References
- An, G., Ebert, P.R., Mitra, A., and Ha, S.B. (1989). Binary vectors. In Plant Molecular Biology Manual. (Dordrecht: Kluwer Academic Publisher A3). pp.1-19.
- An, G., Jeong, D.H., Jung, K.H., and Lee, S. (2005a). Reverse genetic approaches for functional genomics of rice. Plant Mol. Biol. 59, 111-123. https://doi.org/10.1007/s11103-004-4037-y
- An, G., Lee, S., Kim, S.H., and Kim, S.R. (2005b). Molecular genetics using T-DNA in rice. Plant Cell Physiol. 46, 14-22. https://doi.org/10.1093/pcp/pci502
- Cho, L.H., Yoon, J., Pasriga, R., and An, G. (2016). Homodimerization of Ehd1 is required to induce flowering in rice. Plant Physiol. 170, 2159-2171. https://doi.org/10.1104/pp.15.01723
- Cho, L.H., Yoon, J., and An, G. (2017). The control of flowering time by environmental factors. Plant J. 90, 708-719. https://doi.org/10.1111/tpj.13461
- Corbesier, L., Vincent, C., Jang, S., Fornara, F., Fan, Q., Searle, I., Giakountis, A., Farrona, S., Gissot, L., Turnbull, C., and Coupland, G. (2007). FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 316, 1030-1033. https://doi.org/10.1126/science.1141752
- Dangl, M., Brosch, G., Haas, H., Loidl, P., and Lusser, A. (2001). Comparative analysis of HD2 type histone deacetylases in higher plants. Planta 213, 280-285. https://doi.org/10.1007/s004250000506
- Ding, B., Bellizzi Mdel, R., Ning, Y., Meyers, B.C., and Wang, G.L. (2012). HDT701, a histone H4 deacetylase, negatively regulates plant innate immunity by modulating histone H4 acetylation of defense-related genes in rice. Plant Cell 24, 3783-3794. https://doi.org/10.1105/tpc.112.101972
- Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-Iike gene expression independently of Hd1. Genes Dev. 18, 926-936. https://doi.org/10.1101/gad.1189604
- Fowler, S., Lee, K., Onouchi, H., Samach, A., Richardson, K., Coupland, G., and Putterill, J. (1999). GIGANTEA: a circadian clock-controlled gene that regulates photoperiodic flowering in Arabidopsis and encodes a protein with several possible membranespanning domains. EMBO J. 18, 4679-4688. https://doi.org/10.1093/emboj/18.17.4679
- Fu, W., Wu, K., and Duan, J. (2007). Sequence and expression analysis of histone deacetylases in rice. Biochem. Biophys. Res. Commun. 356, 843-850. https://doi.org/10.1016/j.bbrc.2007.03.010
- Haring, M., Offermann, S., Danker, T., Horst, I., Peterhansel, C., and Stam, M. (2007). Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization. Plant Methods 3, 1-16. https://doi.org/10.1186/1746-4811-3-1
- Hayama, R., Yokoi, S., Tamaki, S., Yano, M., and Shimamoto, K. (2003). Adaptation of photoperiodic control pathways produces short-day flowering in rice. Nature 422, 719-722. https://doi.org/10.1038/nature01549
- He, Y., Michaels, S.D., and Amasino, R.M. (2003). Regulation of flowering time by histone acetylation in Arabidopsis. Science 302, 1751-1754. https://doi.org/10.1126/science.1091109
- Hu, Y., Qin, F., Huang, L., Sun, Q., Li, C., Zhao, Y., and Zhou, D.X. (2009). Rice histone deacetylase genes display specific expression patterns and developmental functions. Biochem. Biophys. Res. Commun. 388, 266-271. https://doi.org/10.1016/j.bbrc.2009.07.162
- Ishikawa, R., Aoki, M., Kurotani, K., Yokoi, S., Shinomura, T., Takano, M., and Shimamoto, K. (2011). Phytochrome B regulates Heading date 1(Hd1)-mediated expression of rice florigen Hd3a and critical day length in rice. Mol. Genet. Genom. 285, 461-470. https://doi.org/10.1007/s00438-011-0621-4
- Jeon, J.S., Lee, S., Jung, K.H., Jun, S.H., Jeong, D.H., Lee, J., Kim, C., Jang, S., Lee, S., Yang, K., et al. (2000). T-DNA insertional mutagenesis for functional genomics in rice. Plant J. 22, 561-570. https://doi.org/10.1046/j.1365-313x.2000.00767.x
- Jeong, D.H., An, S., Kang, H.G., Moon, S., Han, J.J., Park, S., Lee, H.S., An, K., and An, G. (2002). T-DNA insertional mutagenesis for activation tagging in rice. Plant Physiol. 130, 1636-1644. https://doi.org/10.1104/pp.014357
- Jeong, D.H., An, S., Park, S., Kang, H.G., Park, G.G., Kim, S.R., Sim, J., Kim, Y.O., Kim, M.K., Kim, S.R., et al. (2006). Generation of a flanking sequence-tag database for activation-tagging lines in japonica rice. Plant J. 45, 123-132. https://doi.org/10.1111/j.1365-313X.2005.02610.x
- Kim, S.R., Lee, D.Y., Yang, J.I., Moon, S., and An, G. (2009) Cloning vectors for rice. J. Plant Biol. 52, 73-78. https://doi.org/10.1007/s12374-008-9008-4
- Kim, S.L., Choi, M., Jung, K.H., and An, G. (2013). Analysis of the early-flowering mechanisms and generation of T-DNA tagging lines in Kitaake, a model rice cultivar, J. Exp. Bot. 64, 4169-4182. https://doi.org/10.1093/jxb/ert226
- Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K. (2008). Hd3a and RFT1 are essential for flowering in rice. Development 135, 767-774. https://doi.org/10.1242/dev.008631
- Lee, Y.S., and An, G. (2015). OsGI controls flowering time by modulating rhythmic flowering time regulators preferentially under short day in rice. J. Plant Biol. 58, 137-145. https://doi.org/10.1007/s12374-015-0007-y
- Lee, Y.S., Jeong, D.H., Lee, D.Y., Yi, J., Ryu, C.H., Kim, S.L., Jeong, H.J., Choi, S.C., Jin, P., Yang, J., et al. (2010). OsCOL4 is a constitutive flowering repressor upstream of Ehd1 and downstream of OsphyB. Plant J. 63, 18-30.
- Lee, Y.S., Lee, D.Y., Cho, L.H., and An, G. (2014). Rice miR172 induces flowering by suppressing OsIDS1 and SNB, two AP2 genes that negatively regulate expression of Ehd1 and florigens. Rice. 7, 31. https://doi.org/10.1186/s12284-014-0031-4
- Lee, Y.S., Yi, J., Jung, K.H., and An, G. (2016) Comparison of rice flowering-time genes under paddy conditions. J. Plant Biol. 59, 238-246. https://doi.org/10.1007/s12374-016-0029-0
- Li, C., Huang, L., Xu, C., Zhao, Y., and Zhou, D.X. (2011). Altered levels of histone deacetylase OsHDT1 affect differential gene expression patterns in hybrid rice. PLoS One 6, e21789. https://doi.org/10.1371/journal.pone.0021789
- Luo, M., Wang, Y.Y., Liu, X., Yang, S., Lu, Q., Cui, Y., and Wu, K. (2012). HD2C interacts with HDA6 and is involved in ABA and salt stress response in Arabidopsis. J. Exp. Bot. 63, 3297-3306. https://doi.org/10.1093/jxb/ers059
- Luo, M., Tai, R., Yu, C.W., Yang, S., Chen, C.Y., Lin, W.D., Schmidt, W., and Wu, K. (2015). Regulation of flowering time by the histone deacetylase HDA5 in Arabidopsis. Plant J. 82, 925-936. https://doi.org/10.1111/tpj.12868
- Miao, J., Guo, D., Zhang, J., Huang, Q., Qin, G., Zhang, X., Wan, J., Gu, H., and Qu, L.J. (2013). Targeted mutagenesis in rice using the CRISPR-Cas system. Cell Res. 23, 1233-1236. https://doi.org/10.1038/cr.2013.123
- Morita, S., Wada, H., and Matsue, Y. (2017). Countermeasures for heat damage in rice grain quality under climate change. Plant Prod. Sci. 19, 1-11.
- Naito, Y., Hino, K., Bono, H., and Ui-Tei, K. (2015). CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics 31, 1120-1123. https://doi.org/10.1093/bioinformatics/btu743
- Nishida, H., Inoue, H., Okumoto, Y., and Tanisakao, T. (2002). A novel gene ef1-h conferring an extremely long basic vegetative growth period in rice. Crop Sci. 42, 348-354.
- Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Childs, K., Thibaud-Nissen, F., Malek, R.L., Lee, Y., Zheng, L., et al. (2007).The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res. 35, D883-D887. https://doi.org/10.1093/nar/gkl976
- Pandey, R., MuEller, A., Napoli, C.A., Selinger, D.A., Pikaard, C.S., Richards, E.J., Bender, J., Mount, D.W., and Jorgensen, R.A. (2002). Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res. 30, 5036-5055. https://doi.org/10.1093/nar/gkf660
- Park, D.H., Somers, D.E., Kim, Y.S., Choy, Y.H., Lim, H.K., Soh, M.S., Kim, H.J., Kay, S.A., and Nam, H.G. (1999). Control of circadian rhythms and photoperiodic flowering by the Arabidopsis GIGANTEA gene. Science 285, 1579-1582. https://doi.org/10.1126/science.285.5433.1579
- Peng, L.T., Shi, Z.Y., Li, L., Shen, G.Z., and Zhang, J.L. (2007). Ectopic expression of OsLFL1 in rice represses Ehd1 by binding on its promoter. Biochem. Biophys. Res. Commun. 360, 251-256. https://doi.org/10.1016/j.bbrc.2007.06.041
- Peng, L.T., Shi, Z.Y., Li, L., Shen, G.Z., and Zhang, J.L. (2008). Overexpression of transcription factor OsLFL1 delays flowering time in Oryza sativa. Plant Physiol. 165, 876-885. https://doi.org/10.1016/j.jplph.2007.07.010
- Ryu, C.H., Lee, S., Cho, L.H., Kim, S.L., Lee, Y.S., Choi, S.C., Jeong, H.J., Yi, J., Park, S.J., Han, C.D., et al. (2009). OsMADS50 and OsMADS56 function antagonistically in regulating long day (LD)-dependent flowering in rice. Plant Cell Environ. 32, 1412-1427. https://doi.org/10.1111/j.1365-3040.2009.02008.x
- Saito, H., Ogiso-Tanaka, E., Okumoto, Y., Yoshitake, Y., Izumi, H., Yokoo, T., Matsubara, K., Hori, K., Yano, M., Inoue, H., et al. (2012). Ef7 encodes an ELF3-likeprotein and promotes rice flowering by negatively regulating the floral repressor gene Ghd7 under both short- and long-day conditions, Plant Cell Physiol. 53, 717-728. https://doi.org/10.1093/pcp/pcs029
- Samach, A., Onouchi, H., Gold, S.E., Ditta, G.S., Schwarz-Sommer, Z.,Yanofsky, M.F., and Coupland, G. (2000). Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis. Science 288, 1613-1616. https://doi.org/10.1126/science.288.5471.1613
- Sridha, S., and Wu, K. (2006). Identification of AtHD2C as a novel regulator of abscisic acid responses in Arabidopsis. Plant J. 46, 124-133. https://doi.org/10.1111/j.1365-313X.2006.02678.x
- Sun, C., Chen, D., Fang, J., Wang, P., Deng, X., and Chu, C. (2014). Understanding the genetic and epigenetic architecture in complex network of rice flowering pathways. Protein Cell 5, 889-898. https://doi.org/10.1007/s13238-014-0068-6
- Tamaki, S., Matsuo, S., Wong, H.L., Yokoi, S., and Shimamoto, K. (2007). Hd3a protein is a mobile flowering signal in rice. Science 316, 1033-1036. https://doi.org/10.1126/science.1141753
- Tanaka, T., Antonio, B.A., Kikuchi, S., Matsumoto, T., Nagamura, Y., Numa, H., Sakai, H,. Wu, J., Itoh, T., Sasaki, T., et al. (2008). The rice annotation project database (RAP-DB): 2008 update. Nucleic Acids Res. 36, D1028-D1033.
- Ueno, Y., Ishikawa, T., Watanabe, K., Terakura, S., Iwakawa, H., Okada, K., Machida, C., and Machida, Y. (2007). Histone deacetylases and ASYMMETRIC LEAVES2 are involved in the establishment of polarity in leaves of Arabidopsis. Plant Cell 19, 445-457. https://doi.org/10.1105/tpc.106.042325
- Wei, J., Wu, Y., Cho, L.H., Yoon, J., Choi, H., Yoon, H., Jin, P., Yi, J., Lee, Y.S., Jeong, H.J., et al. (2017). Identification of root-preferential transcription factors in rice by analyzing GUS expression patterns of T-DNA tagging lines. J. Plant Biol. 60, 268-277. https://doi.org/10.1007/s12374-016-0597-z
- Wu, K., Tian, L., Malik, K., Brown, D., and Miki, B. (2000). Functional analysis of HD2 histone deacetylase homologues in Arabidopsis thaliana. Plant J. 22, 19-27. https://doi.org/10.1046/j.1365-313x.2000.00711.x
- Wu, K., Zhang, L., Zhou, C., Yu, C.W., and Chaikam, V. (2008). HDA6 is required for jasmonate response, senescence and flowering in Arabidopsis. J. Exp. Bot. 59, 225-234. https://doi.org/10.1093/jxb/erm300
- Xue, W., Xing, Y., Weng, X., Zhao, Y., Tang, W., Wang, L., Zhou, H., Yu, S., Xu, C., Li, X., et al. (2008). Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice, Nat. Genet. 40, 761-767. https://doi.org/10.1038/ng.143
- Yanovsky, M.J., and Kay, S.A. (2002). Molecular basis of seasonal time measurement in Arabidopsis. Nature 419, 308-312. https://doi.org/10.1038/nature00996
- Yoon, J., Cho, L.H., Kim, S.L., Choi, H., Koh, H.J., and An, G. (2014). The BEL1-type homeobox gene SH5 induces seed shattering by enhancing abscission-zone development and inhibiting lignin biosynthesis. Plant J. 79, 717-728. https://doi.org/10.1111/tpj.12581
- Yoon, J., Cho, L.H., Antt, H.W., Koh, H.J., and An, G. (2017). KNOX protein OSH15 induces grain shattering by repressing lignin biosynthesis genes. Plant Physiol. 174, 312-325. https://doi.org/10.1104/pp.17.00298
- Yi, J., and An, G. (2013). Utilization of T-DNA tagging lines in rice. J. Plant Biol. 56, 85-90. https://doi.org/10.1007/s12374-013-0905-9
- Zhang, J., Zhou, X., Yan, W., Zhang, Z., Lu, L., Han, Z., Zhao, H., Liu, H., Song, P., Hu, Y., et al. (2015). Combinations of the Ghd7, Ghd8 and Hd1 genes largely define the ecogeographical adaptation and yield potential of cultivated rice. New Phytol. 1056-1066.
- Zhang, Z., Hu, W., Shen, G., Liu, H., Hu, Y., Zhou, X., Liu, T., and Xing, Y. (2017). Alternative functions of Hd1 in repressing or promoting heading are determined by Ghd7 status under long-day conditions. Sci. Rep. 7, 5388. https://doi.org/10.1038/s41598-017-05873-1
- Zhao, X.L., Shi, Z.Y., Peng, L.T., Shen, G.Z., and Zhang, J.L. (2011). An atypical HLH protein OsLF in rice regulates flowering time and interacts with OsPIL13 and OsPIL15. N. Biotechnol. 28, 788-797. https://doi.org/10.1016/j.nbt.2011.04.006
- Zhao, J., Zhang, J., Zhang, W., Wu, K., Zheng, F., Tian, L., Liu, X., and Duan, J. (2015). Expression and functional analysis of the plant-specific histone deacetylase HDT701 in rice. Front. Plant Sci. 5, 764.
- Zhu, Q.H, and Helliwell, C.A. (2011). Regulation of flowering time and floral patterning by miR172. J. Exp. Bot. 62, 487-495. https://doi.org/10.1093/jxb/erq295
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