Rice genomics moves ahead

Molecular Breeding

Volumn 26, Issue 2, 2010, Pages 257-273

  Raghuvanshi, Saurabh ^a   Kapoor, Meenu ^b   Tyagi, Shashi ^c   Kapoor, Sanjay ^a   Khurana, Paramjit ^a   Khurana, Jitendra ^a   Tyagi, Akhilesh ^d  

^a UNIVERSITY OF DELHI   (India)

^b GURU GOBIND SINGH INDRAPRASTHA UNIVERSITY   (India)

^c UNIVERSITY OF DELHI   (India)

^d NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

Epigenomics; Gene function; Genome analysis; Genomics assisted breeding; Rice; Transcriptomics

Indexed keywords

FOOD SUPPLY; GENES;

EPIGENOMICS; FOOD SECURITY; GENE FUNCTION; GENOME ANALYSIS; GENOME SEQUENCES; GENOMIC-ASSISTED BREEDING; GENOMICS; RICE; RICE GENOMES; TRANSCRIPTOMICS;

GENOME;

EID: 77955056912     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-009-9367-7     Document Type: Article

References (192)

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: 467-485.
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: 822-828.
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: 242.
4. Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 12: 1021-1029.
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: 128-133.
6. Bennetzen JL, Ramakrishana W (2002) Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Mol Biol 48: 821-827.
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: 732-736.
8. Bolot S, Abrouk M, Masood-Quraishi U et al (2009) The 'inner circle' of the cereal genomes. Curr Opin Plant Biol 12: 119-125.
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: 704-717.
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: 630-634.
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: 673-683.
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: 16491-16498.
13. Chan SW, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6: 351-360.
14. Chen M, Presting G, Barbazuk WB et al (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14: 537-545.
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: 389-397.
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: 294-297.
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: 557-572.
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 524847.
19. Cui X, Xu J, Asghar R et al (2005) Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit. Bioinformatics 21: 3852-3858.
20. Cui X, Xu XM, Mu DS et al (2008) Genomic analysis of rice microRNA promoters and clusters. Gene 431: 61-66.
21. Dardick C, Chen J, Richter T et al (2007) The rice protein kinase database for the rice kinome. Plant Physiol 143: 579-586.
22. Davierwala AP, Reddy AP, Lagu MD et al (2001) Marker assisted selection of bacterial blight resistance genes in rice. Biochem Genet 39: 261-278.
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: 627-632.
24. Devos KM (2005) Updating the 'crop circle'. Curr Opin Plant Biol 8: 155-162.
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: 9-22.
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: 149-163.
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-D995.
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: 825-834.
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: 13.
30. Eisen JA, Fraser CM (2003) Phylogenomics: intersection of evolution and genomics. Science 300: 1706-1707.
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: 1768-1774.
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: 213-226.
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: 1812-1819.
34. Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3: 329-341.
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: 1342-1353.
36. Feuillet C, Keller B (2002) Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann Bot 89: 3-10.
37. Finnegan EJ, Kovac KA (2000) Plant DNA methyltransferases. Plant Mol Biol 43: 189-201.
38. Fischle W, Wang Y, Allis CD (2003) Binary switches and modification cassettes in histone biology and beyond. Nature 425: 475-479.
39. Fitzgerald MA, McCouch SR, Hall RD (2009) Not just a grain of rice: the quest for quality. Trends Plant Sci 14: 133-139.
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: 271-277.
41. Furutani I, Sukegawa S, Kyozuka J (2006) Genome-wide analysis of spatial and temporal gene expression in rice panicle. Plant J 46: 503-511.
42. Goff SA, Ricke D, Lan TH et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100.
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: 890-897.
44. Griffiths-Jones S, Saini HK, van Dongen S et al (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-D158.
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: 163-185.
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. 12.
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: 371-384.
48. Han B, Zhang Q (2008) Rice genome research; current status and future perspectives. Plant Genome 1: 71-76.
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: 373-380.
50. Han F, Kilian A, Chen JP et al (1999) Sequence analysis of a rice BAC covering the syntenous barley Rpg1 region. Genome 42: 1071-1076.
51. Hazen SP, Kay SA (2003) Gene arrays are not just for measuring gene expression. Trends Plant Sci 8: 413-416.
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: 1429-1450.
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: 7783-7788.
54. Hirochika H, Guiderdoni E, An G et al (2004) Rice mutant resources for gene discovery. Plant Mol Biol 54: 325-334.
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: 1121-1128.
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: 1275-1283.
57. Huang X, Qian Q, Liu Z et al (2009) Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet 41: 494-497.
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: 856-875.
59. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
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: 113-120.
61. Jabbari K, Cruveiller S, Clay O et al (2004) The new genes of rice: a closer look. Trends Plant Sci 9: 281-285.
62. Jackson JP, Lindroth AM, Cao X et al (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416: 556-560.
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: 965-977.
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: 1467-1483.
65. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293: 1074-1080.
66. Jiang N, Bao Z, Zhang X et al (2003) An active DNA transposon family in rice. Nature 421: 163-167.
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: 258-263.
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: 1007-1014.
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: 91-101.
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: 451.
71. Kathuria H, Giri J, Tyagi H et al (2007) Advances in transgenic rice biotechnology. Crit Rev Plant Sci 26: 65-103.
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: 889-905.
73. Kazazian HH Jr (2004) Mobile elements: drivers of genome evolution. Science 303: 1626-1632.
74. Keller B, Feuillet C (2000) Colinearity and gene density in grass genomes. Trends Plant Sci 5: 246-251.
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: 376-379.
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 31-54.
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: 347-354.
78. Krishnan A, Guiderdoni E, An G et al (2009) Mutant resources in rice for functional genomics of the grasses. Plant Physiol 149: 165-170.
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-D1027.
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: 370-375.
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: R52.
82. Li L, Wang X, Stolc V et al (2006) Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 38: 124-129.
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: e294.
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: 259-276.
85. Lindroth AM, Cao X, Jackson JP et al (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292: 2077-2080.
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: 107-118.
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: 685-689.
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: 296-305.
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: 2705-2718.
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: 723-728.
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: 4951-4956.
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: 118.
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: 2071-2076.
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: 6842-6852.
95. Mathieu O, Reinders J, Caikovski M et al (2007) Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130: 851-862.
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 348621.
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: 469-474.
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: 297-318.
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: 381-391.
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 Issue.
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: 539-549.
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. 22.
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: 1771-1780.
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: 139-148.
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: 43-51.
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: 5836-5841.
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: 14867-14871.
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-D735.
109. Nakazaki T, Okumoto Y, Horibata A et al (2003) Mobilization of a transposon in the rice genome. Nature 421: 170-172.
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: 91.
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: 333-350.
112. Nobuta K, Venu RC, Lu C et al (2007) An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol 25: 473-477.
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: 2583-2594.
114. O'Donnell KA, Boeke JD (2007) Mighty Piwis defend the germline against genome intruders. Cell 129: 37-44.
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-D887.
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: 341-357.
117. Ozsolak F, Platt AR, Jones DR et al (2009) Direct RNA sequencing. Nature 461: 814-818.
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: 9903-9908.
119. Paterson AH, Bowers JE, Bruggmann R et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.
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: 627-636.
121. Picault N, Chaparro C, Piegu B et al (2009) Identification of an active LTR retrotransposon in rice. Plant J 58: 754-765.
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: 61-76.
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: 1755-1767.
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: 493-505.
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: 95-104.
126. Rensink WA, Buell CR (2005) Microarray expression profiling resources for plant genomics. Trends Plant Sci 10: 603-609.
127. Rice Annotation Project (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res 17: 175-183.
128. Rice Annotation Project (2008) The rice annotation project database (RAP-DB): 2008 update. Nucleic Acids Res 36: D1028-D1033.
129. Sakamoto T, Matsuoka M (2008) Identifying and exploiting grain yield genes in rice. Curr Opin Plant Biol 11: 209-214.
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: 396-409.
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: 792-797.
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: 615-624.
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: e1235.
134. Schena M, Shalon D, Davis RW et al (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470.
135. Schwab R, Ossowski S, Riester M et al (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18: 1121-1133.
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: 1198-1205.
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: 599-607.
138. Shimono M, Sugano S, Nakayama A et al (2007) Rice WRKY45 plays a crucial role in benzothiadiazole-inducible blast resistance. Plant Cell 19: 2064-2076.
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: 1067-1074.
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: 102-117.
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: 17-35.
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: 203.
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: 1055-1061.
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: 97-108.
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: 1599-1610.
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: 137-149.
147. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403: 42-45.
148. Sunkar R, Girke T, Jain PK et al (2005) Cloning and characterization of microRNAs from rice. Plant Cell 17: 1397-1411.
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: 1407-1416.
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: 6805-6810.
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: 337-349.
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: 20.
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-D1000.
154. Throude M, Bolot S, Bosio M et al (2009) Structure and expression analysis of rice paleo duplications. Nucleic Acid Res 37: 1248-1259.
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: 1005-1009.
156. Vaucheret H (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 20: 759-771.
157. Vazquez F, Vaucheret H, Rajagopalan R et al (2004) Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 16: 69-79.
158. Velculescu VE, Zhang L, Vogelstein B et al (1995) Serial analysis of gene expression. Science 270: 484-487.
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: 421-431.
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: 301-307.
161. Vij S, Gupta V, Kumar D et al (2006) Decoding the rice genome. BioEssays 28: 421-432.
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: 732-750.
163. Wang SM (2007) Understanding SAGE data. Trends Genet 23: 42-50.
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: 721-737.
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: 85-91.
166. Wang Z, Gerstein M, Snyder M (2009b) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
167. Warthmann N, Chen H, Ossowski S et al (2008) Highly specific gene silencing by artificial miRNAs in rice. PLoS One 3: e1829.
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: 7695-7701.
169. Wortman JR, Haas BJ, Hannick LI et al (2003) Annotation of the Arabidopsis genome. Plant Physiol 132: 461-468.
170. Wu J, Maehara T, Shimokawa T et al (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14: 525-535.
171. Xiao W, Custard KD, Brown RC et al (2006) DNA methylation is critical for Arabidopsis embryogenesis and seed viability. Plant Cell 18: 805-814.
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: 1947-1959.
173. ′-flanking regions. Biosci Biotechnol Biochem 68: 1315-1323.
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: 258-277.
175. Yamamoto K, Sasaki T (1997) Large-scale EST sequencing in rice. Plant Mol Biol 35: 135-144.
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: 1774-1782.
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: 336-344.
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: 468-478.
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: 161-172.
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: 367-370.
181. Yazaki J, Kishimoto N, Nagata Y et al (2003) Genomics approach to abscisic acid- and gibberellin-responsive genes in rice. DNA Res 10: 249-261.
182. Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92.
183. Yu J, Wang J, Lin W et al (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3: e38.
184. Yuan Q, Ouyang S, Wang A et al (2005) The Institute for Genomic Research Osa1 rice genome annotation database. Plant Physiol 138: 18-26.
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: 600-605.
186. Zhang B, Pan X, Cannon CH et al (2006b) Conservation and divergence of plant microRNA genes. Plant J 46: 243-259.
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: 715-719.
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-D382.
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: 29.
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: 591-608.
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: 1456-1465.
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: 1983-1992.