Basu D, Dehesh K, Schneider-Poetsch H J, Harrington S E, McCouch S R, Quail P H. 2000. Rice PHYC gene: Structure, expression, map position and evolution. Plant Mol Biol, 44: 27–42.Briggs W R, Huala E. 1999. Blue-light photoreceptors in higher plants. Annu Rev Cell Dev Biol, 15: 33–62.Chen H, Zhang J, Neff M M, Hong S W, Zhang H, Deng X W, Xiong L. 2008. Integration of light and abscisic acid signaling during seed germination and early seedling development. Proc Natl Acad Sci USA, 105: 4495–4500.Correll M J, Kiss J Z. 2005. The roles of phytochromes in elongation and gravitropism of roots. Plant Cell Physiol, 46: 317–323.De Simone S, Oka Y, Inoue Y. 2000. Photoperceptive site of the photoinduction of root hairs in lettuce (Lactuca sativa L. cv. Grand Rapids) seedlings under low pH conditions. J Plant Res, 113: 55–62.Dehesh K, Tepperman J, Christensen A H, Quail P H. 1991. phyB is evolutionarily conserved and constitutively expressed in rice seedling shoots. Mol Gen Genet, 225: 305–313.Devlin P F, Yanovsky M J, Kay S A. 2003. A genomic analysis of the shade avoidance response in Arabidopsis. Plant Physiol, 133: 1617–1629.Franklin K A, Quail P H. 2010. Phytochrome functions in Arabidopsis development. J Exp Bot, 61: 11–24.Iwamoto M, Kiyota S, Hanada A, Yamaguchi S, Takano M. 2011. The multiple contributions of phytochromes to the control of internode elongation in rice. Plant Physiol, 157: 1187–1195.Jumtee K, Okazawa A, Harada K, Fukusaki E, Takano M, Kobayashi A. 2009. Comprehensive metabolite profiling of phyA phyB phyC triple mutants to reveal their associated metabolic phenotype in rice leaves. J Biosci Bioeng, 108: 151–159.Kay S A, Keith B, Shinozaki K, Chua N H. 1989. The sequence of the rice phytochrome gene. Nucl Acids Res, 17: 2865–2866.Kiss J Z, Miller K M, Ogden L A, Roth K K. 2002. Phototropism and gravitropism in lateral roots of Arabidopsis. Plant Cell Physiol, 43: 35–43.Kurata T, Yamamoto K T. 1997. Light-stimulated root elongation in Arabidopsis thaliana. J Plant Physiol, 151: 346–351.Lin R C, Wang H Y. 2005. Two homologous ATP-binding cassette transporter proteins, AtMDR1 and AtPGP1, regulate Arabidopsis photomorphogenesis and root development by mediating polar auxin transport. Plant Physiol, 138: 949–964.Liu J, Liu Y M, Takano M, Wang B, Xie X Z. 2010. Involvement of phytochromes in gibberellin-mediated photomorphogenesis in rice seedlings. Chin Sci Bull, 55: 2384–2390. (in Chinese)Molas M L, Kiss J Z, Correll M J. 2006. Gene profiling of the red light signalling pathways in roots. J Exp Bot, 57: 3217–3229.Nagatani A, Reed J W, Chory J. 1993. Isolation and initial characterization of Arabidopsis mutants that are deficient in phytochrome A. Plant Physiol, 102: 269–277.Nagatani A. 2004. Light-regulated nuclear localization of phytochromes. Curr Opin Plant Biol, 7: 708–711.Neff M M, Fankhauser C, Chory J. 2000. Light: An indicator of time and place. Genes Dev, 14: 257–271.Oh E, Kang H, Yamaguchi S, Park J, Lee D, Kamiya Y, Choi G. 2009. Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis. Plant Cell, 21: 403–419.Ohno Y, Fujiwara A. 1967. Photoinhibition of elongation of roots in rice seedlings. Plant Cell Physiol, 8: 141–150.Okada K, Shimura Y. 1992. Mutational analysis of root gravitropism and phototropism of Arabidopsis thaliana seedlings. Funct Plant Biol, 19: 439–448.Osugi A, Itoh H, Ikeda-Kawakatsu K, Takano M, Izawa T. 2011. Molecular dissection of the roles of phytochrome in photoperiodic flowering in rice. Plant Physiol, 157: 1128–1137. Riemann M, Muller A, Korte A, Furuya M, Weiler E W, Nick P. 2003. Impaired induction of the jasmonate pathway in the rice mutant hebiba. Plant Physiol, 133(4): 1820–1830. Saab I N, Sharp R E, Pritchard J, Voetberg G S. 1990. Increased endogenous abscisic acid maintains primary root growth and inhibits shoot growth of maize seedlings at low water potentials. Plant Physiol, 93: 1329–1336.Salisbury F J, Hall A, Grierson C S, Halliday K J. 2007. Phytochrome coordinates Arabidopsis shoot and root development. Plant J, 50: 429–438.Seo M, Hanada A, Kuwahara A, Endo A, Okamoto M, Yamauchi Y, North H, Marion-Poll A, Sun T P, Koshiba T, Kamiya Y, Yamaguchi S, Nambara E. 2006. Regulation of hormone metabolism in Arabidopsis seeds: Phytochrome regulation of abscisic acid metabolism and abscisic acid regulation of gibberellin metabolism. Plant J, 48: 354–366.Shimizu H, Tanabata T, Xie X Z, Inagaki N, Takano M, Shinomura T, Yamamoto K T. 2009. Phytochrome-mediated growth inhibition of seminal roots in rice seedlings. Physiol Plant, 137: 289–297.Shimizu H, Shinomura T, Yamamoto K T. 2010. Similarities and differences between phytochrome-mediated growth inhibition of coleoptiles and seminal roots in rice seedlings. Plant Signal Behav, 5(2): 134–135. Sidler M, Hassa P, Hasan S, Ringli C, Dudler R. 1998. Involvement of an ABC transporter in a developmental pathway regulating hypocotyl cell elongation in the light. Plant Cell, 10: 1623– 1636.Sun Q, Yoda K, Suzuki M, Suzuki H. 2003. Vascular tissue in the stem and roots of woody plants can conduct light. J Exp Bot, 54: 1627–1635.Svyatyna K, Riemann M. 2012. Light-dependent regulation of the jasmonate pathway. Protoplasma, 249(Suppl. 2): 137–145.Takano M, Kanegae H, Shinomura T, Miyao A, Hirochika H, Furuya M. 2001. Isolation and characterization of rice phytochrome A mutants. Plant Cell, 13: 521–534.Takano M, Inagaki N, Xie X Z, Yuzurihara N, Hihara F, Ishizuka T, Yano M, Nishimura M, Miyao A, Hirochika H, Shinomura T. 2005. Distinct and cooperative functions of phytochromes A, B, and C in the control of deetiolation and flowering in rice. Plant Cell, 17: 3311–3325.Takano M, Inagaki N, Xie X Z, Kiyota S, Baba-Kasai A, Tanabata T, Shinomura T. 2009. Phytochromes are the sole photoreceptors for perceiving red/far-red light in rice. Proc Natl Acad Sci USA, 106: 14705–14710.Tian Q, Uhlir N J, Reed J W. 2002. Arabidopsis SHY2/IAA3 inhibits auxin-regulated gene expression. Plant Cell, 14: 301–319.Xie X Z, Shinomura T, Inagaki N, Kiyota S, Takano M. 2007. Phytochrome-mediated inhibition of coleoptile growth in rice: Age-dependency and action spectra. Photochem Photobiol, 83: 131–138.Xie X Z, Xue Y J, Zhou J J, Zhang B, Chang H, Takano M. 2011. Phytochromes regulate SA and JA signaling pathways in rice and are required for developmentally controlled resistance to Magnaporthe grisea. Mol Plant, 4(4): 688–696. |