References

Large scale production of Tos17 insertion lines and their analysis:
Miyao A, Tanaka K, Murata K, Sawaki H, Takeda S, Abe K, Shinozuka Y, Onosato K, Hirochika H. 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(8):1771-1780, 2003.
Large scale phenotyping of our insertion lines:
Miyao A, Iwasaki Y, Kitano H, Itoh JI, Maekawa M, Murata K, Yatou O, Nagato Y, Hirochika H. A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes. Plant Mol Biol. 63(5):625-635, 2007.
Method for flanking sequence analysis:
Miyao A, Yamazaki M, and Hirochika H, Systematic screening of mutants of rice by sequencing retrotransposon-insertion sites, Plant Biotechnology, 15(4):253-256, 1998.
Finding of retrotransposon Tos17:
Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M. Retrotransposons of rice involved in mutations induced by tissue culture, Proc Natl Acad Sci U S A., 93(15):7783-7788, 1996.
Distribution of Tos17 insertions on the IRGSP Build 3 sequence of rice genome:
International Rice Genome Sequencing Project, The map-based sequence of the rice genome. Nature 436(7052):793-800, 2005.
Review:
Hirochika H, Guiderdoni E, An G, Hsing YI, Eun MY, Han CD, Upadhyaya N, Ramachandran S, Zhang Q, Pereira A, Sundaresan V, Leung H. Rice mutant resources for gene discovery. Plant Mol Biol. 54(3):325-34, 2004.
Review:
Hirochika H., Contribution of the Tos17 retrotransposon to rice functional genomics, Curr Opin Plant Biol, 4(2):118-122, 2001.
Review:
Hirochika H., Retrotransposons of rice: their regulation and use for genome analysis, Plant Mol Biol., 35(1-2):231-240, 1997.
Book Chapter:
Miyao, A. (2024). Somaclonal Variation in Rice: Retrotransposon Tos17 and Structural Variation with NGS Analysis. In: Sanchez-Romero, C. (eds) Somaclonal Variation: Basic and Practical Aspects. Springer, Cham.
Computer system (software):
FreeBSD (Oparating System), PostgreSQL (Relational Database), Apache (Web Server), BLAST, EMBOSS, Primer3
Studies using our mutant lines.
[Google scholar]
Takahashi A, Hayashi N, Miyao A, Hirochika H, Unique features of the rice blast resistance Pish locus revealed by large scale retrotransposon-tagging, BMC Plant Biol., 10:175, 2010.
Hirose T, Zhang Z, Miyao A, Hirochika H, Ohsugi R, Terao T, Disruption of a gene for rice sucrose transporter, OsSUT1, impairs pollen function but pollen maturation is unaffected, J Exp Bot.,61(13):3639-3646, 2010.
Kishi-Kaboshi M, Okada K, Kurimoto L, Murakami S, Umezawa T, Shibuya N, Yamane H, Miyao A, Takatsuji H, Takahashi A, Hirochika H, A rice fungal MAMP-responsive MAPK cascade regulates metabolic flow to antimicrobial metabolite synthesis, Plant J., 63(4):599-612, 2010.
Sugimoto K, Takeuchi Y, Ebana K, Miyao A, Hirochika H, Naho Hara N, Ishiyama K, Kobayashi M, Ban Y, Hattori T, Yano M, Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proceedings of the National Academy of Sciences of the United States of America 107(13):5792-5797, 2010.
Chen H, Tamai A, Mori M, Ugaki M, Tanaka Y, Samadder P.P, Miyao A, Hirochika H, Yamaoka N, Nishiguchi M, Analysis of rice RNA-dependent RNA polymerase 1 (OsRDR1) in virus-mediated RNA silencing after particle bombardment. Journal of General Plant Pathology 76(2):152-160, 2010.
Wang M, Wang K, Tang D, Wei C, Li M, Shen Y, Chi Z, Gu M, Cheng Z, The central element protein ZEP1 of the synaptonemal complex regulates the number of crossovers during meiosis in rice, Plant Cell, 22(2):417-430, 2010.
Asano K, Miyao A, Hirochika H, Kitano H, Matsuoka M, Ashikari M, SSD1, which encodes a plant-specific novel protein, controls plant elongation by regulating cell division in rice. Proceedings of the Japan Academy, Series B 86(3):265-273, 2010.
Yoshii M, Yamazaki M, Rakwal R, Kishi-Kaboshi M, Miyao A, Hirochika H, The NAC transcription factor RIM1 of rice is a new regulator of jasmonate signaling. The Plant Journal 61(5):804-815, 2010.
Kobayashi K, Maekawa M, Miyao A, Hirochika H, Kyozuka J, PANICLE PHYTOMER2 (PAP2), encoding a SEPALLATA subfamily MADS-box protein, positively controls spikelet meristem identity in rice. Plant and Cell Physiology 51(1):47-57, 2010.
Ohmori S, Kimizu M, Sugita M, Miyao A, Hirochika H, Uchida E, Nagato Y, Yoshida H, MOSAIC FLORAL ORGANS1, an AGL6-like MADS box gene, regulates floral organ identity and meristem fate in rice. The Plant Cell 21(10):3008-3025, 2009.
Tsuda K, Ito Y, Yamaki S, Miyao A, Hirochika H, Kurata N, Isolation and mapping of three rice mutants that showed ectopic expression of KNOX genes in leaves. Plant Science 177(2):131-135, 2009.
Fujita N, Toyosawa Y, Utsumi Y, Higuchi T, Hanashiro I, Ikegami A, Akuzawa S, Yoshida M, Mori A, Inomata K, Itoh R, Miyao A, Hirochika H, Satoh H, Nakamura Y, Characterization of pullulanase (PUL)-deficient mutants of rice (Oryza sativa L.) and the function of PUL on starch biosynthesis in the developing rice endosperm. Journal of Experimental Botany 60(3):1009-1023, 2009.
Yoshii M, Shimizu T, Yamazaki M, Higashi T, Miyao A, Hirochika H, Omura T, Disruption of a novel gene for a NAC-domain protein in rice confers resistance to Rice dwarf virus. The Plant Journal 57(4):615-625, 2009.
Fujii S, Yamada M, Toriyama K, Cytoplasmic male sterility-related protein kinase, OsNek3, is regulated downstream of mitochondrial protein phosphatase 2C, DCW11, Plant Cell Physiol., 50(4):828-837, 2009.
Jiang CJ, Shimono M, Maeda S, Inoue H, Mori M, Hasegawa M, Sugano S, Takatsuji H, Suppression of the rice fatty-acid desaturase gene OsSSI2 enhances resistance to blast and leaf blight diseases in rice, Mol Plant Microbe Interact., 22(7):820-829, 2009.
Dai X, You C, Wang L, Chen G, Zhang Q, Wu C, Molecular characterization, expression pattern, and function analysis of the OsBC1L family in rice, Plant Mol Biol. 71(4-5):469-481, 2009.
Gutjahr C, Banba M, Croset V, An K, Miyao A, An G, Hirochika H, Imaizumi-Anraku H, Paszkowski U, Arbuscular mycorrhiza-specific signaling in rice transcends the common symbiosis signaling pathway. Plant Cell. 20(11):2989-3005,2008.
Banba M, Gutjahr C, Miyao A, Hirochika H, Paszkowski U, Kouchi H, Imaizumi-Anraku H, Divergence of evolutionary ways among common sym genes: CASTOR and CCaMK show functional conservation between two symbiosis systems and constitute the root of a common signaling pathway. Plant Cell Physiol. 49(11):1659-71, 2008.
Lee SK, Jeon JS, Bornke F, Voll L, Cho JI, Goh CH, Jeong SW, Park YI, Kim SJ, Choi SB, Miyao A, Hirochika H, An G, Cho MH, Bhoo SH, Sonnewald U, Hahn TR, Loss of cytosolic fructose-1,6-bisphosphatase limits photosynthetic sucrose synthesis and causes severe growth retardations in rice (Oryza sativa). Plant Cell Environ. 31(12):1851-63, 2008.
Chen H, Samadder PP, Tanaka Y, Ohira T, Okuizumi H, Yamaoka N, Miyao A, Hirochika H, Ohira T, Tsuchimoto S, Ohtsubo H, Nishiguchi M, OsRecQ1, a QDE-3 homologue in rice, is required for RNA silencing induced by particle bombardment for inverted repeat DNA, but not for double-stranded RNA. Plant J. 56(2):274-86, 2008.
Riemann M, Riemann M, Takano M, Rice JASMONATE RESISTANT 1 is involved in phytochrome and jasmonate signalling. Plant Cell Environ. 31(6):783-792, 2008.
Takahashi A, Agrawal GK, Yamazaki M, Onosato K, Miyao A, Kawasaki T, Shimamoto K, Hirochika H. Rice Pti1a negatively regulates RAR1-dependent defense responses. Plant Cell. 19(9):2940-2951, 2007.
Chen C, Ane' JM, Zhu H, OsIPD3, an ortholog of the Medicago truncatula DMI3 interacting protein IPD3, is required for mycorrhizal symbiosis in rice, New Phytol., 180(2):311-315, 2008.
Goh CH, Jang S, Jung S, Kim HS, Kang HG, Park YI, Bae HJ, Lee CH, An G, Rice phot1a mutation reduces plant growth by affecting photosynthetic responses to light during early seedling growth, Plant Mol Biol., 69(5):605-619, 2008.
Nonomura K, Morohoshi A, Nakano M, Eiguchi M, Miyao A, Hirochika H, Kurata N, 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(8):2583-2594, 2007.
Tozawa Y, Teraishi M, Sasaki T, Sonoike K, Nishiyama Y, Itaya M, Miyao A, Hirochika H, The plastid sigma factor SIG1 maintains photosystem I activity via regulated expression of the psaA operon in rice chloroplasts. Plant J. 52(1):124-132, 2007.
Fujita N, Yoshida M, Kondo T, Saito K, Utsumi Y, Tokunaga T, Nishi A, Satoh H, Park JH, Jane JL, Miyao A, Hirochika H, Nakamura Y, Characterization of SSIIIa-deficient mutants of rice: the function of SSIIIa and pleiotropic effects by SSIIIa deficiency in the rice endosperm.Plant Physiol. 144(4):2009-2023, 2007.
Horie T, Costa A, Kim TH, Han MJ, Horie R, Leung HY, Miyao A, Hirochika H, An G, Schroeder JI. Rice OsHKT2;1 transporter mediates large Na(+) influx component into K(+)-starved roots for growth. EMBO J. 26(12):3003-3014, 2007.
Katou S, Kuroda K, Seo S, Yanagawa Y, Tsuge T, Yamazaki M, Miyao A, Hirochika H, Ohashi Y, A calmodulin-binding mitogen-activated protein kinase phosphatase is induced by wounding and regulates the activities of stress-related mitogen-activated protein kinases in rice. Plant Cell Physiol. 48(2):332-344, 2007.
Rice Annotation Project, Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing YI, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T, Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res. 17(2):175-183, 2007.
Saika H, Okamoto M, Miyoshi K, Kushiro T, Shinoda S, Jikumaru Y, Fujimoto M, Arikawa T, Takahashi H, Ando M, Arimura S, Miyao A, Hirochika H, Kamiya Y, Tsutsumi N, Nambara E, Nakazono M, Ethylene promotes submergence-induced expression of OsABA8ox1, a gene that encodes ABA 8'-hydroxylase in rice. Plant Cell Physiol. 48(2):287-298, 2007.
Kubota Y, Miyao A, Hirochika H, Tozawa Y, Yasuda H, Tsunoyama Y, Niwa Y, Imamura S, Shirai M, Asayama M, Two Novel Nuclear Genes, OsSIG5 and OsSIG6, Encoding Potential Plastid Sigma Factors of RNA Polymerase in Rice: Tissue-Specific and Light-Responsive Gene Expression. Plant Cell Physiol. 48(1):186-192, 2007.
Fujita N, Yoshida M, Asakura N, Ohdan T, Miyao A, Hirochika H, Nakamura Y. Function and characterization of starch synthase I using mutants in rice. Plant Physiol. 140(3):1070-84, 2006.
Yamaguchi T, Lee DY, Miyao A, Hirochika H, An G, Hirano HY, Functional Diversification of the Two C-Class MADS Box Genes OSMADS3 and OSMADS58 in Oryza sativa. Plant Cell, 18(1):15-28, 2006.
Takano M, Inagaki N, Xie X, Yuzurihara N, Hihara F, Ishizuka T, Yano M, Nishimura M, Miyao A, Hirochika H, Shinomura T, Distinct and cooperative functions of phytochromes a, B, and C in the control of deetiolation and flowering in rice. Plant Cell. 17(12):3311-25, 2005.
Agrawal GK, Abe K, Yamazaki M, Miyao A, Hirochika H, Conservation of the E-function for floral organ identity in rice revealed by the analysis of tissue culture-induced loss-of-function mutants of the OsMADS1 gene. Plant Mol Biol. 59(1):125-35, 2005.
Kikui S, Sasaki T, Maekawa M, Miyao A, Hirochika H, Matsumoto H, Yamamoto Y, Physiological and genetic analyses of aluminium tolerance in rice, focusing on root growth during germination. J Inorg Biochem. 99(9):1837-44, 2005.
Debi BR, Chhun T, Taketa S, Tsurumi S, Xia K, Miyao A, Hirochika H, Ichii M, Defects in root development and gravity response in the aem1 mutant of rice are associated with reduced auxin efflux. J Plant Physiol. 162(6):678-85, 2005.
Lee S, Kim JH, Yoo ES, Lee CH, Hirochika H, An G, Differential regulation of chlorophyll a oxygenase genes in rice. Plant Mol Biol. 57(6):805-18, 2005.
Kurusu T, Yagala T, Miyao A, Hirochika H, Kuchitsu K, Identification of a putative voltage-gated Ca2+ channel as a key regulator of elicitor-induced hypersensitive cell death and mitogen-activated protein kinase activation in rice. Plant J. 42(6):798-809, 2005.
Kurusu T, Sakurai Y, Miyao A, Hirochika H, Kuchitsu K, Identification of a putative voltage-gated Ca2+ -permeable channel (OsTPC1) involved in Ca2+ influx and regulation of growth and development in rice. Plant Cell Physiol. 45(6):693-702, 2004.
Sakamoto T, Miura K, Itoh H, Tatsumi T, Ueguchi-Tanaka M, Ishiyama K, Kobayashi M, Agrawal GK, Takeda S, Abe K, Miyao A, Hirochika H, Kitano H, Ashikari M, Matsuoka M, An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiol. 134(4):1642-53, 2004.
Nonomura K, Nakano M, Fukuda T, Eiguchi M, Miyao A, Hirochika H, Kurata N., 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(4):1008-20, 2004.
Fukuda A, Nakamura A, Tagiri A, Tanaka H, Miyao A, Hirochika H, Tanaka Y, Function, intracellular localization and the importance in salt tolerance of a vacuolar Na⁺/H⁺ antiporter from rice. Plant Cell Physiol. 45(2):146-59, 2004.
Nonomura KI, Nakano M, Murata K, Miyoshi K, Eiguchi M, Miyao A, Hirochika H, Kurata N, An insertional mutation in the rice PAIR2 gene, the ortholog of Arabidopsis ASY1, results in a defect in homologous chromosome pairing during meiosis, Mol Genet Genomics. 271: 121-129, 2004.
Kaneko M, Inukai Y, Ueguchi-Tanaka M, Itoh H, Izawa T, Kobayashi Y, Hattori T, Miyao A, Hirochika H, Ashikari M, Matsuoka M, Loss-of-function mutations of the rice GAMYB gene impair α-amylase expression in aleurone and flower development, Plant Cell, 16(1):33-44, 2004.
Tanaka K, Murata K, Yamazaki M, Onosato K, Miyao A, Hirochika H, Three distinct rice cellulose synthase catalytic subunit genes required for cellulose synthesis in the secondary wall, Plant Physiol., 133(1):73-83, 2003.
Nonomura K, Miyoshi K, Eiguchi M, Suzuki T, Miyao A, Hirochika H, Kurata N, 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(8):1728-1739, 2003.
Jung KH, Hur J, Ryu CH, Choi Y, Chung YY, Miyao A, Hirochika H, An G, Characterization of a rice chlorophyll-deficient mutant using the T-DNA gene-trap system, Plant Cell Physiol, 44(5):463-472, 2003.
Yamazaki M, Tsugawa H, Miyao A, Yano M, Wu J, Yamamoto S, Matsumoto T, Sasaki T, Hirochika H,The rice retrotransposon Tos17 prefers low-copy-number sequences as integration targets, Mol Genet Genomics, 265(2):336-344, 2001.
Takano M, Kanegae H, Shinomura T, Miyao A, Hirochika H, Furuya M, Isolation and characterization of rice phytochrome A mutants, Plant Cell, 13(3):521-534, 2001.
Agrawal GK, Yamazaki M, Kobayashi M, Hirochika R, Miyao A, Hirochika H, 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(3):1248-1257, 2001.
Sato Y, Sentoku N, Miura Y, Hirochika H, Kitano H, Matsuoka M, Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants, EMBO J., 18(4):992-1002, 1999.

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