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6. References
Antonio, B.A., Inoue, T., Kajiya, H., Nagamura, Y., Kurata, N., Minobe, Y., Yano, M., Nakagahra, M., and Sasaki, T., 1996, Comparison of genetic distance and order of genetic markers in five populations of rice, Genome 39:946–956.
Antonio, B.A., Sakata, K., and Sasaki, T., 2000, Rice at the forefront of plant genome informatics, Genome Informatics 11:3–11.
Ashikari, M., Wu, J., Yano, M., Sasaki, T., and Yoshimura, A., 1999, Rice gibberellin-insensitive dwarf mutant gene Dwarf1 encodes the alpha-subunit of GTP-binding protein, Proc. Natl. Acad. Sci. USA 96:10284–10289.
Baba, T., Katagiri, S., Tanoue, H., Tanaka, R., Chiden, Y., Saji, S., Hamada, M., Nakashima, M., Okamoto, M., Hayashi, M., Yoshiki, S., Karasawa, W., Honda, M., Ichikawa, Y., Arita, K., Ikeno, M., Ohta, T., Umehara, Y., Matsumoto, T., de Jong, P., and Sasaki, T., 2000, Construction and characterization of rice genome libraries: PAC library of japonica variety, Nipponbare and BAC library of indica variety, NIAR Bull. 14:41–49.
Barry, G., 2001, The use of the Monsanto draft rice genome sequence in research, Plant Physiol. 125:1164–1165.
Feng, Q., Zhang, Y., Hao, P., Wang, S., Fu, G., Huang, Y., Li, Y., Zhu, J., Liu, Y., Hu, X., Jia, P., Zhang, Y., Zhao, Q., Ying, K., Yu, S., Tang, Y., Weng, Q., Zhang, L., Lu, Y., Mu, J., Lu, Y., Zhang, L.S., Yu, Z., Fan, D., Liu, X., Lu, T., Li, C., Wu, Y., Sun, T., Lei, H., Li, T., Hu, H., Guan, J., Wu, M., Zhang, R., Zhou, B., Chen, Z., Chen, L., Jin, Z., Wang, R., Yin, H., Cai, Z., Ren, S., Lv, G., Gu, W., Zhu, G., Tu, Y., Jia, J., Zhang, Y., Chen, J., Kang, H., Chen, X., Shao, C., Sun, Y., Hu, Q., Zhang, X., Zhang, W., Wang, L., Ding, C., Sheng, H., Gu, J., Chen, S., Ni, L., Zhu, F., Chen, W., Lan, L., Lai, Y., Cheng, Z., Gu, M., Jiang, J., Li, J., Hong, G., Xue, Y., and Han, B., 2002, Sequence and analysis of rice chromosome 4, Nature 420:316–320.
Goff, S.A., Ricke, D., Lan, T.H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., Hadley, D., Hutchison, D., Martin, C., Katagiri, F., Lange, B.M., Moughamer, T., Xia, Y., Budworth, P., Zhong, J., Miguel, T., Paszkowski, U., Zhang, S., Colbert, M., Sun, W., Chen, L., Cooper, B., Park, S., Wood, T.C., Mao, L., Quail, P., Wing, R., Dean, R., Yu, Y., Zharkikh, A., Shen, R., Sahasrabudhe, S., Thomas, A., Cannings, R. Gutin, A., Pruss, D., Reid, J., Tavtigian, S., Mitchell, J., Eldredge, G., Scholl, T., Miller, R.M., Bhatnagar, S. Adey, N., Rubano, T., Tusneem, N., Robinson, R., Feldhaus, J. Macalma, T., Oliphant, A., and Briggs, S., 2002, A draft sequence of the rice genome (Oryza sativa L. ssp. japonica), Science 296:92–100.
Harris, S.B., 2002, Virtual rice, EMBO Reports 3:511–513.
Harushima, Y., Yano, M., Shomura, A., Sato, M., Shimano, T., Kuboki, Y., Yamamoto, T., Lin, S.Y., Antonio, B.A., Parco, A., Kajiya, H., Huang, N., Yamamoto, K., Nagamura, Y., Kurata, N., Khush, G.S., and Sasaki, T., 1998, A high-density rice genetic linkage map with 2,275 markers using a single F2 population, Genetics 148:479–494.
Hirochika, H., 2001, Contribution of the Tos17 retrotransposon to rice functional genoics, Curr. Opin. Plant Biol. 4:118–122.
Higo, K., Ugawa, Y., Iwamoto, M., and Korenaga, T., 1999, Plant cis-acting regulatory DNA elements (PLACE) database, Nucleic Acids Res. 27:297–300.
Kikuchi, S., Satouh, K., Nagata, T., Kawagashira, N., Doi, K., Kishimoto, N., Yazaki, J., Ishikawa, M., Yamada, H., Ooka, H., Hotta, I., Kojima, K., Namiki, T., Ohneda, E., Yahagi, W., Suzuki, K., Li, C.J., Ohtsuki, K., Shishiki, T., Otomo, Y., Murakami, K., Iida, Y., Sugano, S., Fujimura, T., Suzuki, Y., Tsunoda, Y., Kurosaki, T., Kodama, T., Masuda, H., Kobayashi, M., Xie, Q., Lu, M., Narikawa, R., Sugiyama, A., Mizuno, K., Yokomizo, S., Niikura, J., Ikeda, R., Ishibiki, J., Kawamata, M., Akemi, Y., Miura, J., Kusumegi, T., Oka, M., Ryu, R., Ueda, M., Matsubara, K., Kawai, J., Carninci, P., Adachi, J., Aizawa, K., arakawa, T., Fukuda, S., Hara. A., Hashidume, W., Hayatsu, N., Imotani, K., Ishii, Y., Itoh, M., Kagawa, I., Kondo, S., Konno, H., Miyazaki, A., Osato, N., Ota, Y., Saito, R., Sasaki, D., Sato, K., Shibata, K. Shinagawa, A., Shiraki, T., Yoshino, M., and Hayashizaki, Y., 2003, Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice, Science 301:376–379.
Kojima, S., Takahashi, Y., Kobayashi, Y., Monna, L., Sasaki, T., Araki, T., and Yano, M. 2002, Hd3a, a rice ortholog of the ArabidopsisFT gene, promotes transition to flowering downstream of Hd1 under short-day condition, Plant Cell Physiol. 43:1096–1105.
Kurata, N., Nagamura, Y., Yamamoto, K., Harushima, Y., Sue, N., Wu, J., Antonio, B.A., Shomura, A,. Shimizu, T., Lin, S.Y., Fukuda, A., Shimano, T., Kuboki, Y., Toyama, T., Miyamoto, Y., Kirihara, T., Hayasaka, K., Miyao, A., Monna, L., Zhong, H.S., Tamura, Y., Wang, Z.X., Momma, T., Umehara, Y., Yano, M., Sasaki, T., and Minobe, Y., 1994b, A 300 kilobase interval genetic map of rice including 883 expressed sequences, Nature Genetics 8:365–372.
Kurata, N., Moore, G., Nagamura, Y., Foote, T., Yano, M., Minobe, Y., and Gale, M., 1994a, Conservation of genome structure between rice and wheat, Bio/Technology 12:276–278.
Lin, S.Y., Sasaki, T., and Yano, M., 1998, Mapping quantitative trait loci controlling seed dormancy and heading date using backcross inbred lines in rice, Oryza sativa L., Theor. Appl. Genet. 96:997–1003.
Moore, G., Devos, K.M., Wang, Z., and Gale, M.D., 1995, Grasses, line up and form a circle, Current Biol. 5: 737–739.
Saji, S., Umehara, Y., Antonio, B.A., Yamane, H., Tanoue, H., Baba, T., Aoki, H., Ishige, N., Wu, J., Koike, K., Matsumoto, T., and Sasaki, T., 2001, A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes, Genome 44:32–37.
Sakata, K., Nagamura, Y., Numa, H., Antonio, B.A., Nagasaki, H., Idonuma, A., Watanabe, W., Shimizu, Y., Horiuchi, I., Matsumoto, T., Sasaki, T., and Higo, K., 2002, Rice GAAS: an automated annotation system and database for rice genome sequence, Nucleic Acids Res. 30:98–102.
Sakata, K., Antonio, B.A., Mukai, Y., Nagasaki, H., Sakai, Y., Makino, K., and Sasaki, T., 2000, INE: a rice genome database with an integrated map view, Nucleic Acids Res. 28:97–101.
Sasaki, T., Matsumoto, T., Yamamoto, Y., Sakata, K., Baba, T., Katayose, Y., Wu, J., Niimura, Y., Cheng, Z., Nagamura, Y., Antonio, B.A., Kanamori, H., Hosokawa, S., Masukawa, M., Arikawa, K., Chiden, Y., Hayashi, M., Okamoto, M., Ando, T., Aoki, H., Arita, K., Hamada, M., Harada, C., Hijishita, S., Honda, M., Ichikawa, Y., Idonuma, A., Iijima, M., Ikeda, M., Ikeno, M., Ito, S., Ito, T., Ito, Y., Ito, Y., Iwabuchi, A., Kamiya, K., Karasawa, W., Katagiri, S., Kikuta, A., Kobayashi, N., Kono, I., Machita, K., Maehara, T., Mizuno, H., Mizubayashi, T., Mukai, Y., Nagasaki, H., Nakashima, M., Nakama, Y., Nakamichi, Y., Nakamura, M., Namiki, N., Negishi, M., Ohta, I., Ono, N., Saji, S., Sakai, K., Shibata, M., Shimokawa, T., Shomura, A., Song, J., Takazaki, Y., Terasawa, K., Tsuji, K., Waki, K., Yamagata, H., Yamane, H., Yoshiki, S., Yoshihara, R., Yukawa, K., Zhong, H., Iwama, H., Endo, T., Ito, H., Hahn, J.H., Kim, H.I., Eun, M.Y., Yano, M., Jiming, J., and Gojobori, T., 2002, The genome sequence and structure of rice chromosome 1, Nature 420:312–316.
Sasaki, T., and Burr, B., 2000, International rice genome sequencing project: the effort to completely sequence the rice genome, Curr. Opin. Plant Biol. 3:138–141.
Sasaki, T., 1999, Rice genome research in Japan as a frontrunner in crop genomics. Sci Technol. Jpn. 18:18–21.
Takahashi, Y., Shomura, A., Sasaki, T., and Yano, M., 2001, Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the a subunit of protein kinase CK2, Proc. Natl. Acad. Sci. USA 98:7922–7927.
Takeuchi, Y., Hayasaka, H., Chiba, B., Tanaka, I., Shimano, T., Yamagishi, M., Nagano, K., Sasaki, S., and Yano, M., 2001, Mapping quantitative trait loci controlling cool-temperature tolerance at booting stage using doubled-haploid lines of temperate japonica rice cultivars, Breed. Sci. 51:191–197.
Wang, Z.X., Yano, M., Yamanouchi, U., Iwamoto, M., Monna, L., Hayasaka, H., Katayose, Y., and Sasaki, T., 1999, The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes, Plant J. 19:55–64.
Wu, J., Maehara, T., Shimokawa, T., Yamamoto, S., Harada, C., Takazaki, Y., Ono, N., Mukai, Y., Koike, K., Yazaki, J., Fujii, F., Shomura, A., Ando, T., Kono, I., Waki, K., Yamamoto, K., Yano, M., Matsumoto, T., and Sasaki, T., 2002, A comprehensive rice transcript map containing 6591 expressed sequence tag sites, Plant Cell 14:525–535.
Yamamoto, K., and Sasaki, T., 1997, Large-scale EST sequencing in rice. Plant Mol. Biol. 35:135–144.
Yano, M., and Sasaki, T., 1997, genetic and molecular dissection of quantitative traits in rice, Plant Mol. Biol. 35:145–153.
Yano, M., Katayose, Y., Ashikari, M., Yamanouchi, U., Monna, L., Fuse, T., Baba, T., Yamamoto, K., Umehara, Y., Nagamura, Y., and Sasaki, T., 2000, Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS, Plant Cell 12:2473–248.
Yazaki, J., Kishimoto, N., Nakamura, K., Fujii, F., Shimbo, K., Otsuka, Y., Wu, J., Yamamoto, K., Sakata, K., Sasaki, T., and Kikuchi, S., 2000, Embarking on rice functional genomics via cDNA microarray: Use of 3′ UTR probes for specific gene expression analysis, DNA Res. 7:367–370.
Yazaki, J., Kishimoto, N., Ishikawa, M., and Kikuchi, S., 2002, Rice Expression Database: the gateway to rice functional genomics, Trends Plant Sci. 7:563–564.
Yazaki, J., Kojima, K., Suzuki, K., Kishimoto, N., and Kikuchi, S., The Rice PIPELINE: a unification tool for plant functional genomics, (in preparation).
Yoshimura, S., Yamanouchi, U., Katayose, Y., Toki, S., Wang, Z.X., Kono, I., Kurata, N., Yano, M., Iwata, N., and Sasaki, T., 1998, Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation, Proc. Natl. Acad. Sci. USA 95:1663–1668.
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Antonio, B.A., Nagamura, Y., Namiki, N., Matsumoto, T., Sasaki, T. (2005). Rice Genome Sequencing and Data Mining Resources. In: Gustafson, J.P., Shoemaker, R., Snape, J.W. (eds) Genome Exploitation. Springer, Boston, MA. https://doi.org/10.1007/0-387-24187-6_1
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