons for molecular analysis and genetic enhancement not only for rice but also for other cereal crops. In the post-genomic era, significant progress has been made on defining transcriptome and epigenome as well as gene discovery by way of forward and reverse genetic approaches. Efforts are on to fill the gap between the genome and the phenotype. This may lead to regular practice of genomics-assisted breeding of rice.

Keywords

Gene function Genome analysis Epigenomics Transcriptomics Genomics-assisted breeding Rice 

Notes

Acknowledgments

Our research is supported by DBT, DST and UGC, Government of India.

References

  1. Agarwal P, Arora R, Ray S et al (2007) Genome-wide identification of C2H2 zinc-finger gene family in rice and their phylogeny and expression analysis. Plant Mol Biol 65:467–485PubMedGoogle Scholar
  2. Armstead IP, Turner LB, Farrell M et al (2004) Synteny between a major heading-date QTL in perennial ryegrass (Lolium perenne L.) and the Hd3 heading-date locus in rice. Theor Appl Genet 108:822–828PubMedGoogle Scholar
  3. Arora R, Agarwal P, Ray S et al (2007) MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics 8:242PubMedGoogle Scholar
  4. Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 12:1021–1029PubMedGoogle Scholar
  5. Bennetzen JL, Ma J (2003) The genome colinearity of rice and other grasses on the basis of genome sequence analysis. Curr Opin Plant Biol 6:128–133PubMedGoogle Scholar
  6. Bennetzen JL, Ramakrishana W (2002) Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Mol Biol 48:821–827PubMedGoogle Scholar
  7. Bennetzen JL, Coleman C, Liu R et al (2004) Consistent over-estimation of gene number in complex plant genomes. Curr Opin Plant Biol 7:732–736PubMedGoogle Scholar
  8. Bolot S, Abrouk M, Masood-Quraishi U et al (2009) The ‘inner circle’ of the cereal genomes. Curr Opin Plant Biol 12:119–125PubMedGoogle Scholar
  9. Bossolini E, Wicker T, Knobel PA et al (2007) Comparison of orthologous loci from small grass genomes Brachypodium and rice: implications for wheat genomics and grass genome annotation. Plant J 49:704–717PubMedGoogle Scholar
  10. Brenner S, Johnson M, Bridgham J et al (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18:630–634PubMedGoogle Scholar
  11. Brunner S, Keller B, Feuillet C (2003) A large rearrangement involving genes and low-copy DNA interrupts the microcolinearity between rice and barley at the Rph7 locus. Genetics 164:673–683PubMedGoogle Scholar
  12. Cao X, Jacobsen SE (2002) Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci USA 4:16491–16498Google Scholar
  13. Chan SW, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6:351–360PubMedGoogle Scholar
  14. Chen M, Presting G, Barbazuk WB et al (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14:537–545PubMedGoogle Scholar
  15. Cho Y-I, Park C-W, Kwon S-W et al (2004) Key DNA markers for predicting heterosis in F1 hybrids of japonica rice. Breed Sci 54:389–397Google Scholar
  16. Civán P, Svec M (2009) Genome-wide analysis of rice (Oryza sativa L. subsp. japonica) TATA box and Y Patch promoter elements. Genome 52:294–297PubMedGoogle Scholar
  17. Collard BC, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 363:557–572PubMedGoogle Scholar
  18. Collard BCY, Cruz CMV, McNally KL et al (2008) Rice molecular breeding laboratories in the genomic era: current status and future considerations. Int J Plant Genomics, Article Id 524847Google Scholar
  19. Cui X, Xu J, Asghar R et al (2005) Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit. Bioinformatics 21:3852–3858PubMedGoogle Scholar
  20. Cui X, Xu XM, Mu DS et al (2008) Genomic analysis of rice microRNA promoters and clusters. Gene 431:61–66PubMedGoogle Scholar
  21. Dardick C, Chen J, Richter T et al (2007) The rice protein kinase database for the rice kinome. Plant Physiol 143:579–586PubMedGoogle Scholar
  22. Davierwala AP, Reddy AP, Lagu MD et al (2001) Marker assisted selection of bacterial blight resistance genes in rice. Biochem Genet 39:261–278PubMedGoogle Scholar
  23. De Hoon M, Hayashizaki Y (2008) Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference. Biotechniques 44:627–632PubMedGoogle Scholar
  24. Devos KM (2005) Updating the ‘crop circle’. Curr Opin Plant Biol 8:155–162PubMedGoogle Scholar
  25. Ding Y, Wang X, Su L et al (2007) SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice. Plant Cell 19:9–22PubMedGoogle Scholar
  26. Ding X, Hou X, Xie K et al (2009) Genome-wide identification of BURP domain-containing genes in rice reveals a gene family with diverse structures and responses to abiotic stresses. Planta 230:149–163PubMedGoogle Scholar
  27. Droc G, Périn C, Fromentin S et al (2009) OryGenesDB (2008) update: database interoperability for functional genomics of rice. Nucleic Acids Res 37:D992–D995PubMedGoogle Scholar
  28. Dunford RP, Yano M, Kurata N et al (2002) Comparative mapping of the barley Ppd-Hi photoperiod response gene region which lies close to a junction between two rice linkage segments. Genetics 161:825–834PubMedGoogle Scholar
  29. Edwards JD, Janda J, Sweeney MT et al (2008) Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice. Plant Methods 4:13PubMedGoogle Scholar
  30. Eisen JA, Fraser CM (2003) Phylogenomics: intersection of evolution and genomics. Science 300:1706–1707PubMedGoogle Scholar
  31. Emery JF, Floyd SK, Alvarez J et al (2003) Radial patterning of Arabidopsis shoots by classIII HD-ZIP and KANADI genes. Curr Biol 13:1768–1774PubMedGoogle Scholar
  32. Endo M, Tsuchiya T, Saito H et al (2004) Identification and molecular characterization of novel anther-specific genes in Oryza sativa L. by using cDNA microarray. Genes Genet Syst 79:213–226PubMedGoogle Scholar
  33. Feltus FA, Wan J, Schulze SR et al (2004) An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res 14:1812–1819PubMedGoogle Scholar
  34. Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329–341PubMedGoogle Scholar
  35. Feuillet C, Keller B (1999) High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci USA 96:1342–1353Google Scholar
  36. Feuillet C, Keller B (2002) Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann Bot 89:3–10PubMedGoogle Scholar
  37. Finnegan EJ, Kovac KA (2000) Plant DNA methyltransferases. Plant Mol Biol 43:189–201PubMedGoogle Scholar
  38. Fischle W, Wang Y, Allis CD (2003) Binary switches and modification cassettes in histone biology and beyond. Nature 425:475–479PubMedGoogle Scholar
  39. Fitzgerald MA, McCouch SR, Hall RD (2009) Not just a grain of rice: the quest for quality. Trends Plant Sci 14:133–139PubMedGoogle Scholar
  40. Fukuoka S, Inoue T, Miyao A et al (1994) Mapping of sequence-tagged sites in rice by single strand conformation polymorphism. DNA Res 1:271–277PubMedGoogle Scholar
  41. Furutani I, Sukegawa S, Kyozuka J (2006) Genome-wide analysis of spatial and temporal gene expression in rice panicle. Plant J 46:503–511PubMedGoogle Scholar
  42. Goff SA, Ricke D, Lan TH et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100PubMedGoogle Scholar
  43. Gowda M, Jantasuriyarat C, Dean RA et al (2004) Robust-LongSAGE (RL-SAGE): a substantially improved LongSAGE method for gene discovery and transcriptome analysis. Plant Physiol 134:890–897PubMedGoogle Scholar
  44. Griffiths-Jones S, Saini HK, Van Dongen S et al (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–D158PubMedGoogle Scholar
  45. Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185Google Scholar
  46. Haas BJ, Volfovsky N, Town CD et al (2002) Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol 3:0029.1–0029.12Google Scholar
  47. Hackauf B, Rudd S, van der Voort JR et al (2008) Comparative mapping of DNA sequences in rye (Secale cereale L.) in relation to the rice genome. Theor Appl Genet 118:371–384PubMedGoogle Scholar
  48. Han B, Zhang Q (2008) Rice genome research; current status and future perspectives. Plant Genome 1:71–76Google Scholar
  49. Han F, Kleinhofs A, Ullrich SE et al (1998) Synteny with rice-analysis of barley malting quality QTLs and RPG4 chromosomal regions. Genome 41:373–380Google Scholar
  50. Han F, Kilian A, Chen JP et al (1999) Sequence analysis of a rice BAC covering the syntenous barley Rpg1 region. Genome 42:1071–1076PubMedGoogle Scholar
  51. Hazen SP, Kay SA (2003) Gene arrays are not just for measuring gene expression. Trends Plant Sci 8:413–416PubMedGoogle Scholar
  52. Hirano K, Aya K, Hobo T et al (2008) Comprehensive transcriptome analysis of phytohormone biosynthesis and signaling genes in microspore/pollen and tapetum of rice. Plant Cell Physiol 49:1429–1450PubMedGoogle Scholar
  53. Hirochika H, Sugimoto K, Otsuki Y et al (1996) Autonomous retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci USA 93:7783–7788PubMedGoogle Scholar
  54. Hirochika H, Guiderdoni E, An G et al (2004) Rice mutant resources for gene discovery. Plant Mol Biol 54:325–334PubMedGoogle Scholar
  55. Hittalmani S, Parco A, Mew TV et al (2000) Fine mapping and DNA marker-assisted pyramiding of the three major genes for blast resistance in rice. Theor Appl Genet 100:1121–1128Google Scholar
  56. Hoecker N, Keller B, Muthreich N et al (2008) Comparison of maize (Zea mays L.) F1-hybrid and parental inbred line primary root transcriptomes suggests organ-specific patterns of nonadditive gene expression and conserved expression trends. Genetics 179:1275–1283PubMedGoogle Scholar
  57. Huang X, Qian Q, Liu Z et al (2009) Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet 41:494–497PubMedGoogle Scholar
  58. Imanishi T, Itoh T, Suzuki Y et al (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol 2:856–875Google Scholar
  59. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800Google Scholar
  60. Izawa T, Takahashi Y, Yano M (2003) Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis. Curr Opin Plant Biol 6:113–120PubMedGoogle Scholar
  61. Jabbari K, Cruveiller S, Clay O et al (2004) The new genes of rice: a closer look. Trends Plant Sci 9:281–285PubMedGoogle Scholar
  62. Jackson JP, Lindroth AM, Cao X et al (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416:556–560PubMedGoogle Scholar
  63. Jain S, Jain RK, McCouch SR (2004) Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theor Appl Genet 109:965–977PubMedGoogle Scholar
  64. Jain M, Nijhawan A, Arora R et al (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 143:1467–1483PubMedGoogle Scholar
  65. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080PubMedGoogle Scholar
  66. Jiang N, Bao Z, Zhang X et al (2003) An active DNA transposon family in rice. Nature 421:163–167PubMedGoogle Scholar
  67. Jiao Y, Tausta SL, Gandotra N et al (2009) A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet 41:258–263PubMedGoogle Scholar
  68. Jongeneel CV, Delorenzi M, Iseli C et al (2005) An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res 15:1007–1014PubMedGoogle Scholar
  69. 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
  70. Kapoor M, Arora R, Lama T et al (2008) Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analysis during reproductive development and stress in rice. BMC Genomics 9:451PubMedGoogle Scholar
  71. Kathuria H, Giri J, Tyagi H et al (2007) Advances in transgenic rice biotechnology. Crit Rev Plant Sci 26:65–103Google Scholar
  72. Kawasaki S, Borchert C, Deyholos M et al (2001) Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13:889–905PubMedGoogle Scholar
  73. Kazazian HH Jr (2004) Mobile elements: drivers of genome evolution. Science 303:1626–1632PubMedGoogle Scholar
  74. Keller B, Feuillet C (2000) Colinearity and gene density in grass genomes. Trends Plant Sci 5:246–251PubMedGoogle Scholar
  75. Kikuchi S, Satoh K, Nagata T et al (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301:376–379PubMedGoogle Scholar
  76. Kikuchi S, Wang G-L, Li L (2007) Genome-wide RNA expression profile in rice. In: Upadhyaya N (ed) Rice functional genomics: challenges, progress and prospects. Springer, New York, pp 31–54Google Scholar
  77. Kim KM, Cho SK, Shin SH et al (2005) Analysis of differentially expressed transcripts of fungal elicitor and wound-treated wild rice (Oryza grandiglumis). J Plant Res 118:347–354PubMedGoogle Scholar
  78. Krishnan A, Guiderdoni E, An G et al (2009) Mutant resources in rice for functional genomics of the grasses. Plant Physiol 149:165–170PubMedGoogle Scholar
  79. 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:D1022–D1027PubMedGoogle Scholar
  80. Leister D, Kurth J, Laurie DA et al (1998) Rapid reorganization of resistance gene homologues in cereal genomes. Proc Natl Acad Sci USA 95:370–375PubMedGoogle Scholar
  81. Li L, Wang X, Xia M et al (2005) Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol 6:R52PubMedGoogle Scholar
  82. Li L, Wang X, Stolc V et al (2006) Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 38:124–129PubMedGoogle Scholar
  83. Li L, Wang X, Sasidharan R et al (2007) Global identification and characterization of transcriptionally active regions in the rice genome. PLoS ONE 2:e294PubMedGoogle Scholar
  84. Li X, Wang X, He K et al (2008) High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation and gene expression. Plant Cell 20:259–276PubMedGoogle Scholar
  85. Lindroth AM, Cao X, Jackson JP et al (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292:2077–2080PubMedGoogle Scholar
  86. Lister R, Gregory BD, Ecker JR (2009) Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr Opin Plant Biol 12:107–118PubMedGoogle Scholar
  87. Liu J, Hara C, Umeda M et al (1995) Analysis of randomly isolated cDNAs from developing endosperm of rice (Oryza sativa L.): evaluation of expressed sequence tags, and expression levels of mRNAs. Plant Mol Biol 29:685–689PubMedGoogle Scholar
  88. Liu B, Li P, Li X et al (2005) Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in rice. Plant Physiol 139:296–305PubMedGoogle Scholar
  89. Liu B, Chen Z, Song X et al (2007) Oryza sativa Dicer-like4 reveals a key role for small interfering RNA silencing in plant development. Plant Cell 19:2705–2718PubMedGoogle Scholar
  90. Liu Q, Zhang YC, Wang CY et al (2009) Expression analysis of phytohormone-regulated microRNAs in rice, implying their regulation roles in plant hormone signaling. FEBS Lett 583:723–728PubMedGoogle Scholar
  91. Lu C, Jeong DH, Kulkarni K et al (2008a) Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proc Natl Acad Sci USA 105:4951–4956PubMedGoogle Scholar
  92. Lu T, Huang X, Zhu C et al (2008b) RICD: a rice indica cDNA database resource for rice functional genomics. BMC Plant Biol 8:118PubMedGoogle Scholar
  93. Lu F, Ammiraju JS, Sanyal A et al (2009) Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 106:2071–2076PubMedGoogle Scholar
  94. Malagnac F, Bartee L, Bender J (2002) An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J 21:6842–6852PubMedGoogle Scholar
  95. Mathieu O, Reinders J, Caikovski M et al (2007) Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130:851–862PubMedGoogle Scholar
  96. Matsumoto T, Wu J, Antonio B et al (2008) Development in rice genome research based on accurate genome sequence. Int J Plant Genomics, Article Id 348621Google Scholar
  97. Matsumura H, Bin Nasir KH, Yoshida K et al (2006) SuperSAGE array: the direct use of 26-base-pair transcript tags in oligonucleotide arrays. Nat Methods 3:469–474PubMedGoogle Scholar
  98. Meins F Jr, Si-Ammour A, Blevins T et al (2005) RNA silencing systems and their relevance to plant development. Annu Rev Cell Dev Biol 21:297–318PubMedGoogle Scholar
  99. Meyer S, Pospisil H, Scholten S (2007) Heterosis associated gene expression in maize embryos 6 days after fertilization exhibits additive, dominant and overdominant pattern. Plant Mol Biol 63:381–391PubMedGoogle Scholar
  100. Mihara M, Itoh T, Izawa T (2009) SALAD database: a motif-based database o f protein annotations for plant comparative genomics. Nucleic Acids Res Database IssueGoogle Scholar
  101. Miki D, Shimamoto K (2008) De novo DNA methylation induced by siRNA targeted to endogenous transcribed sequences is gene-specific and OsMet1-independent in rice. Plant J 56:539–549PubMedGoogle Scholar
  102. Misra S, Crosby M, Mungall C et al (2002) Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol 3:0083.1–0083.22Google Scholar
  103. Miyao A, Tanaka K, Murata K et al (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 15:1771–1780PubMedGoogle Scholar
  104. Monna L, Miyao A, Inoue T et al (1994) Determination of RAPD markers in rice and their conversion into sequence tagged sites (STSs) and STS-specific primers. DNA Res 1:139–148PubMedGoogle Scholar
  105. Monna L, Ohta R, Masuda H et al (2006) Genome-wide searching of single-nucleotide polymorphisms among eight distantly and closely related rice cultivars (Oryza sativa L.) and a wild accession (Oryza rufipogon Griff.). DNA Res 13:43–51PubMedGoogle Scholar
  106. Nagaraju J, Kathirvel M, Kumar RR et al (2002) Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence-based ISSR-PCR and SSR markers. Proc Natl Acad Sci USA 99:5836–5841PubMedGoogle Scholar
  107. Nagasaki H, Itoh J, Hayashi K et al (2007) The small interfering RNA production pathway is required for shoot meristem initiation in rice. Proc Natl Acad Sci USA 104:14867–14871PubMedGoogle Scholar
  108. Nakano M, Nobuta K, Vemaraju K et al (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res 34:D731–D735PubMedGoogle Scholar
  109. Nakazaki T, Okumoto Y, Horibata A et al (2003) Mobilization of a transposon in the rice genome. Nature 421:170–172PubMedGoogle Scholar
  110. Ngezahayo F, Xu C, Wang H et al (2009) Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice. BMC Plant Mol Biol 9:91Google Scholar
  111. Nijhawan A, Jain M, Tyagi AK et al (2008) A genomic survey and gene expression analysis of basic leucine zipper (bZIP) transcription factor family in rice. Plant Physiol 146:333–350PubMedGoogle Scholar
  112. Nobuta K, Venu RC, Lu C et al (2007) An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol 25:473–477PubMedGoogle Scholar
  113. Nonomura K, Morohoshi A, Nakano M et al (2007) A germ cell-specific gene of the ARGONAUTE family is essential for the progression of premeiotic mitosis and meiosis during sporogenesis in rice. Plant Cell 19:2583–2594PubMedGoogle Scholar
  114. O’Donnell KA, Boeke JD (2007) Mighty Piwis defend the germline against genome intruders. Cell 129:37–44PubMedGoogle Scholar
  115. Ouyang S, Zhu W, Hamilton J et al (2007) The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res 35:D883–D887PubMedGoogle Scholar
  116. Ouyang Y, Chen J, Xie W et al (2009) Comprehensive sequence and expression profile analysis of Hsp20 gene family in rice. Plant Mol Biol 70:341–357PubMedGoogle Scholar
  117. Ozsolak F, Platt AR, Jones DR et al (2009) Direct RNA sequencing. Nature 461:814–818PubMedGoogle Scholar
  118. Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 101:9903–9908PubMedGoogle Scholar
  119. Paterson AH, Bowers JE, Bruggmann R et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556PubMedGoogle Scholar
  120. Perez LM, Redona ED, Mendioro MS et al (2008) Introgression of Xa4, Xa7 and Xa21 for resistance to bacterial blight in thermosensitive genetic male sterile rice (Oryza sativa L.) for the development of two-line hybrids. Euphytica 164:627–636Google Scholar
  121. Picault N, Chaparro C, Piegu B et al (2009) Identification of an active LTR retrotransposon in rice. Plant J 58:754–765PubMedGoogle Scholar
  122. Prigge MJ, Otsuga D, Alonso JM et al (2005) Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development. Plant Cell 17:61–76PubMedGoogle Scholar
  123. Rabbani MA, Maruyama K, Abe H et al (2003) Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol 133:1755–1767PubMedGoogle Scholar
  124. Ray S, Agarwal P, Arora R et al (2007) Expression analysis of calcium-dependent protein kinase gene family during reproductive development and abiotic stress conditions in rice (Oryza sativa L. ssp. indica). Mol Genet Genomics 278:493–505PubMedGoogle Scholar
  125. Reinartz J, Bruyns E, Lin JZ et al (2002) Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. Brief Funct Genomics Proteomics 1:95–104Google Scholar
  126. Rensink WA, Buell CR (2005) Microarray expression profiling resources for plant genomics. Trends Plant Sci 10:603–609PubMedGoogle Scholar
  127. Rice Annotation Project (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res 17:175–183Google Scholar
  128. Rice Annotation Project (2008) The rice annotation project database (RAP-DB): 2008 update. Nucleic Acids Res 36:D1028–D1033Google Scholar
  129. Sakamoto T, Matsuoka M (2008) Identifying and exploiting grain yield genes in rice. Curr Opin Plant Biol 11:209–214PubMedGoogle Scholar
  130. Salse J, Peigu B, Cooke R et al (2004) New in silico insight into the synteny between rice (Oryza saliva L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome. Plant J 38:396–409PubMedGoogle Scholar
  131. Sanchez AC, Brar DS, Huang N et al (2000) Sequence tagged site marker-assisted selection for three blight resistant genes in rice. Crop Sci 40:792–797Google Scholar
  132. Sasaki T, Song J, Koga-Ban Y et al (1994) Toward cataloguing all rice genes: large-scale sequencing of randomly chosen rice cDNAs from a callus cDNA library. Plant J 6:615–624PubMedGoogle Scholar
  133. 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:e1235PubMedGoogle Scholar
  134. Schena M, Shalon D, Davis RW et al (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470PubMedGoogle Scholar
  135. Schwab R, Ossowski S, Riester M et al (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18:1121–1133PubMedGoogle Scholar
  136. Shen YJ, Jiang H, Jin JP et al (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135:1198–1205PubMedGoogle Scholar
  137. Shim KS, Cho SK, Jeung JU et al (2004) Identification of fungal (Magnaporthe grisea) stress-induced genes in wild rice (Oryza minuta). Plant Cell Rep 22:599–607PubMedGoogle Scholar
  138. Shimono M, Sugano S, Nakayama A et al (2007) Rice WRKY45 plays a crucial role in benzothiadiazole-inducible blast resistance. Plant Cell 19:2064–2076PubMedGoogle Scholar
  139. Shirasawa K, Maeda H, Monna L et al (2007) The number of genes having different alleles between rice cultivars estimated by SNP analysis. Theor Appl Genet 115:1067–1074PubMedGoogle Scholar
  140. Singh NK, Raghuvanshi S, Srivastava SK et al (2004) Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny. Funct Integr Genomics 4:102–117PubMedGoogle Scholar
  141. Singh NK, Dalal V, Batra K et al (2007) Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes. Funct Integr Genomics 7:17–35PubMedGoogle Scholar
  142. Skvortsov D, Abdueva D, Stitzer M et al (2007) Using expression arrays for copy number detection: an example from E. coli. BMC Bioinformatics 8:203PubMedGoogle Scholar
  143. Soderlund C, Haller K, Pampanwar V et al (2006) MGOS: a resource for studying Magnaporthe grisea and Oryza sativa interactions. Mol Plant Microbe Interact 19:1055–1061PubMedGoogle Scholar
  144. Song BK, Hein I, Druka A et al (2008) The 172-kb genomic region of the O. rufipogon yld1.1 locus: comparative sequence analysis with O. sativa ssp. japonica and O. sativa ssp. indica. Funct Integr Genomics 9:97–108PubMedGoogle Scholar
  145. Stein LD, Mungall C, Shu S et al (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12:1599–1610PubMedGoogle Scholar
  146. Stolc V, Li L, Wang X et al (2005) A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray. Plant Mol Biol 59:137–149PubMedGoogle Scholar
  147. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403:42–45Google Scholar
  148. Sunkar R, Girke T, Jain PK et al (2005) Cloning and characterization of microRNAs from rice. Plant Cell 17:1397–1411PubMedGoogle Scholar
  149. Suwabe K, Suzuki G, Takahashi H et al (2008) Separated transcriptomes of male gametophyte and tapetum in rice: validity of a laser microdissection (LM) microarray. Plant Cell Physiol 49:1407–1416PubMedGoogle Scholar
  150. Swanson-Wagner RA, Jia Y, DeCook R et al (2006) All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents. Proc Natl Acad Sci USA 103:6805–6810PubMedGoogle Scholar
  151. Teerawanichpan P, Chandrasekharan MB, Jiang Y et al (2004) Characterization of two rice DNA methyltransferase genes and RNAi-mediated reactivation of a silenced transgene in rice callus. Planta 218:337–349PubMedGoogle Scholar
  152. The Rice Chromosome 11 and 12 Sequencing Consortia (2005) The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biol 3:20Google Scholar
  153. Thongjuea S, Ruanjaichon V, Bruskiewich R et al (2009) RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome. Nucleic Acids Res 37:D996–D1000PubMedGoogle Scholar
  154. Throude M, Bolot S, Bosio M et al (2009) Structure and expression analysis of rice paleo duplications. Nucleic Acid Res 37:1248–1259PubMedGoogle Scholar
  155. Uchimiya H, Kidou S, Shimazaki T et al (1992) Random sequencing of cDNA libraries reveals a variety of expressed genes in cultured cells of rice (Oryza sativa L.). Plant J 2:1005–1009Google Scholar
  156. Vaucheret H (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 20:759–771PubMedGoogle Scholar
  157. Vazquez F, Vaucheret H, Rajagopalan R et al (2004) Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 16:69–79PubMedGoogle Scholar
  158. Velculescu VE, Zhang L, Vogelstein B et al (1995) Serial analysis of gene expression. Science 270:484–487PubMedGoogle Scholar
  159. Venu RC, Jia Y, Gowda M et al (2007) RL-SAGE and microarray analysis of the rice transcriptome after Rhizocotonia solani infection. Mol Genet Genomics 278:421–431PubMedGoogle Scholar
  160. Vij S, Tyagi AK (2008) A20/AN1 zinc-finger domain-containing proteins in plants and animals represent common elements in stress response. Funct Integr Genomics 8:301–307PubMedGoogle Scholar
  161. Vij S, Gupta V, Kumar D et al (2006) Decoding the rice genome. BioEssays 28:421–432PubMedGoogle Scholar
  162. Vij S, Giri J, Dansana P et al (2008) The receptor-like cytoplasmic kinase (OsRLCK) gene family in rice: organization, phylogenetic relationship, and expression during development and stress. Mol Plant 1:732–750PubMedGoogle Scholar
  163. Wang SM (2007) Understanding SAGE data. Trends Genet 23:42–50PubMedGoogle Scholar
  164. Wang Z, Liang Y, Li C et al (2005) Microarray analysis of gene expression involved in anther development in rice (Oryza sativa L.). Plant Mol Biol 58:721–737PubMedGoogle Scholar
  165. Wang J, Nakazaki T, Chen S et al (2009a) Identification and characterization of the erect-pose panicle gene EP conferring high grain yield in rice (Oryza sativa L.). Theor Appl Genet 119:85–91PubMedGoogle Scholar
  166. Wang Z, Gerstein M, Snyder M (2009b) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63PubMedGoogle Scholar
  167. Warthmann N, Chen H, Ossowski S et al (2008) Highly specific gene silencing by artificial miRNAs in rice. PLoS One 3:e1829PubMedGoogle Scholar
  168. Wei G, Tao Y, Liu G et al (2009) A transcriptomic analysis of superhybrid rice LYP9 and its parents. Proc Natl Acad Sci USA 106:7695–7701PubMedGoogle Scholar
  169. Wortman JR, Haas BJ, Hannick LI et al (2003) Annotation of the Arabidopsis genome. Plant Physiol 132:461–468PubMedGoogle Scholar
  170. Wu J, Maehara T, Shimokawa T et al (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14:525–535PubMedGoogle Scholar
  171. Xiao W, Custard KD, Brown RC et al (2006) DNA methylation is critical for Arabidopsis embryogenesis and seed viability. Plant Cell 18:805–814PubMedGoogle Scholar
  172. Xu Y, Beachell H, McCouch SR (2004) A marker-based approach to broadening the genetic base of rice in the USA. Crop Sci 44:1947–1959CrossRefGoogle Scholar
  173. Yamaguchi T, Nakayama K, Hayashi T et al (2004) cDNA microarray analysis of rice anther genes under chilling stress at the microsporogenesis stage revealed two genes with DNA transposon Castaway in the 5-flanking regions. Biosci Biotechnol Biochem 68:1315–1323PubMedGoogle Scholar
  174. Yamakawa H, Hirose T, Kuroda M et al (2007) Comprehensive expression profiling of rice grain filling-related genes under high temperature using DNA microarray. Plant Physiol 144:258–277PubMedGoogle Scholar
  175. Yamamoto K, Sasaki T (1997) Large-scale EST sequencing in rice. Plant Mol Biol 35:135–144PubMedGoogle Scholar
  176. Yamauchi T, Moritoh S, Johzuka-Hisatomi Y et al (2008) Alternative splicing of the rice OsMET1 genes encoding maintenance DNA methyltransferase. J Plant Physiol 165:1774–1782PubMedGoogle Scholar
  177. Yamazaki M, Tsugava H, Miyao A et al (2001) The rice retrotransposon Tos17 prefers low-copy number sequences as integration targets. Mol Genet Genomics 265:336–344PubMedGoogle Scholar
  178. Yang GX, Jan A, Shen SH et al (2004) Microarray analysis of brassinosteroids- and gibberellin-regulated gene expression in rice seedlings. Mol Genet Genomics 271:468–478PubMedGoogle Scholar
  179. Yang Z, Gao Q, Sun C et al (2009) Molecular evolution and functional divergence of HAK potassium transporter gene family in rice (Oryza sativa L.). J Genet Genomics 36:161–172PubMedGoogle Scholar
  180. Yazaki J, Kishimoto N, Nakamura K et al (2000) Embarking on rice functional genomics via cDNA microarray: use of 3′ UTR probes for specific gene expression analysis. DNA Res 7:367–370PubMedGoogle Scholar
  181. Yazaki J, Kishimoto N, Nagata Y et al (2003) Genomics approach to abscisic acid- and gibberellin-responsive genes in rice. DNA Res 10:249–261PubMedGoogle Scholar
  182. Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92PubMedGoogle Scholar
  183. Yu J, Wang J, Lin W et al (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3:e38PubMedGoogle Scholar
  184. Yuan Q, Ouyang S, Wang A et al (2005) The Institute for Genomic Research Osa1 rice genome annotation database. Plant Physiol 138:18–26PubMedGoogle Scholar
  185. Zhang J, Li X, Jiang G et al (2006a) Pyramiding of Xa7 and Xa21 for the improvement of disease resistance to bacterial blight in hybrid rice. Plant Breed 125:600–605Google Scholar
  186. Zhang B, Pan X, Cannon CH et al (2006b) Conservation and divergence of plant microRNA genes. Plant J 46:243–259PubMedGoogle Scholar
  187. Zhang Q, Li J, Xue Y et al (2008) Rice 2020; a call for international coordinated effort in rice functional genomics. Mol Plant 1:715–719PubMedGoogle Scholar
  188. Zhao W, Wang J, He X et al (2004) BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res 32:D377–D382PubMedGoogle Scholar
  189. Zhao B, Ge L, Liang K et al (2009) Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor. BMC Mol Biol 10:29PubMedGoogle Scholar
  190. Zhou J, Wang X, Jiao Y et al (2007) Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. Plant Mol Biol 63:591–608PubMedGoogle Scholar
  191. Zhu Q-H, Spriggs A, Matthew L et al (2008) A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res 18:1456–1465PubMedGoogle Scholar
  192. Zwick MS, Islam-Faridi MN, Czeschin DG et al (1998) Physical mapping of the liguleless linkage group in Sorghum bicolor using rice RFLP-selected sorghum BACs. Genetics 148:1983–1992PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Saurabh Raghuvanshi
    • 1
  • Meenu Kapoor
    • 2
  • Shashi Tyagi
    • 3
  • Sanjay Kapoor
    • 1
  • Paramjit Khurana
    • 1
  • Jitendra Khurana
    • 1
  • Akhilesh Tyagi
    • 4
    Email author
  1. 1.Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular BiologyUniversity of DelhiNew DelhiIndia
  2. 2.University School of Biotechnology, GGS Indraprastha UniversityDelhiIndia
  3. 3.Botany DepartmentGargi CollegeNew DelhiIndia
  4. 4.National Institute of Plant Genome ResearchNew DelhiIndia

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