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2020

Murai M., Rana B. B., Takamure I., Nakazawa H., Bhattarai M. (2020)
Lateness gene concerning photosensitivity increases yield, by applying low
to high levels of fertilization, in rice, a preliminary report.
Journal of Nepal Agricultural Research Council 6: 136-145.
Kuniyoshi D., Masuda I., Kanaoka Y., Shimazaki-Kishi Y., Okamoto Y., Yasui
H., Yamamoto T., Nagaki K., Hoshino Y., Koide Y., Takamure I., Kishima Y.
(2020)
Diploid male gametes circumvent hybrid sterility between Asian and African
rice species.
Frontiers in Plant Science 11, 579305.
Koide Y., Kuniyoshi D., Kishima Y. (2020)
Fertile Tetraploids: New Resources for Future Rice Breeding?
Frontiers in Plant Science 11, 1231.
Koide Y. (2020)
Evolution of the "Neutral": Diverse forms of wide-compatibility haplotypes
at the locus for reproductive isolation.
Molecular Plant 13: 539-540.
山本敏央，古田智敬，小川大輔，米丸淳一，國吉大地，貴島祐治 (2020)
イネ育種における遺伝的多様性を拡大するための２，３のアプローチ．
作物研究 65: 83-87.
Encabo J. R., Macalalad-Cabral R. J. A., Matres J. M. K., Coronejo S. C. T. P.,
Jonson G. B., Kishima Y., Henry A., Choi I.R. (2020)
Infection with an asymptomatic virus in rice results in a delayed drought
response.
Functional Plant Biology 47, 239-249.

2019

Tam N.T., Dwiyanti M.S., Koide Y., Nagano A.J., Ky H., Tin H.Q., Hien N.L.,
Dung L.V., Kishima Y. (2019)
Profiling SNP and nucleotide diversity to characterize Mekong Delta ricelandrace in Southeast Asian populations.
The Plant Genome 12, 190042.
Koide Y., Sakaguchi S., Uchiyama T., Ota Y., Tezuka A., Nagano A.J., Ishiguro
S., Takamure I., Kishima Y. (2019)
Genetic properties responsible for the transgressive segregation of days toheading in rice.
G3 Genes|Genomes|Genetics 9, 1655-1662.

Saito N., Encabo J.R., Chen S., Jonson G., Kishima Y., Choi I.R. (2019)
Innate vulnerability of Oryza glaberrima to rice tungro bacilliform virus.
Japan Agricultural Research Quarterly 53, 1-6.
Lee K.J.I., Bushell C., Koide Y., Fozard J.A., Piao C., Yu M., Newman J.,
Whitewoods C., Avondo J., Kennaway R., Marée A.F.M., Cui M., Coen E.

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Shaping of a three-dimensional carnivorous trap through modulation of aplanar growth mechanism.
PLOS Biology 17(10), e3000427.
Rana B.B., Kamimukai M., Bhattarai M., Koide Y., Murai M. (2019)
Responses of earliness and lateness genes for heading to different
photoperiods, and specific response of a gene or a pair of genes to short
day length in rice.
Hereditas 156, 36.
Koide Y., Onishi K., Hayashi Y., Abe T., Fukuta Y., Okumoto Y., Kanazawa A.
(2019)
Recent progress in overcoming interspecific hybrid sterility in rice.
RIKEN Accelerator Progress Report 52
小出陽平 (2019)
イネ種間雑種の生殖隔離障壁の打破に関する遺伝育種学的研究
育種学研究 21, 141-145.

2018

Kanaoka Y., Kuniyoshi D., Inada E., Koide Y., Okamoto Y., Yasui H., Kishima
Y. (2018)
Anther culture in rice proportionally rescues microspores according to
gametophytic gene effect and enhances genetic study of hybrid sterility.
Plant Methods 14, 102.
Chen S., Saito N., Encabo J.R., Yamada K., Choi I.R., Kishima Y. (2018)
Ancient endogenous pararetroviruses in Oryza genomes provide Insights
into the heterogeneity of viral gene macroevolution.
Genome Biology and Evolution 10, 2686-2696.
Fujita, D., Koide, Y., Kobayashi, N. (2018)
Genetic dissection of agronomic traits in introgression lines andimprovement of an elite Indica rice variety.
Japan Agricultural Research Quarterly 52, 91-103.
Koide, Y., Ogino, A., Yoshikawa, T., Kitashima, Y., Saito, N., Kanaoka, Y.,
Onishi, K., Yoshitake, T., Tsukiyama, T., Saito, H., Teraishi, M., Yamagata,Y., Uemura, A., Takagi, H., Hayashi, Y., Abe, T., Fukuta, Y., Okumoto, Y.,
Kanazawa, A. (2018)
Lineage-specific gene acquisition or loss is involved in interspecific hybrid
sterility in rice.
Proceedings of the National Academy of Sciences of the UnitedStates of America 115, E1955-E1962.
Koide, Y., Obara, M., Yanagihara, S., Fukuta, Y. (2018)
Identification of QTLs for agronomic characteristics in an upland New Ricefor Africa (NERICA) variety.
Japan Agricultural Research Quarterly 52, 29-37.

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2017

Chen, S., Zheng, H., Kishima, Y. (2017)
Genomic fossils reveal adaptation of non-autonomous pararetroviruses
driven by concerted evolution of noncoding regulatory sequences.
PLOS Pathogens e1006413.
Zhou, H., Kishima, Y. (2017)
Alternative plant host defense against transposon activities occurs at the
post-translational stage.
Plant Signaling & Behavior 13, e1318238.
Zhou, H., Hirata, M., Osawa, R., Fujino, K., Kishima, Y. (2017)
Detainment of Tam3 transposase at plasma membrane by its BED-zincfinger domain.
Plant Physiology 173, 1492-1501.
Kinoshita, N., Kato,M., Koyasaki, K., Kawashima T., Nishimura, T.,
Hirayama, Y., Takamure, I., Sato, T., Kato K. (2017)
Identification of quantitative trait loci for rice grain quality and yieldrelated traits in two closely related Oryza sativa L. subsp. japonica
cultivars grown near the northernmost limit for rice paddy cultivation.
Breeding Science 67, 191–206.
Ogiso-Tanaka, E., Tanaka, T., Tanaka, K., Nonoue, Y., Sasaki, T., Fushimi,E., Koide, Y., Okumoto, Y., Yano, M., Saito, H. (2017)
Detection of novel QTLs qDTH4.5 and qDTH6.3, which confer late heading
under short-day conditions, by SSR marker-based and QTL-seq analysis.
Breeding Science 67, 101-109.

2016

Chen, S., Kishima, Y. (2016)
Endogenous pararetroviruses in rice genomes as a fossil record useful forthe emerging field of paleovirology.
Molecular Plant Pathology 17, 1317-1320.
Matsuda, A., Takano, S., Sato, M., Furukawa, K., Nagasawa, H., Yoshikawa,
S., Kasuga, J., Tokuji, Y., Yazaki, K., Nakazono, M., Takamure, I., Kato, K.
(2016)
Rice stomatal closure requires guard cell plasma membrane ATP-Binding
cassette transporter RCN1/OsABCG5.
Molecular Plant 9, 417–427.
Yamauchi, T., Tanaka, A., Mori, H., Takamure, I., Kato, K., Nakazono, M.
(2016)
Ethylene-dependent aerenchyma formation in adventitious roots isregulated differently in rice and maize.
Plant, Cell and Environment 39, 2145–2157.

2015

Mikami, T., Kitazaki K., Kishima, Y. (2015)
Cytoplasmic genome diversity in the cultivated apple.

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Horticultural Science 42, 47-51.
Takano, S., Matsuda, S., Funabiki, A., Furukawa, J., Yamauchi, T., Tokuj, Y.,
Nakazono, M., Shinohara, Y., Takamure I., Kato, K. (2015)
The rice RCN11/OsXylT,β1,2-xylosyltransferase, is involved in plantdevelopment and growth in response to multiple abiotic stresses and ABA
sensitivity during seed germination.
Plant Science 236, 75-88.

2014

Chen, S., Liu, R., Koyanagi, K.O., Kishima, Y. (2014)
Rice genomes recorded ancient pararetrovirus activities: virus genealogy
and multiple origins of endogenization during rice speciation.
Virology 471-473, 141-152.
Ishiguro, S., Ogasawara, K., Fujino, K., Sato, Y., Kishima, Y. (2014)
Low temperature-responsive changes in the anther transcriptome’s repeat
sequences are indicative of stress sensitivity and pollen sterility in ricestrains.
Plant Physiology 164, 671-682.
Ota, Y., Ishiguro, S., Aoyama, E., Aiba, R., Iwashiro, R., Tanabata, T.,
Takamure, I., Fujino, K., Kishima, Y. (2014)
Isolation of a major genetic interaction associated with an extreme
phenotype using assorted F2 populations in rice.
Molecular Breeding 33, 997-1003.
Liu, R., Kishima, Y. (2014)
Chapter 12 “Establishment of endogenous pararetroviruses in the ricegenome”
Plant Virus-Host Interaction: Molecular Approaches and Viral
Evolution: ed Gaur, R.K., Hohn, T., Sharma, P., pp 229-240, Elsevier New
York.
Shiono, K., Ando, M., Nishiuchi, S., Takahashi, H., Watanabe, K.,
Nakamura, M., Matsuo, Y., Yasuno, N., Yamanouchi, U., Fujimoto, M.,
Takanashi, H., Ranathunge, K., Franke, R. B., Shitan, N., Nishizawa, N. K.,
Takamure, I., Yano, M., Tsutsumi, N., Schreiber, L., Yazaki, K., Nakazono,
M., Kato, K. (2014)
RCN1/OsABCG5, an ATP- binding cassette (ABC) transporter, is requiredfor hypodermal suberization of roots in rice (Oryza sativa).
The Plant Journal 80, 40-51
Matsuda, S., Nagasawa, H., Yamashiro, N., Yasuno, N., Watanabe, T.,
Kitazawa, H., Takano, S., Tokuji, Y., Tani, M., Takamure, I., Kato, K. (2014)
Rice RCN1/OsABCG5 mutation alters accumulation of essential andnonessential minerals and causes high Na/K ratio resulting in a saltsensitive phenotype.
Plant Science 224, 103-111.

2013

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Kitazaki, K., Ishiguro, S., Kato, S., Wakatsuki, A., Kishima, Y., Mikami, T.
(2013)
Cytoplasmic diversity and possible maternal lineages in apples as revealedby analysis of the mitochondrial cox1 and atp9 loci.
Scientia Horticulturae 164, 209-212.
Uchiyama, T., Hiura, S., Ebinuma, I., Senda, M., Mikami, T., Martin, C.,Kishima, Y. (2013)
A pair of transposons coordinately suppresses gene expression,
independent of pathways mediated by siRNA in Antirrhinum.
New Phytologist 197, 431-440.
Funabiki, A., Takano, S., Matsuda, S., Tokuji, Y., Takamure, I., Kato, K.
(2013)The rice REDUCED CULM NUMBER11 gene controls vegetative growthunder low-temperature conditions in paddy fields independent of
RCN1/OsABCG5.
Plant Science 211, 70–76.
Takano-Kai, N., Jiang, H., Powell, A., McCouch, S., Takamure, I., Furuya,N., Doi, K., Yoshimura, A. (2013)
Multiple and independent origins of short seeded alleles of GS3 in rice.
Breeding Science 63, 77–85.

2012

Liu, R., Koyanagi, K.O., Chen, S., Kishima, Y. (2012)
Evolutionary force of AT-rich repeats to trap genomic and episomal DNAs in
the rice genome: lessons from endogenous pararetrovirus.
The Plant Journal 72, 817-828.
Kato, S., Kitazaki, K., Wakatsuki, A., Kishima, Y., Mikami, T. (2012)
An apple atp9 pseudogene is maintained at high copy number in ‘Golden
Delicious’ -type mitochondria but is present substoichiometrically in‘Delicious’-type mitochondria.
Scientia Horticulturae 134, 237-230.
Matsuda, S., Funabiki, A., Furukawa, K., Komori, N., Koike, M., Tokuji, Y.,
Takamure, I., Kato, K. (2012)
Genome-wide analysis and expression Analysis profiling of half-size ABC
protein subgroup G in rice in Response to abiotic stress and phytohormone
treatments.
Molecular Genetics and Genomics 287, 819–835.
Ureshi, A., Matuda, S. Ohashi, E., Onishi, K., Takamure, I., Kato, K. (2012)
Rice RCN1/OsABCG5 mutation is associated with the root development inresponse to nutrient shortage.
Plant Root 6, 28-35.
Koide, Y., Shinya, Y., Ikenaga, M., Sawamura, N., Matsubara, K., Onishi, K.,
Kanazawa, A., Sano, Y. (2012).

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Complex genetic nature of sex-independent transmission ratio distortion in
Asian rice species: the involvement of unlinked modifiers and sex-specificmechanisms.
Heredity 108, 242-247.

2011

Fujino, K., Hashida, SN., Ogawa, T., Natsume, T., Uchiyama, T., Mikami, T.,
Kishima, Y. (2011)
Temperature controls nuclear import of Tam3 transposase in Antirrhinum.
The Plant Journal 65, 146-155.
Wakatsuki, A., Kitazaki, K., Kato, S., Kishima, Y., Mikami, T. (2011)
An intact mitochondrial cox1 gene and a pseudogene with different
genomic configurations are present in apple cultivars ‘Golden Delicious’and ‘Delicious’: Evolutionary aspects.
Scientia Horticulturae 130, 49-53.

2010 - 2000

Hu, Z., Yan, H., Yang, J., Yamaguchi, S., Maekawa, M., Takamure, I.,
Tsutsumi, N., Kyozuka, J., Nakazono, M. (2010) Strigolactones negatively
regulate mesocotyl elongation in rice during germination and growth indarkness. Plant Cell Physiology 51, 1136‒1142.
貴島祐治、堀田夕夏、石黒聖也、山村和照、塙章、内藤聡、佐野芳雄 (2010) トランス
ポゾンを指標にしたコシヒカリ品種内の遺伝的差異 育種学研究 12, 81-86.
Hagiwara, WE., Uwatoko, N., Sasaki, A., Matsubara, K., Nagano, H., Onishi,K., Sano, Y. (2009) Diversification in flowering time due to tandem FT-likegene duplication, generating novel Mendelian factors in wild and cultivatedrice. Molecular Ecology 18, 1537-1549.
Yasuno, N., Takamure, I., Kidou, S., Tokuji, Y., Ureshi, A., Funabiki, A.,
Ashikaga, K., Yamanouchi, U, Yano, M., Kato, K. (2009) Rice shootbranching requires an ATP-binding cassette subfamily G protein. New
Phytologist 182, 91–101.
Ariyaratne, M., Takamure, I., Kato, K. (2009) Shoot branching control by
reduced culm number 4 in rice (Oryza sativa L.). Plant Science 176, 744‒
748.
Uchiyama, T., Fujino, K., Ogawa, T., Wakatsuki, A., Kishima, Y., Mikami, T.,
Sano, Y. (2009) Stable transcription activities dependent on an orientationof Tam3 transposon insertions into Antirrhinum and yeast promoters occur
only within chromatin. Plant Physiology 151, 1557-1569.
Koide, Y., Ikenaga, M., Sawamura, N., Nishimoto, D., Matsubara, K., Onishi,K., Kanazawa, A., Sano, Y. (2008) The evolution of sex-independenttransmission ratio distortion involving multiple allelic interactions at asingle locus in rice. Genetics 180, 409-420.

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Koide, Y., Onishi, K., Nishimoto, D., Baruah, AR., Kanazawa, A., Sano, Y.
(2008) Sex-independent transmission ratio distortion system responsible
for reproductive barriers between Asian and African rice species. New
Phytologist 179, 888-900.
Uchiyama, T., Saito, Y., Kuwabara, H., Fujino, K., Kishima, Y., Martin, C.,
Sano, Y. (2008) Multiple regulatory mechanisms influence the activity ofthe transposon, Tam3, of Antirrhinum. New Phytologist 179, 343-355.
Koide, Y., Ikenaga, M., Shinya, Y., Matsubara, K., Sano, Y. (2008) Twoloosely linked genes controlling the female specificity for crossincompatibility in rice. Euphytica 164, 753-760.
Yan, H., Saika, H., Maekawa, M., Takamure, I., Tsutsumi, N., Kyozuka, J.,
Nakazono, M. (2007) Rice tillering dwarf mutant dwarf3 has increased leaf
longevity during darkness-induced senescence or hydrogen peroxideinduced cell death. Genes and Genetic Systems 82, 361-366.
Furukawa, T., Maekawa, M., Oki, T., Suda, I., Iida, S., Shimada, H.,
Takamure, I., Kadowaki, K. (2007) The Rc and Rd genes are involved inproanthocyanidin synthesis in rice pericarp. The Plant Journal 49, 91102.
Takata, M., Kiyohara, A., Takasu, A., Kishima, Y., Ohtsubo, H., Sano, Y.
(2007) Rice transposable elements are characterized by various
methylation environments in the genome. BMC Genomics 8, 469.
Noro, Y., Takano-Shimizu, T., Syono, K., Kishima, Y., Sano, Y. (2007)
Genetic variations in rice in vitro cultures at the EPSPs - RPS20 region.
Theoretical and Applied Genetics 114, 705-711.
Yasuno, N., Yasui, Y., Takamure, I., Kato, K. (2007) Genetic interaction
between 2 tillering genes, ruduced culm number 1 (rcn1) and tilleringdwarfgene d3, in rice. Journal of Heredity 98, 169-172.
Hashida, SN., Uchiyama, T., Martin, C., Kishima, Y., Sano, Y., Mikami, T.
(2006) The temperature-dependent change in methylation of the
Antirrhinum transposon tam3 is controlled by the activity of its
transposase. The Plant Cell 18, 104-118.
Hagiwara, W. E., Onishi, K., Takamure, I., Sano, Y. (2006) Transgressive
segregation due to linked QTLs for grain characteristics of rice. Euphytica
150, 27-35.
Hashida, SN., Kishima, Y., Mikami, T. (2005) DNA methylation is notnecessary for the inactivation of the Tam3 transposon at non-permissive
temperature in Antirrhinum. Journal of Plant Physiology 162, 12921296.
Takata, M., Kishima, Y., Sano, Y. (2005) DNA methylation polymorphisms inrice and wild rice strains: Detection of epigenetic markers. Breeding

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Science 55, 57-63.
Kobayashi, S., Noro, Y., Nagano, H., Yoshida, K. T., Takano-Shimizu, T.,
Kishima, Y., Sano, Y. (2005) Evidence for an evolutionary force thatprevents epigenetic silencing between tail-to-tail rice genes with a shortspacer. Gene 346, 231-240.
Maekawa, M., Takamure, I., Ahmed, N., Kyozuka, J. (2005) Bunketsuwaito, one of the tillering dwarfs, is controlled by a single recessive gene inrice (Oryza sativa L.). Breeding Science 55, 193-197.
Ishikawa, S., Maekawa, M., Arite, T., Onishi, K., Takamure, I., Kyozuka, J.
(2005) Suppression of tiller bud activity in tillering dwarf mutants of rice.
Plant and Cell Physiology 46, 79-86.
Saitoh, K., Onishi, K., Mikami, I., Thidar, K., Sano, Y. (2004) Allelicdiversification at the C (OsC1) locus of wild and cultivated rice: Nucleotidechanges associated with phenotypes. Genetics 168, 997-1007.
Kunii, M., Kanda, M., Nagano, H., Uyeda, I., Kishima, Y., Sano, Y. (2004)
Reconstruction of putative DNA virus from endogenous rice tungro
bacilliform virus-like sequences in the rice genome: implications for
integration and evolution. BMC Genomics 5, 80.
Matsubara, K., Khin-Thidar., Sano, Y. (2003) A gene block causing crossincompatibility hidden in wild and cultivated rice. Genetics 165, 343-352.
Takagi, K., Nagano, H., Kishima, Y., Sano, Y. (2003) MITE-transposon
display efficiently detects polymorphisms among the Oryza AA-genome
species. Breeding Science 53, 125-132.
Hashida, S., Kitamura, K., Mikami, T., Kishima, Y. (2003) Temperature shift
coordinately changes the activity and the methylation state of transposon
Tam3 in Antirrhinum majus. Plant Physiology 132, 1207-1216.
Nagano, H., Kunii, M., Azuma, T., Kishima, Y., Sano, Y. (2002)
Characterization of the repetitive sequences in a 200-kb region around therice waxy locus: diversity of transposable elements and presence of veiled
repetitive sequences. Genes and Genetic Systems 77, 69-79.
Murai, M., Takamure, I., Sato, S., Tokutome, T., Sato, Y. (2002) Effects ofthe dwarfing gene originating from 'Dee-geo-woo-gen' on yield and its
related traits in rice. Breeding Science 52, 95-100.
Kitamura, K., Hashida, S., Mikami, T., Kishima, Y. (2001) Position effect of
the excision frequency of the Antirrhinum transposon Tam3: implications
for the degree of position-dependent methylation in the ends of theelement. Plant Molecular Biology 47, 475-490.
Nagano, H., Kawasaki, S., Kishima, Y., Sano, Y. (2000) Structuraldifferences in the vicinity of the waxy locus among the Oryza species with

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the AA-genome: identification of variable regions. Theoretical andApplied Genetics 100, 376-383.

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