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  • Agrawal, G.K., Yamazaki, M., Kobayashi, M., Hirochika, R., Miyao, A. and Hirochika, H. (2001) Screening of the rice viviparous mutants generated by endogenous retrotransposon Tos17 insertion. Tagging of a zeaxanthin epoxidase gene and a novel OsTATC gene. Plant Physiol. 125, 12481257.
  • Bari, R., Datt Pant, B., Stitt, M. and Scheible, W.-R.D. (2006) PHO2, MicroRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol. 141, 988999.
  • Berruyer, R., Adreit, H., Milazzo, J., Gaillard, S., Berger, A., Dioh, W., Lebrun, M.H. and Tharreau, D. (2003) Identification and fine mapping of Pi33 the rice resistance gene corresponding to the Magnaporthe grisea avirulence gene ACE1. Theor. Appl. Genet. 107, 11391147.
  • Bruce, M., Hess, A., Bai, J., Mauleon, R., Diaz, M.G., Sugiyama, N., Bordeos, A., Wang, G.-L., Leung, H. and Leach, J. (2009) Detection of genomic deletions in rice using oligonucleotide microarrays. BMC Genomics, 10, 129.
  • Chern, C.-G., Fan, M.-J., Yu, S.-M., Hour, A.-L., Lu, P.-C., Lin, Y.-C., Wei, F.-J., Huang, S.-C., Chen, S., Lai, M.-H., Tseng, C.-S., Yen, H.-M., Jwo, W.-S., Wu, C.-C., Yang, T.-L., Li, L.-S., Kuo, Y.-C., Li, S.-M., Li, C.-P., Wey, C.-K., Trisiriroj, A., Lee, H.-F. and Hsing, Y.-I. (2007) A rice phenomics study—phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population. Plant Mol. Biol. 65, 427438.
  • Chin, H.G., Choe, M.S., Lee, S.-H., Park, S.H., Park, S.H., Koo, J.C., Kim, N.Y., Lee, J.J., Oh, B.G., Yi, G.H., Kim, S.C., Choi, H.C., Cho, M.J. and Han, C.-D. (1999) Molecular analysis of rice plants harboring an Ac/Ds transposable element-mediated gene trapping system. Plant J. 19, 615623.
  • Delteil, A., Blein, M., Faivre-Rampant, O., Guellim, A., Estevan, J., Hirsch, J., Bevitori, R., Michel, C. and Morel, J.-B. (2012) Building a mutant resource for the study of disease resistance in rice reveals the pivotal role of several genes involved in defence. Mol. Plant Pathol. 13, 7282.
  • Droc, G., Ruiz, M., Larmande, P., Pereira, A., Piffanelli, P., Morel, J.B., Dievart, A., Courtois, B., Guiderdoni, E. and Périn, C. (2006) OryGenesDB: a database for rice reverse genetics. Nucleic Acids Res. 34, 736740.
  • Droc, G., Périn, C., Fromentin, S.B. and Larmande, P. (2009) OryGenesDB 2008 update: database interoperability for functional genomics of rice. Nucleic Acids Res. 37, 992995.
  • Fujiwara, T., Maisonneuve, S., Isshiki, M., Mizutani, M., Chen, L., Wong, H.L., Kawasaki, T. and Shimamoto, K. (2010) Sekiguchi lesion gene encodes a cytochrome P450 monooxygenase that catalyzes conversion of tryptamine to serotonin in rice. J. Biol. Chem. 285, 1130811313.
  • Hirochika, H. (2001) Contribution of the Tos17 retrotransposon to rice functional genomics. Curr. Opin. Plant Biol. 4, 118122.
  • Hirochika, H., Sugimoto, K., Otsuki, Y., Tsugawa, H. and Kanda, M. (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc. Natl Acad. Sci. USA, 93, 77837788.
  • Hu, H., Dai, M., Yao, J., Xiao, B., Li, X., Zhang, Q. and Xiong, L. (2006) Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc. Natl Acad. Sci. USA, 103, 1298712992.
  • Iida, S. and Terada, R. (2005) Modification of endogenous natural genes by gene targeting in rice and other higher plants. Plant Mol. Biol. 59, 205219.
  • Ikeda, A., Ueguchi-Tanaka, M., Sonoda, Y., Kitano, H., Koshioka, M., Futsuhara, Y., Matsuoka, M. and Yamaguchi, J. (2001) Slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8. Plant Cell, 13, 9991010.
  • Itaya, K. and Ui, M. (1966) A new micromethod for the colorimetric determination of inorganic phosphate. Clin. Chim. Acta., 14, 361366.
  • Jaiswal, P., Avraham, S., Ilic, K., Kellogg, E.A., McCouch, S., Pujar, A., Reiser, L., Rhee, S.Y., Sachs, M.M., Schaeffer, M., Stein, L., Stevens, P., Vincent, L., Ware, D. and Zapata, F. (2005) Plant ontology (PO): a controlled vocabulary of plant structures and growth stages. Comp. Funct. Genomics, 6, 388397.
  • Jefferson, R.A. (1987) Assaying chimeric genes in plants from gene fusion system. Plant Mol. Biol. Rep. 5, 387405.
  • Jeon, J.S., Lee, S., Jung, K.H., Jun, S.H., Jeong, D.H., Lee, J., Kim, C., Jang, S., Lee, S., Yang, K., Nam, J., An, K., Han, M.J., Sung, R.J., Choi, H.S., Yu, J.H., Choi, J.H., Cho, S.Y., Cha, S.S., Kim, S.I. and An, G. (2000) T-DNA insertional mutagenesis for functional genomics in rice. Plant J. 22, 561570.
  • Jeong, D.H., An, S.Y., Kang, H.G., Moon, S., Han, J.J., Park, S., Lee, H.S., An, K.S. and An, G.H. (2002) T-DNA insertional mutagenesis for activation tagging in rice. Plant Physiol. 130, 16361644.
  • Jiang, C., Mithani, A., Gan, X., Belfield, E.J., Klingler, J.P., Zhu, J.-K., Ragoussis, J., Mott, R. and Harberd, N.P. (2012) Regenerant arabidopsis lineages display a distinct genome-wide spectrum of mutations conferring variant phenotypes. Curr. Biol. 21, 13851390.
  • Johnson, A.A.T., Hibberd, J.M., Gay, C., Essah, P.A., Haseloff, J., Tester, M. and Guiderdoni, E. (2005) Spatial control of transgene expression in rice (Oryza sativa L.) using the GAL4 enhancer trapping system. Plant J. 41, 779789.
  • Jung, K.H., Hur, J., Ryu, C.H., Choi, Y., Chung, Y.Y., Miyao, A., Hirochika, H. and An, G.H. (2003) Characterization of a rice chlorophyll-deficient mutant using the T-DNA gene-trap system. Plant Cell Physiol. 44, 463472.
  • Kolesnik, T., Szeverenyi, I., Bachmann, D., Kumar, C.S., Jiang, S., Ramamoorthy, R., Cai, M., Ma, Z.G., Sundaresan, V. and Ramachandran, S. (2004) Establishing an efficient Ac/Ds tagging system in rice: large-scale analysis of Ds flanking sequences. Plant J. 37, 301314.
  • Krishnan, A., Guiderdoni, E., An, G., Hsing, Y.-I.C., Han, C.-D., Lee, M.C., Yu, S.-M., Upadhyaya, N., Ramachandran, S., Zhang, Q., Sundaresan, V., Hirochika, H., Leung, H. and Pereira, A. (2009) Mutant resources in rice for functional genomics of the grasses. Plant Physiol. 149, 165170.
  • Kumar, C.S., Wing, R.A. and Sundaresan, V. (2005) Efficient insertional mutagenesis in rice using the maize En/Spm elements. Plant J. 44, 879892.
  • Larmande, P., Gay, C., Lorieux, M., Perin, C., Bouniol, M., Droc, G., Sallaud, C., Perez, P., Barnola, I., Biderre-Petit, C., Martin, J., Morel, J.B., Johnson, A.A.T., Bourgis, F., Ghesquiere, A., Ruiz, M., Courtois, B. and Guiderdoni, E. (2008) Oryza tag line, a phenotypic mutant database for the genoplante rice insertion line library. Nucleic Acids Res. 36, D1022D1027.
  • Lee, S., Kim, J., Son, J.S., Nam, J., Jeong, D.H., Lee, K., Jang, S., Yoo, J., Lee, J., Lee, D.Y., Kang, H.G. and An, G.H. (2003) Systematic reverse genetic screening of T-DNA tagged genes in rice for functional genomic analyses: MADS-box genes as a test case. Plant Cell Physiol. 44, 14031411.
  • Lee, S., Jung, K.H., An, G.H. and Chung, Y.Y. (2004a) Isolation and characterization of a rice cysteine protease gene, OSCP1, using T-DNA gene-trap system. Plant Mol. Biol. 54, 755765.
  • Lee, S.C., Huh, K.W., An, K., An, G. and Kim, S.R. (2004b) Ectopic expression of a cold-inducible transcription factor, CBF1/DREB1b, in transgenic rice (Oryza sativa L.). Mol. Cells, 18, 107114.
  • Li, J., Jiang, D., Zhou, H., Li, F., Yang, J., Hong, L., Fu, X., Li, Z., Liu, Z., Li, J. and Zhuang, C. (2011) Expression of RNA-interference/antisense transgenes by the cognate promoters of target genes is a better gene-silencing strategy to study gene functions in rice. PLoS One, 6, e17444.
  • Lorrain, S., Vailleau, F., Balagué, C. and Roby, D. (2003) Lesion mimic mutants: keys for deciphering cell death and defense pathways in plants? Trends Plant Sci. 8, 263271.
  • Matsumoto, T., Wu, J.Z., Kanamori, H., Katayose, Y., Fujisawa, M., Namiki, N., Mizuno, H., Yamamoto, K., Antonio, B.A., Baba, T., Sakata, K., Nagamura, Y., Aoki, H., Arikawa, K., Arita, K., Bito, T., Chiden, Y., Fujitsuka, N., Fukunaka, R., Hamada, M., Harada, C., Hayashi, A., Hijishita, S., Honda, M., Hosokawa, S., Ichikawa, Y., Idonuma, A., Iijima, M., Ikeda, M., Ikeno, M., Ito, K., Ito, S., Ito, T., Ito, Y., Ito, Y., Iwabuchi, A., Kamiya, K., Karasawa, W., Kurita, K., Katagiri, S., Kikuta, A., Kobayashi, H., Kobayashi, N., Machita, K., Maehara, T., Masukawa, M., Mizubayashi, T., Mukai, Y., Nagasaki, H., Nagata, Y., Naito, S., Nakashima, M., Nakama, Y., Nakamichi, Y., Nakamura, M., Meguro, A., Negishi, M., Ohta, I., Ohta, T., Okamoto, M., Ono, N., Saji, S., Sakaguchi, M., Sakai, K., Shibata, M., Shimokawa, T., Song, J.Y., Takazaki, Y., Terasawa, K., Tsugane, M., Tsuji, K., Ueda, S., Waki, K., Yamagata, H., Yamamoto, M., Yamamoto, S., Yamane, H., Yoshiki, S., Yoshihara, R., Yukawa, K., Zhong, H.S., Yano, M., Sasaki, T., Yuan, Q.P., Shu, O.T., Liu, J., Jones, K.M., Gansberger, K., Moffat, K., Hill, J., Bera, J., Fadrosh, D., Jin, S.H., Johri, S., Kim, M., Overton, L., Reardon, M., Tsitrin, T., Vuong, H., Weaver, B., Ciecko, A., Tallon, L., Jackson, J., Pai, G., Van Aken, S., Utterback, T., Reidmuller, S., Feldblyum, T., Hsiao, J., Zismann, V., Iobst, S., de Vazeille, A.R., Buell, C.R., Ying, K., Li, Y., Lu, T.T., Huang, Y.C., Zhao, Q., Feng, Q., Zhang, L., Zhu, J.J., Weng, Q.J., Mu, J., Lu, Y.Q., Fan, D.L., Liu, Y.L., Guan, J.P., Zhang, Y.J., Yu, S.L., Liu, X.H., Zhang, Y., Hong, G.F., Han, B., Choisne, N., Demange, N., Orjeda, G., Samain, S., Cattolico, L., Pelletier, E., Couloux, A., Segurens, B., Wincker, P., D’Hont, A., Scarpelli, C., Weissenbach, J., Salanoubat, M., Quetier, F., Yu, Y., Kim, H.R., Rambo, T., Currie, J., Collura, K., Luo, M.Z., Yang, T.J., Ammiraju, J.S.S., Engler, F., Soderlund, C., Wing, R.A., Palmer, L.E., de la Bastide, M., Spiegel, L., Nascimento, L., Zutavern, T., O’Shaughnessy, A., Dike, S., Dedhia, N., Preston, R., Balija, V., McCombie, W.R., Chow, T.Y., Chen, H.H., Chung, M.C., Chen, C.S., Shaw, J.F., Wu, H.P., Hsiao, K.J., Chao, Y.T., Chu, M.K., Cheng, C.H., Hour, A.L., Lee, P.F., Lin, S.J., Lin, Y.C., Liou, J.Y., Liu, S.M., Hsing, Y.I., Raghuvanshi, S., Mohanty, A., Bharti, A.K., Gaur, A., Gupta, V., Kumar, D., Ravi, V., Vij, S., Kapur, A., Khurana, P., Khurana, P., Khurana, J.P., Tyagi, A.K., Gaikwad, K., Singh, A., Dalal, V., Srivastava, S., Dixit, A., Pal, A.K., Ghazi, I.A., Yadav, M., Pandit, A., Bhargava, A., Sureshbabu, K., Batra, K., Sharma, T.R., Mohapatra, T., Singh, N.K., Messing, J., Nelson, A.B., Fuks, G., Kavchok, S., Keizer, G., Llaca, E.L.V., Song, R.T., Tanyolac, B., Young, S., Il, K.H., Hahn, J.H., Sangsakoo, G., Vanavichit, A., de Mattos, L.A.T., Zimmer, P.D., Malone, G., Dellagostin, O., de Oliveira, A.C., Bevan, M., Bancroft, I., Minx, P., Cordum, H., Wilson, R., Cheng, Z.K., Jin, W.W., Jiang, J.M., Leong, S.A., Iwama, H., Gojobori, T., Itoh, T., Niimura, Y., Fujii, Y., Habara, T., Sakai, H., Sato, Y., Wilson, G., Kumar, K., McCouch, S., Juretic, N., Hoen, D., Wright, S., Bruskiewich, R., Bureau, T., Miyao, A., Hirochika, H., Nishikawa, T., Kadowaki, K., Sugiura, M. and Project I.R.G.S. (2005) The map-based sequence of the rice genome. Nature, 436, 793800.
  • Miyao, A., Tanaka, K., Murata, K., Sawaki, H., Takeda, S., Abe, K., Shinozuka, Y., Onosato, K. and 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, 17711780.
  • Miyao, A., Iwasaki, Y., Kitano, H., Itoh, J., Maekawa, M., Murata, K., Yatou, O., Nagato, Y. and 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, 625635.
  • Miyao, A., Nakagome, M., Ohnuma, T., Yamagata, H., Kanamori, H., Katayose, Y., Takahashi, A., Matsumoto, T. and Hirochika, H. (2012) Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing. Plant Cell Physiol. 53, 256264.
  • Mori, M., Tomita, C., Sugimoto, K., Hasegawa, M., Hayashi, N., Dubouzet, J., Ochiai, H., Sekimoto, H., Hirochika, H. and Kikuchi, S. (2007) Isolation and molecular characterization of a Spotted leaf 18 mutant by modified activation-tagging in rice. Plant Mol. Biol. 63, 847860.
  • Nonomura, K.I., Miyoshi, K., Eiguchi, M., Suzuki, T., Miyao, A., Hirochika, H. and Kurata, N. (2003) The MSP1 gene is necessary to restrict the number of cells entering into male and female sporogenesis and to initiate anther wall formation in rice. Plant Cell, 15, 17281739.
  • Nonomura, K.L., Nakano, M., Fukuda, T., Eiguchi, M., Miyao, A., Hirochika, H. and Kurata, N. (2004) The novel gene HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS1 of rice encodes a putative coiled-coil protein required for homologous chromosome pairing in meiosis. Plant Cell, 16, 10081020.
  • O’Malley, R.C. and Ecker, J.R. (2010) Linking genotype to phenotype using the Arabidopsis unimutant collection. Plant J. 61, 928940.
  • Parker, D., Beckmann, M., Zubair, H., Enot, D.P., Caracuel-Rios, Z., Overy, D.P., Snowdon, S., Talbot, N.J. and Draper, J. (2009) Metabolomic analysis reveals a common pattern of metabolic re-programming during invasion of three host plant species by Magnaporthe grisea. Plant J. 59, 723737.
  • Piffanelli, P., Droc, G., Mieulet, D., Lanau, N., Bès, M., Bourgeois, E., Rouvière, C., Gavory, F., Cruaud, C., Ghesquière, A. and Guiderdoni, E. (2007) Large-scale characterization of Tos17 insertion sites in a rice T-DNA mutant library. Plant Mol. Biol. 65, 587601.
  • Ribot, C., Hirsch, J., Balzergue, S., Tharreau, D., Nottéghem, J.-L., Lebrun, M.-H. and Morel, J.-B. (2008) Susceptibility of rice to the blast fungus, Magnaporthe grisea. J. Plant Physiol. 165, 114124.
  • Sabot, F., Picault, N., El-Baidouri, M., Llauro, C., Chaparro, C., Piegu, B., Roulin, A., Guiderdoni, E., Delabastide, M., McCombie, R. and Panaud, O. (2011) Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data. Plant J. 66, 241246.
  • Sallaud, C., Meynard, D., van Boxtel, J., Gay, C., Bes, M., Brizard, J.P., Larmande, P., Ortega, D., Raynal, M., Portefaix, M., Ouwerkerk, P.B., Rueb, S., Delseny, M. and Guiderdoni, E. (2003) Highly efficient production and characterization of T-DNA plants for rice (Oryza sativa L.) functional genomics. Theor. Appl. Genet. 106, 13961408.
  • Sallaud, C., Gay, C., Larmande, P., Bes, M., Piffanelli, P., Piegu, B., Droc, G., Regad, F., Bourgeois, E., Meynard, D., Perin, C., Sabau, X., Ghesquiere, A., Glaszmann, J.C., Delseny, M. and Guiderdoni, E. (2004) High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics. Plant J. 39, 450464.
  • Sukekiyo, Y. and Kimura, Y. (1991) Somaclonal variation in protoplast-derived rice plants. Gamma Field Symposia, 30, 4358.
  • Till, B., Cooper, J., Tai, T., Colowit, P., Greene, E., Henikoff, S. and Comai, L. (2007) Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol. 7, 19.
  • Wang, X.E., Basnayake, B.M.V.S., Zhang, H., Li, G., Li, W., Virk, N., Mengiste, T. and Song, F. (2009) The arabidopsis ATAF1, a NAC transcription factor, is a negative regulator of defense responses against necrotrophic fungal and bacterial pathogens. Mol. Plant Microbe Interact. 22, 12271238.
  • Warthmann, N., Chen, H., Ossowski, S., Weigel, D. and Hervé, P. (2008) Highly specific gene silencing by artificial miRNAs in rice. PLoS One, 3, e1829.
  • Wesley, S.V., Helliwell, C.A., Smith, N.A., Wang, M.B., Rouse, D.T., Liu, Q., Gooding, P.S., Singh, S.P., Abbott, D. and Stoutjesdijk, P.A. (2001) Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J. 27, 581590.
  • Wu, J.L., Wu, C., Lei, C., Baraoidan, M., Bordeos, A., Madamba, M.R., Ramos-Pamplona, M., Mauleon, R., Portugal, A. and Ulat, V.J. (2005) Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics. Plant Mol. Biol. 59, 8597.
  • Yamanouchi, U., Yano, M., Lin, H., Ashikari, M. and Yamada, K. (2002) A rice spotted leaf gene, Spl7, encodes a heat stress transcription factor protein. Proc. Natl Acad. Sci. USA, 99, 75307535.
  • Zhang, J., Li, C., Wu, C., Xiong, L., Chen, G., Zhang, Q. and Wang, S. (2006) RMD: a rice mutant database for functional analysis of the rice genome. Nucleic Acids Res. 34, D745D748.
  • Zhang, Q., Li, J., Xue, Y., Han, B. and Deng, X.W. (2008) Rice 2020: a call for an international coordinated effort in rice functional genomics. Mol. Plant, 1, 715719.
  • Zuryn, S., Le Gras, S.P., Jamet, K. and Jarriault, S. (2010) A strategy for direct mapping and identification of mutations by whole-genome sequencing. Genetics, 186, 427430.