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Critical Reviews in Plant Sciences Volume 35, 2016 - Issue 4
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Original Articles

Sub-Functionalization in Rice Gene Families with Regulatory Roles in Abiotic Stress Responses

G. SharmaNational Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
,
J. GiriNational Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
&
A. K. TyagiNational Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India;Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, IndiaCorrespondence[email protected]
Pages 231-285 | Published online: 25 Jan 2017

References

  • Aasland, R., Gibson, T. J., and Stewart, A. F. 1995. The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem. Sci. 20: 56–59.
  • Abbasi, F., Onodera, H., Toki, S., Tanaka, H., and Komatsu, S. 2004. OsCDPK13, a calcium dependent protein kinase gene from rice, is induced by cold and gibberellin in rice leaf sheath. Plant Mol. Biol. 55: 541–552.
  • Abe, H., Urao, T., Ito, T., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. 2003. Arabidopsis AtMYC2 bHLH and AtMYB2 MYB function as transcriptional activators in abscisic acid signaling. Plant Cell 15: 63–78.
  • Achaz, G., Coissac, E., Viari, A., and Netter, P. 2000. Analysis of intrachromosomal duplications in yeast Saccharomyces cerevisiae: a possible model for their origin. Mol. Biol. Evol. 17: 1268–1275.
  • Adams, K. L., and Wendel, J. F. 2005. Polyploidy and genome evolution in plants. Curr. Opin. Plant Biol. 8: 135–141.
  • Agalou, A., Purwantomo, S., Overnas, E., Johannesson, H., Zhu, X., Estiati, A., de Kam, R. J., Engstrom, P., Slamet-Loedin, IH., Zhu, Z., et al. 2008. A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members. Plant Mol. Biol. 66: 87–103.
  • Agarwal, M., Hao, Y., Kapoor, A., Dong, C. H., Fujii, H., Zheng, X., and Zhu, J. K. 2006. A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance. J. Biol. Chem. 281: 37636–37645.
  • Agarwal, P., Arora, R., Ray, S., Singh, A. K., Singh, V. P., Takatsuji, H., Kapoor, S., and Tyagi, A. K. 2007. Genome-wide identification of C2H2 zinc-finger gene family in rice and their phylogeny and expression analysis. Plant Mol. Biol. 65: 467–485.
  • Ahmad, F., Huang, X., Lan, H. X., Huma, T., Bao, Y. M., Huang, J., and Zhang, H. S. 2014. Comprehensive gene expression analysis of the DNA cytosine-5. methyltransferase family in rice Oryza sativa L. Genet. Mol. Res. 13: 5159–5172.
  • Ahn, J. C., Kim, D. W., You, Y. N., Seok, M. S., Park, J. M., Hwang, H., Kim, B. G., Luan, S., Park, H. S., and Cho, H. S. 2010. Classification of rice Oryza sativa L. Japonica nipponbare immunophilins FKBPs, CYPs and expression patterns under water stress. BMC Plant Biol. 10: 253.
  • Aida, M., Ishida, T., Fukaki, H., Fujisawa, H., and Tasaka, M. 1997. Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. Plant Cell 9: 841–857.
  • Alba, M., and Pages, M. 1998. Plant proteins containing the RNA-recognition motif. Trends Plant Sci. 3: 15–21.
  • Albrecht, V., Ritz, O., Linder, S., Harter, K., and Kudla, J. 2001. The NAF domain defines a novel protein-protein interaction module conserved in Ca2+-regulated kinases. EMBO J. 20: 1051–1063.
  • Allan, A. C., Hellens, R. P., and Laing, W. A. 2008. MYB transcription factors that colour our fruit. Trends Plant Sci. 13: 99–102.
  • Allwood, E. G., Anthony, R. G., Smertenko, A. P., Reichelt, S., Drobak, B. K., Doonan, J. H., and Weeds, A. G., Hussey, P. J. 2002. Regulation of the pollen-specific actin-depolymerizing factor LlADF1. Plant Cell 14: 2915–2927.
  • Ambawat, S., Sharma, P., Yadav, N. R., and Yadav, R. C. 2013. MYB transcription factor genes as regulators for plant responses: an overview. Physiol. Mol. Biol. Plants. 19: 307–321.
  • Ambrosone, A., Costa, A., Leoneb, A., and Grillo, S. 2012. Beyond transcription: RNA-binding proteins as emerging regulators of plant response to environmental constraints. Plant Sci. 182: 12–18.
  • Amrutha, R. N., Sekhar, P. N., Varshney, R. K., and Kishor, P. B. K. 2007. Genome-wide analysis and identification of genes related to potassium transporter families in rice Oryza sativa L. Plant Sci. 172: 708–721.
  • An, L., Zhou, Z., Sun, L., Yan, A., Xi, W., Yu, N., Cai, W., Chen, X., Yu, H., Schiefelbein, J., et al. 2012. A zinc finger protein gene ZFP5 integrates phytohormone signaling to control root hair development in Arabidopsis. Plant J. 72: 474–490.
  • Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815.
  • Asano, T., Hataka, M., Nakamura, H., Aoki, N., Komatsu, S., Ichikawa, H., Hirochika, H., and Ohsug, R. 2011. Functional characterisation of OsCPK21., a calcium-dependent protein kinase that confers salt tolerance in rice. Plant Mol. Biol. 75: 179–191.
  • Asano, T., Hayashi, N., Kobayashi, M., Aoki, N., Miyao, A., Mitsuhara, I., Ichikawa, H., Komatsu, S., Hirochika, H., Kikuchi, S., et al. 2012. A rice calcium-dependent protein kinase OsCPK12 oppositely modulates salt-stress tolerance and blast disease resistance. Plant J. 69: 26–36.
  • Asano, T., Tanaka, N., Yang, G., Hayashi, N., and Komatsu, S. 2005. Genome-wide identification of the rice calcium-dependent protein kinase and its closely related kinase gene families: comprehensive analysis of the CDPKs gene family in rice. Plant Cell Physiol. 46: 356–366.
  • Ashley, M. K., Grant, M., and Grabov, A. 2006. Plant responses to potassium deficiencies: a role for potassium transport proteins. J. Exp. Bot. 57: 425–436.
  • Babu, M. M., Iyer, L. M., Balaji, S., and Aravind, L. 2006. The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucl. Acids Res. 34: 6505–6520.
  • Bae, H., Kin, S. K., Cho, S. K., Kang, B. G., and Kim, T. K. 2011. Overexpression of OsRDCP1., a rice RING domain-containing E3 ubiquitin ligase., increased tolerance to drought stress in rice Oryza sativa L. Plant Sci. 180: 775–782.
  • Bafee, S. O. 2013. Phylogeny of the plant salinity tolerance related HKT genes. Int. J. Biol. 5: 64–68.
  • Bai, M. Y., Zhang, L. Y., Gampala, S. S., Zhu, S. W., Song, W. Y., Chong, K., and Wang, Z. Y. 2007. Functions of OsBZR1 and 14-3-3 proteins in brassinosteroid signaling in rice. Proc. Natl. Acad. Sci. U S A 104: 13839–13844.
  • Bai, Y., Meng, Y., Huang, D., Qi, Y., and Chen, M. 2011. Origin and evolutionary analysis of the plant-specific TIFY transcription factor family. Genomics 98: 128–136.
  • Bakshi, M., and Oelmüller, R. 2014. WRKY transcription factors. Plant Signal. Behav. 9: e27700.
  • Barrera-Figueroa, BE., Gao, L., Wu, Z., Zhou, X., Zhu, J., Jin, H., Liu, R., and Zhu, J. K. 2012. High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice. BMC Plant Biol. 12: 132.
  • Bartel, D. P. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281–297.
  • Basu, S., and Roychoudhury, A. 2014. Expression profiling of abiotic stress-inducible genes in response to multiple stresses in rice Oryza sativa L. varieties with contrasting level of stress tolerance. Biomed. Res. Int. 706890.
  • Bateman, A. 2002. The SGS3 protein involved in PTGS finds a family. BMC Bioinformat. 3: 21.
  • Batistič, O., and Kudla, J. 2009. Plant calcineurin B-like proteins and their interacting protein kinases. Biochem. Biophys. Acta 1793: 985–992.
  • Baumberger, N., and Baulcombe, D. C. 2005. Arabidopsis ARGONAUTE1 is an RNA slicer that selectively recruits microRNAs and short interfering RNAs. Proc. Natl. Acad. Sci. U S A 102: 11928–11933.
  • Baumgarten, A., Cannon, S., Spangler, R., and May, G. 2003. Genome-level evolution of resistance genes in Arabidopsis thaliana. Genetics 165: 309–319.
  • Becchetti, A., Gamel, K., and Torre, V. 1999. Cyclic nucleotide-gated channels. Pore topology studied through the accessibility of reporter cysteines. J. Gen. Physiol. 114: 377–392.
  • Bella, J., Hindle, K. L., McEwan, P. A., and Lovell, S. C. 2008. The leucine-rich repeat structure. Cell Mol. Life Sci. 65: 2307–2333.
  • Berg, J. M., and Shi, Y. 1996. The galvanization of biology: a growing appreciation for the roles of zinc. Science 271: 1081–1085.
  • Berthomieu, P., Conejero, G., Nublat, A., Brackenbury, W. J., Lambert, C., Savio, C., Uozumi, N., Oiki, S., Yamada, K., Cellier, F., et al. 2003. Functional analysis of AtHKT1 in Arabidopsis shows that Na+ recirculation by the phloem is crucial for salt tolerance. EMBO J. 22: 2004–2014.
  • Bienz, M., and Pelham, H. R. 1987. Mechanisms of heat-shock gene activation in higher eukaryotes. Adv. Genet. 24: 31–72.
  • Bindokas, V. P., and Miller, R. J. 1995. Excitotoxic degeneration is initiated at non random sites in cultured rat cerebellar neurons. J. Neurosci. 15: 6999–7011.
  • Bogamuwa, S. P., and Jang, J. C. 2014. Tandem CCCH zinc finger proteins in plant growth, development and stress response. Plant Cell Physiol. 55: 1367–1375.
  • Boonburapong, B., and Buaboocha, T. 2007. Genome-wide identification and analyses of the rice calmodulin and related potential calcium sensor proteins. BMC Plant Biol. 7: 4.
  • Boore, L. J. 2003. The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of duterostome animals. Comp. Genomics 2000: 133–147.
  • Brodersen, P., Sakvarelidze-Achard, L., Bruun-Rasmussen, M., Dunoyer, P., Yamamoto, Y. Y., Sieburth, L., and Voinnet, O. 2008. Widespread translational inhibition by plant miRNAs and siRNAs. Science 320: 1185–1190.
  • Broekaert, I., Lee, H. I., Kush, A., Chua, N. H., and Raikhel, N. 1990. Wound-induced accumulation of mRNA containing a hevein sequence in laticifers of rubber tree Hevea brasiliensis. Proc. Natl. Acad. Sci. U S A 87: 7633–7637.
  • Buljan, M., and Bateman, A. 2009. The evolution of protein domain families. Biochem. Soc. Trans. 37: 751–755.
  • Burd, C. G., and Dreyfuss, G. 1994. Conserved structures and diversity of functions of RNA-binding proteins. Science 265: 615–621.
  • Burglin, T. R. 1997. Analysis of TALE superclass homeobox genes MEIS, PBC, KNOX, Iroquois, TGIF reveals a novel domain conserved between plants and animals. Nucleic Acids Res. 25: 4173–4180.
  • Cambi, A., Koopman, M., and Figdor, C. G. 2005. How C-type lectins detect pathogens. Cell Microbiol. 7: 481–488.
  • Campo, S., Baldrich, P., Messeguer, J., Lalanne, E., Coca, M., San, and Segundo, B. 2014. Overexpression of a calcium-dependent protein kinase confers salt and drought tolerance in rice by preventing membrane lipid peroxidation. Plant Physiol. 165: 688–704.
  • Canella, D., Gilmour, S. J., Kuhn, L. A., and Thomashow, M. F. 2010. DNA binding by the Arabidopsis CBF1 transcription factor requires the PKKP/RAGRxKFxETRHP signature sequence. Biochim.Biophys. Acta 1799: 454–462.
  • Cannon, S. B., Mitra, A., Baumgarten, A., Young, N. D., and May, G. 2004. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol. 4: 10.
  • Cao, X., Springer, N. M., Muszynski, M. G., Phillips, R. L., Kaeppler, S., and Jacobsen, S. E. 2000. Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc. Natl. Acad. Sci. U S A 97: 4979–4984.
  • Carafoli, E., Santella, L., Branca, D., and Brini, M. 2001. Generation, control, and processing of cellular calcium signals. Crit. Rev. Biochem. Mol. Biol. 36: 107–260.
  • Carretero-Paulet, L., Galstyan, A., Roig-Villanova, I., Martinez-Garcia, J. F., Bilbao-Castro, J. R., and Robertson, D. L. 2010. Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae. Plant Physiol. 153: 1398–1412.
  • Cashikar, AG., Duennwald, M., and Lindquist, S. L. 2005. A chaperone pathway in protein disaggregation. Hsp26 alters the nature of protein aggregates to facilitate reactivation by Hsp104. J. Biol. Chem. 280: 23869–23875.
  • Castilhos, G., Lazzarotto, F., Spagnolo-Fonini, L., Bodanese-Zanettini, M. H., and Margis-Pinheiro, M. 2014. Possible roles of basic helix-loop-helix transcription factors in adaptation to drought. Plant Sci. 223: 1–7.
  • Chan, R. L., Gago, G. M., Palena, C. M., and Gonzalez, D. H. 1998. Homeoboxes in plant development. Biochim. Biophys. Acta 1442: 1–19.
  • Chandler, J., Nardmann, J., and Werr, W. 2008. Plant development revolves around axes. Trends Plant Sci. 13: 78–84.
  • Chattopadhyaya, R., Meador, W. E., Means, A. R., and Quiocho, F. A. 1992. Calmodulin structure refined at 1.7 A resolution. J. Mol .Biol. 228: 1177–1192.
  • Chauhan, H., Khurana, N., Agarwal, P., and Khurana, P. 2011. Heat shock factors in rice Oryza sativa L. genome-wide expression analysis during reproductive development and abiotic stress. Mol. Genet. Genomics 286: 171–187.
  • Chen, F., Li, Q., Sun, L., and He, Z. 2006. The rice 14-3-3 gene family and its involvement in responses to biotic and abiotic stress. DNA Res. 13: 53–63.
  • Chen, H., Chen, W., Zhou, J., He, H., Chen, L., Chen, H., and Deng, X. W. 2012. Basic leucine zipper transcription factor OsbZIP16 positively regulates drought resistance in rice. Plant Sci. 193–194: 8–17.
  • Chen, M., and Bennetzen, J. L. 1996. Sequence composition and organization in the Sh2/A1-homologous region of rice. Plant Mol. Biol. 32: 999–1001.
  • Chen, Q., Wang, Q., Xiong, L., and Lou, Z. 2011. A structural view of the conserved domain of rice stress-responsive NAC1. Protein Cell 2: 55–63.
  • Chen, X., Wang, Y., Lv, B., Li, J., Luo, L., Lu, S., Zhang, X., Ma, H., and Ming, F. 2014. The NAC family transcription factor OsNAP confers abiotic stress response through the ABA pathway. Plant Cell Physiol. 55: 604–619.
  • Chen, Z. J., and Tian, L. 2007. Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochem. Biophys. Acta 1769: 295–301.
  • Cheng, Q., Zhou, Y., Liu, Z., Zhang, L., Song, G., Guo, Z., Wang, W., Qu, X., Zhu, Y., and Yang, D. 2015. An alternatively spliced heat shock transcription factor, OsHSFA2dI, functions in the heat stress-induced unfolded protein response in rice. Plant Biol. Stuttg. 17: 419–429.
  • Cheng, S., Huang, Y., Zhu, N., and Zhao, Y. 2014. The rice WUSCHEL-related homeobox genes are involved in reproductive organ development, hormone signaling and abiotic stress response. Gene 549: 266–274.
  • Cheng, S., Zhou, DX., and Zhao, Y. 2016. WUSCHEL-related homeobox gene WOX11 increases rice drought resistance by controlling root hair formation and root system development. Plant Signal. Behav. 11: e1130198.
  • Chini, A., Fonseca, S., Fernandez, G., Adie, B., Chico, J. M., Lorenzo, O., Garcia-Casado, G., Lopez-Vidriero, I., Lozano, FM., Ponce, MR., et al. 2007. The JAZ family of repressors is the missing link in jasmonate signalling. Nature 448: 666–671.
  • Chinnusamy, V., Schumaker, K., and Zhu, J. K. 2004. Molecular genetic perspectives on cross-talk and specificity in abiotic stress signalling in plants. J. Exp. Bot. 55: 225–236.
  • Chinnusamy, V., and Zhu, J. K. 2009. RNA-directed DNA methylation and demethylation in plants. Sci. China C. Life Sci. 52: 331–343.
  • Chinpongpanich, A., Wutipraditkul, N., Thairat, S., and Buaboocha, T. 2011. Biophysical characterization of calmodulin and calmodulin-like proteins from rice, Oryza sativa L. Acta Biochim. Biophys. Sin. Shanghai 43: 867–876.
  • Chung, H. J., Sehnke, P. C., and Ferl, R. J. 1999. The 14-3-3 proteins: cellular regulators of plant metabolism. Trends Plant Sci. 4: 367–371.
  • Chung, P. J., Lin, Y. S., Park, S. H., Nahm, B. H., and Kin, J. K. 2009. Subcellular localization of rice histone deacetylases in organelles. FEBS Lett. 583: 2249–2254.
  • Colot, V., and Rossignol, J. L. 1999. Eukaryotic DNA methylation as an evolutionary device. BioEssays 21: 402–411.
  • Cominelli, E., Galbiati, M., Vavasseur, A., Conti, L., Sala, T., Vuylsteke, M., Leonhardt, N., Dellaporta, SL., and Tonelli, C. 2005. A guard-cell-specific MYB transcription factor regulates stomatal movements and plant drought tolerance. Curr. Biol. 15: 1196–1200.
  • Cominelli, E., and Tonelli, C. 2009. A new role for plant R2R3-MYB transcription factors in cell cycle regulation. Cell Res. 19: 1231–1232.
  • Conan, G. C., and Wolfe, K. H. 2008. Turning a hobby into a job: how duplicated genes find new functions. Nat. Rev. Genet. 9: 938–950.
  • Cook, A. J., Gurard-Levin, Z. A., Vassias, I., and Almouzni, G. 2011. A specific function for the histone chaperone NASP to fine-tune a reservoir of soluble H3-H4 in the histone supply chain. Mol. Cell 44: 918–927.
  • Cooper, B., Clarke, J. D., Budworth, P., Kreps, J., Hutchison, D., Park, S., Guimil, S., Dunn, M., Luginbuhl, P., Ellero, C., et al. 2003. A network of rice genes associated with stress response and seed development. Proc. Natl. Acad. Sci. U S A 100: 4945–4950.
  • Cordeiro, A. M., Figueiredo, D. D., Tepperman, J., Borba, A. R., Lourenco, T., Abreu, I. A., Ouwerkerk, P. B., Quail, P. H., Margarida, Oliveira, M., and Saibo, N. J. 2016. Rice phytochrome-interacting factor protein OsPIF14 represses OsDREB1B gene expression through an extended N-box and interacts preferentially with the active form of phytochrome B. Biochim. Biophys. Acta 1859: 393–404.
  • Corpet, A., and Almouzni, G. 2009. Making copies of chromatin: the challenge of nucleosomal organization and epigenetic information. Trends Cell. Biol. 19: 29–41.
  • Cubas, P. 2002. Role of TCP genes in the evolution of morphological characters in angiosperms. Dev. Genet. Plant Evol. 247: 266.
  • Cubas, P., Lauter, N., Doebley, J., and Coen, E. 1999. The TCP domain: a motif found in proteins regulating plant growth and development. Plant J. 18: 215–222.
  • Dansana, P. K., Kothari, K. S., Vij, S., and Tyagi, A. K. 2014. OsiSAP1 overexpression improves water-deficit stress tolerance in transgenic rice by affecting expression of endogenous stress-related genes. Plant Cell Rep. 33: 1425–1440.
  • Darling, D. L., Yingling, J., and Wynshaw-Boris, A. 2005. Role of 14-3-3 proteins in eukaryotic signaling and development. Curr.Top. Dev. Biol. 68: 281–315.
  • Das, P., Nutan, K. K., Singla-Pareek, S. L., and Pareek, A. 2015. Understanding salinity responses and adopting ‘omics-based’ approaches to generate salinity tolerant cultivars of rice. Front. Plant Sci. 6: 712.
  • De Vos, M., Van Oosten, V. R., Van Poecke, R. M., Van Pelt, J. A., Pozo, M. J., Mueller, M. J., Buchala, A. J., Metraux, J. P., Van Loon, L. C., Dicke, M., et al. 2005. Signal signature and transcriptome changes of Arabidopsis during pathogen and insect attack. Mol. Plant Microbe Interact. 18: 923–937.
  • Delaney, K. J., Xu, R., Zhang, J., Li, Q. Q., Yun, K. Y., Falcone, D. L., and Hunt, A. G. 2006. Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit. Plant Physiol. 140: 1507–1521.
  • Deppmann, C. D., Alvania, R. S., and Taparowsky, E. J. 2006. Cross-species annotation of basic leucine zipper factor interactions: insight into the evolution of closed interaction networks. Mol. Biol. Evol. 23: 1480–1492.
  • Desplan, C., Theis, J., and O'Farrell, P. H. 1988. The sequence specificity of homeodomain-DNA interaction. Cell 54: 1081–1090.
  • Dey, A., Samanta, M. K., Gayen, S., Sen, S. K., and Maiti, M. K. 2016. Enhanced gene expression rather than natural polymorphism in coding sequence of the OsbZIP23 determines drought tolerance and yield improvement in rice genotypes. PLoS One 11: e0150763.
  • Dietz, K. J., Vogel, M. O., and Viehhauser, A. 2010. AP2/EREBP transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde. Protoplasma 245: 3–14.
  • Dievart, A., Perin, C., Hirsch, J., Bettembourg, M., Lanau, N., Artu,s, F., Bureau, C., Noel, N., Droc, G., Peyramard, M., et al. 2016. The phenome analysis of mutant alleles in Leucine-Rich Repeat Receptor-Like Kinase genes in rice reveals new potential targets for stress tolerant cereals. Plant Sci. 242: 240–249.
  • Ding, X., Hou, X., Xie, K., and Xiong, L. 2009. Genome-wide identification of BURP domain-containing genes in rice reveals a gene family with diverse structures and responses to abiotic stresses. Planta 230: 149–163.
  • Dipolo, R., and Beauge, L. 2006. Sodium/calcium exchanger: influence of metabolic regulation on ion carrier interactions. Physiol. Rev. 86: 155–203.
  • Doebley, J., Stec, A., and Hubbard, L. 1997. The evolution of apical dominance in maize. Nature 386: 485–488.
  • Dong, A., Xin, H., Yu, Y., Sun, C., Cao, K., and Shen, W. H. 2002. The subcellular localization of an unusual rice calmodulin isoform, OsCaM61, depends on its prenylation status. Plant Mol. Biol. 48: 203–210.
  • Du, L., Jiao, F., Chu, J., Jin, G., Chen, M., and Wu, P. 2007. The two-component signal system in rice Oryza sativa L.: a genome-wide study of cytokinin signal perception and transduction. Genomics 89: 697–707.
  • Duan, M., Huang, P., Yuan, X., Chen, H., Huang, J., and Zhang, H. 2014. CMYB1 encoding a MYB transcriptional activator is involved in abiotic stress and circadian rhythm in rice. Sci. World J. 14: 178038.
  • Duan, W., Sun, B., Li, T. W., Tan, B. J., Lee, M. K., and Teo, T. S. 2000. Cloning and characterization of AWP1, a novel protein that associates with serine/threonine kinase PRK1 in vivo. Gene 256: 113–121.
  • Dubos, C., Stracke, R., Grotewold, E., Weisshaar, B., Martin, C., and Lepiniec, L. 2010. MYB transcription factors in Arabidopsis. Trends Plant Sci. 15: 1360–1385.
  • Dubouzet, J. G., Sakuma, Y., Ito, Y., Kasuga, M., Dubouzet, E. G., Miura, S., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. 2003. OsDREB genes in rice, Oryza sativa L. encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. Plant J. 33: 751–763.
  • Duina, A. A., Chang, H. C., Marsh, J. A., Lindquist, S., and Gaber, R. F. 1996. A cyclophilin function in Hsp90-dependent signal transduction. Science 274: 1713–1715.
  • El-Kereamy, A., Bi, Y. M., Ranathunge, K., Beatty, PH., Good, AG., Rothstein, S. J. 2012. The rice R2R3-MYB transcription factor OsMYB55 is involved in the tolerance to high temperature and modulates amino acid metabolism. PLoS One 7: e52030.
  • Ermolaeva, M. D., Wu, M., Eisen, J. A., and Salzberg, S. L. 2003. The age of the Arabidopsis thaliana genome duplication. Plant Mol. Biol. 51: 859–866.
  • Ernst, H. A., Olsen, A. N., Larsen, S., and Lo Leggio, L. 2004. Structure of the conserved domain of ANAC., a member of the NAC family of transcription factors. EMBO Rep. 5: 297–303.
  • Eulgem, T., Rushton, PJ., Robatzek, S., and Somssich, E. 2000. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 5: 199–206.
  • Eulgem, T., and Somssich, I. E. 2007. Networks of WRKY transcription factors in defense signaling. Curr.Opin. Plant Biol. 10: 366–371.
  • Evans, H. J., and Sorger, G. J. 1966. Role of mineral elements with emphasis on the univalent cations. Ann. Rev. Plant Physiol. 17: 47–76.
  • Faehnle, C. R., and Joshua-Tor, L. 2007. Argonautes confront new small RNAs. Curr Opin Chem. Biol. 11: 569–577.
  • Fang, H., Meng, Q., Xu, J., Tang, H., Tang, S., Zhang, H., and Huang, J. 2015b. Knock-down of stress inducible OsSRFP1 encoding an E3 ubiquitin ligase with transcriptional activation activity confers abiotic stress tolerance through enhancing antioxidant protection in rice. Plant Mol. Biol. 87: 441–458.
  • Fang, Y., Liao, K., Du, H., Xu, Y., Song, H., Li, X., and Xiong, L. 2015a. A stress-responsive NAC transcription factor SNAC3 confers heat and drought tolerance through modulation of reactive oxygen species in rice. J. Exp. Bot. 66: 6803–6817.
  • Fang, Y., Xie, K., and Xiong, L. 2014. Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice. J. Exp. Bot. 65: 2119–2135.
  • Fang, Y., You, J., Xie, K., Xie, W., and Xiong, L. 2008. Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice. Mol. Genet. Genomics 280: 547–563.
  • Feller, A., Machemer, K., Braun, E. L., and Grotewold, E. 2011. Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. Plant J. 66: 94–116.
  • Feng, J. X., Liu, D., Pan, Y., Gong, W., Ma, L. G., Luo, J. C., Deng, X. W., and Zhu, Y. X. 2005. An annotation update via cDNA sequence analysis and comprehensive profiling of developmental, hormonal or environmental responsiveness of the Arabidopsis AP2/EREBP transcription factor gene family. Plant Mol. Biol. 59: 853–868.
  • Feng, Y., Liu, Q., and Xue, Q. 2006. Comparative study of rice and Arabidopsis actin-depolymerizing factors gene families. J. Plant Physiol. 163: 69–79.
  • Finnegan, E. J., and Kovac, K. A. 2000. Plant DNA methyltransferases. Plant Mol. Biol. 43: 189–201.
  • Fischer, G., Wittmann-Liebold, B., Lang, K., Kiefhaber, T., and Schmid, F. X. 1989. Cyclophilin and the peptidyl-prolyl cis-trans isomerase are probably identical proteins. Nature 337: 476–478.
  • Flaus, A., Martin, D. M., Barton, G. J., and Owen-Hughes, T. 2006. Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucl. Acids Res. 34: 2887–2905.
  • Folsom, J. J., Begcy, K., Hao, X., Wang, D., and Walia, H. 2014. Rice fertilization-Independent Endosperm1 regulates seed size under heat stress by controlling early endosperm development. Plant Physiol. 165: 238–248.
  • Freeman, B. C., Toft, D. O., and Morimoto, R. I. 1996. Molecular chaperone machines: chaperone activities of the cyclophilin Cyp-40 and the steroid aporeceptor-associated protein p23. Science 274: 1718–1720.
  • Freemont, P. S. 1993. The RING finger. A novel protein sequence motif related to the zinc finger. Ann. N Y Acad. Sci. 684: 174–192.
  • Freemont, P. S. 2000. Ubiquitination: RING for destruction? Curr. Biol. 10: R84–R87.
  • Fujita, Y., Fujita, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. 2011. ABA-mediated transcriptional regulation in response to osmotic stress in plants. J. Plant Res. 124: 509–525.
  • Fulgosi, H., Soll, J., de Faria Maraschin, S., Korthout, H. A., Wang, M., and Testerink, C. 2002. 14-3-3 proteins and plant development. Plant Mol. Biol. 50: 1019–1029.
  • Gao, J., Zhu, Y., Zhou, W., Molinier, J., Dong, A., and Shen, W. H. 2012. NAP1 family histone chaperones are required for somatic homologous recombination in Arabidopsis. Plant Cell 24: 1437–1447.
  • Gao, L. L., and Xue, H. W. 2012. Global analysis of expression profiles of rice receptor-like kinase genes. Mol. Plant 5: 143–153.
  • Gao, S., Zhang, H., Tian, Y., Li, F., Zhang, Z., Lu, X., Chen, X., and Hunag, R. 2008. Expression of TERF1 in rice regulates expression of stress-responsive genes and enhances tolerance to drought and high-salinity. Plant Cell Rep. 27: 1787–1795.
  • Gao, T., Wu, Y., Zhang, Y., Liu, L., Ning, Y., Wang, D., Tong, H., Chen, S., Chu, C., and Xie, Q. 2011. OsSDIR1 overexpression greatly improves drought tolerance in transgenic rice. Plant Mol. Biol. 76: 145–156.
  • Garciadebla´s, B., Senn, M. E., Banuelos, M. A., and Rodriguez-Navarro, A. 2003. Sodium transport and HKT transporters: the rice model. Plant J. 34: 788–801.
  • Garg, R., Verma, M., Agrawal, S., Shankar, R., Majee, M., and Jain, M. 2014. Deep transcriptome sequencing of wild halophyte rice, Porteresia coarctata, provides novel insights into the salinity and submergence tolerance factors. DNA Res. 21: 69–84.
  • Gehring, W. J., Muller, M., Affolter, M., Percival-Smith, A., Billeter, M., Qian, Y. Q., Otting, G., and Wuthrich, K. 1990. The structure of the homeodomain and its functional implications. Trends Genet. 6: 323–329.
  • Ghosh, A., Kushwaha, H. R., Hasan, M. R., Pareek, A., Sopory, S. K., and Singla-Pareek, S. L. 2016. Presence of unique glyoxalase III proteins in plants indicates the existence of shorter route for methylglyoxal detoxification. Sci. Rep. 6: 18358.
  • Ghosh, A., Pareek, A., Sopory, S. K., and Singla-Pareek, S. L. 2014. A glutathione responsive rice glyoxalase II, OsGLYII-2, functions in salinity adaptation by maintaining better photosynthesis efficiency and anti-oxidant pool. Plant J. 80: 93–105.
  • Gilmour, S. J., and Thomashow, M. F. 1991. Cold acclimation and cold-regulated gene expression in ABA mutants of Arabidopsis thaliana. Plant Mol. Biol. 17: 1233–1240.
  • Gingerich, D. J., Hanada, K., Shiu, S. H., and Vierstra, R. D. 2007. Large-scale., lineage-specific expansion of a bric-a-brac/tramtrack/broad complex ubiquitin-ligase gene family in rice. Plant Cell 19: 2329–2348.
  • Giri, J., Vij, S., Dansana, P. K., and Tyagi, A. K. 2011. Rice A20/AN1 zinc-finger containing stress-associated proteins SAP1/11 and a receptor-like cytoplasmic kinase OsRLCK253 interact via A20 zinc-finger and confer abiotic stress tolerance in transgenic Arabidopsis plants. New Phytol. 191: 721–732.
  • Giri, J., Dansana, P. K., Kothari, K. S., Sharma, G., Vij, S., and Tyagi, A. K. 2013. SAPs as novel regulators of abiotic stress response in plants. BioEssays 35: 639–648.
  • Gorantla, M., Babu, P. R., Lachagari, V. B., Reddy, A. M., Wusirika, R., Bennetzen, J. L., and Reddy, A. R. 2007. Identification of stress-responsive genes in an indica rice Oryza sativa L. using ESTs generated from drought-stressed seedlings. J. Exp. Bot. 58: 253–265.
  • Grabov, A. 2007. Plant KT/KUP/HAK potassium transporters: single family—multiple functions. Ann. Bot. 99: 1035–1041.
  • Gu, Z., Ma, B., Jiang, Y., Chen, Z., Su, Z., and Zhang, H. 2008. Expression analysis of the calcineurin B-like gene family in rice Oryza sativa L. under environmental stresses. Gene 415: 1–12.
  • Guo, J., Wu, J., Ji, Q., Wang, C., Luo, L., Yuan, Y., Wang, Y., and Wang, J. 2008. Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis. J. Genet. Genomics 35: 105–118.
  • Guo, M., Wang, R., Wang, J., Hua, K., Wang, Y., Liu, X., and Yao, S. 2014. ALT1., a Snf2 family chromatin remodeling ATPase, negatively regulates alkaline tolerance through enhanced defense against oxidative stress in rice. PLoS One 9: e112515.
  • Gupta, M., Qiu, X., Wang, L., Xie, W., Zhang, C., Xiong, L., Lian, X., and Zhang, Q. 2008. KT/HAK/KUP potassium transporters gene family and their whole-life cycle expression profile in rice Oryza sativa. Mol. Genet. Genomics 280: 437–452.
  • Gutha, L. R., and Reddy, A. R. 2008. Rice DREB1B promoter shows distinct stress-specific responses, and the overexpression of cDNA in tobacco confers improved abiotic and biotic stress tolerance. Plant Mol. Biol. 68: 533–555.
  • Ha, S., Vankova, R., Yamaguchi-Shinozaki, K., Shinozaki, K., and Tran, L. S. 2012. Cytokinins: metabolism and function in plant adaptation to environmental stresses. Trends Plant Sci. 17: 172–179.
  • Haecker, A., Gross-Hardt, R., Geiges, B., Sarkar, A., Breuninger, H., Herrmann, M., and Laux, T. 2004. Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana. Development 131: 657–668.
  • Hamilton, A. J., and Baulcombe, D. C. 1999. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286: 950–952.
  • Han, R., Jian, C., Lv, J., Yan, Y., Chi, Q., Li, Z., Wang, Q., Zhang, J., Liu, X., and Zhao, H. 2014. Identification and characterization of microRNAs in the flag leaf and developing seed of wheat Triticum aestivum L. BMC Genomics 15: 289.
  • Harmon, A. C., Gribskov, M., and Harper, J. F. 2000. CDPKs—a kinase for every Ca2+ signal? Trends Plant Sci. 5: 154–159.
  • Hattori, J., Boutilier, KA., van Lookeren Campagne, M. M., and Miki, B. L. 1998. A conserved BURP domain defines a novel group of plant proteins with unusual primary structures. Mol. Gen. Genet. 259: 424–428.
  • Haug-Collet, K., Pearson, B., Webel, R., Szerencsei, R. T., Winkfein, R. J., Schnetkamp, P. P. M., and Colley, N. J. 1999. Cloning and characterization of a potassium-dependent sodium/calcium exchanger in Drosophila. J. Cell Biol. 147: 659–669.
  • Hauser, F., and Horie, T. 2010. A conserved primary salt tolerance mechanism mediated by HKT transporters: a mechanism for sodium exclusion and maintenance of high K+/Na+ ratio in leaves during salinity stress. Plant Cell Environ. 33: 552–565.
  • Hazen, S. P., Pathan, M. S., Sanchez, A., Baxter, I., Dunn, M., Estes, B., Chang, H. S., Zhu, T., Kreps, J. A., and Nguyen, H.T. 2005. Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array. Funct.Integr. Genomics 5: 104–116.
  • Hedman, H., Zhu, T., von Arnold, S., and Sohlberg, J. J. 2013. Analysis of the WUSCHEL-RELATED HOMEOBOX gene family in the conifer Picea abies reveals extensive conservation as well as dynamic patterns. BMC Plant Biol. 13: 89.
  • Henderson, I. R., Zhang, X., Lu, C., Johnson, L., Meyers, B. C., Green, P. J., and Jacobsen, S. E. 2006. Dissecting Arabidopsis thaliana DICER function in small RNA processing., gene silencing and DNA methylation patterning. Nat. Genet. 38: 721–725.
  • Henikoff, S., and Comai, L. 1998. A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis. Genetics 149: 307–318.
  • Herve, C., Serres, J., Dabos, P., Canut, H., Barre, A., Rouge, P., and Lescure, B. 1999. Characterization of the Arabidopsis lecRK-a genes: members of a superfamily encoding putative receptors with an extracellular domain homologous to legume lectins. Plant Mol. Biol. 39: 671–682.
  • Himmelbach, A., Hoffmann, T., Leube, M., Hohener, B., and Grill, E. 2002. Homeodomain protein ATHB6 is a target of the protein phosphatase ABI1 and regulates hormone responses in Arabidopsis. EMBO J. 21: 3029–3038.
  • Ho, S. L., Huang, L. F., Lu, C. A., He, S. L., Wang, C. C., Yu, S. P., Chen, J., Yu, S. M. 2013. Sugar starvation- and GA-inducible calcium-dependent protein kinase 1 feedback regulates GA biosynthesis and activates a 14-3-3 protein to confer drought tolerance in rice seedlings. Plant Mol. Biol. 81: 347–361.
  • Hofer, J., Gourlay, C., Michael, A., and Ellis, T. H. 2001. Expression of a class 1 knotted1-like homeobox gene is down-regulated in pea compound leaf primordia. Plant Mol. Biol. 45: 387–398.
  • Hong, J. Y., Chae, M. J., Lee, I. S., Lee, Y. N., Nam, M. H., Kim, D. Y., Byun, M. O., and Yoon, I. S. 2011. Phosphorylation-mediated regulation of a rice ABA responsive element binding factor. Phytochemistry 72: 27–36.
  • Hoque, T. S., Hossain, M. A., Mostofa, M. G., Burritt, D. J., Fujita, M., Tran, L. S. 2016. Methylglyoxal: an emerging signaling molecule in plant abiotic stress responses and tolerance. Front. Plant Sci. 7: 1341.
  • Horie, T., Hauser, F., and Schroeder, J. I. 2009. HKT transporter-mediated salinity resistance mechanisms in Arabidopsis and monocot crop plants. Trends Plant Sci. 14: 660–668.
  • Horie, T., Sugawara, M., Okada, T., Taira, K., Kaothien-Nakayama, P., Katsuhara, M., Shinmyo, A., and Nakayama, H. 2011. Rice sodium-insensitive potassium transporter., OsHAK5., confers increased salt tolerance in tobacco BY2 cells. J. Biosci. Bioeng. 111: 346–356.
  • Horne, S. D., Chowdhury, S. K., and Heng, H. H. 2014. Stress genomic adaptation, and the evolutionary trade-off. Front. Genet. 5: 92.
  • Horowitz, D. S., Lee, E. J., Mabon, S. A., and Misteli, T. 2002. A cyclophilin functions in pre-mRNA splicing. EMBO J. 21: 470–480.
  • Hossain, M. A., Cho, J. I., Han, M., Ahn, C. H., Jeon, J. S., An, G., and Park, P. B. 2010b. The ABRE-binding bZIP transcription factor OsABF2 is a positive regulator of abiotic stress and ABA signaling in rice. J. Plant Physiol. 167: 1512–1520.
  • Hossain, M. A., Lee, Y., Cho, J. I., Ahn, A. H., Lee, S. K., Jeon, J. S., Kang, H., Lee, C. H., An, G., and Park, P. B. 2010a. The bZIP transcription factor OsABF1 is an ABA responsive element binding factor that enhances abiotic stress signalling in rice. Plant Mol. Biol. 72: 557–566.
  • Hu, H., Dai, M., Yao, J., Xiao, B., Li, X., Zhang, Q., and Xiong, L. 2006. Overexpressing a NAM, ATAF, and CUC NAC transcription factor enhances drought resistance and salt tolerance in rice. Proc. Natl. Acad. Sci. U S A 103: 12987–12992.
  • Hu, H., You, J., Fang, Y., Zhu, X., Qi, Z., and Xiong, L. 2008. Characterization of transcription factor gene SNAC2 conferring cold and salt tolerance in rice. Plant Mol. Biol. 67: 169–181.
  • 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.
  • Hu, Y., Zhu, N., Wang, X., Yi, Q., Zhu, D., Lai, Y. and Zhao, Y. 2013. Analysis of rice Snf2 family proteins and their potential roles in epigenetic regulation. Plant Physiol. Biochem. 70: 33–42.
  • Huang, J., Sun, S., Xu, D., Lan, H., Sun, H., Wang, Z., Bao, Y., Wang, J., Tang, H., and Zhang, H. 2012a. A TFIIIA-type zinc finger protein confers multiple abiotic stress tolerances in transgenic rice Oryza sativa L. Plant Mol. Biol. 80: 337–350.
  • Huang, J., Wang, M. M., Jiang, Y., Bao, Y. M., Huang, X., Sun, H., Xu, D. Q., Lan, H. X., and Zhang, H. S. 2008. Expression analysis of rice A20/AN1-type zinc finger genes and characterization of ZFP177 that contributes to temperature stress tolerance. Gene 420: 135–144.
  • Huang, J., Yang, X., Wang, M. M., Tang, H. J., Ding, L. Y., Shen, Y. and Zhang, H. S. 2007. A novel rice C2H2-type zinc finger protein lacking DLN-box/EAR-motif plays a role in salt tolerance. Biochim. Biophys. Acta 1769: 220–227.
  • Huang, X., Duan, M., Liao, J., Yuan, X., Chen, H., Feng, J., Huang, J. and Zhang, H. S. 2014. OsSLI1, a homeodomain containing transcription activator, involves abscisic acid related stress response in rice Oryza sativa L. Sci. World J. 2014: 809353.
  • Huang, Y. C., Huang, W. L., Hong, C. Y., Lur, H. S. and Chang, M. C. 2012b. Comprehensive analysis of differentially expressed rice actin depolymerizing factor gene family and heterologous overexpression of OsADF3 confers Arabidopsis thaliana drought tolerance. Rice 5: 33.
  • Hurst, H. C. 1994. Transcription factors 1: bZIP proteins. Protein Profile 1: 123–168.
  • Hutchison, C. E. and Kieber, J. J. 2002. Cytokinin signaling in Arabidopsis. Plant Cell 14: S47–S59.
  • Hwang, I. and Sheen, J. 2001. Two-component circuitry in Arabidopsis cytokinin signal transduction. Nature 413: 383–389.
  • Hwang, S. G., Kim, D. S., and Jang, C. S. 2011. Comparative analysis of evolutionary dynamics of genes encoding leucine-rich repeat receptor-like kinase between rice and Arabidopsis. Genetica 139: 1023–1032.
  • Hwang, Y. S., Bethke, P. C., Cheong, Y. H., Chang, H. S., Zhu, T., and Jones, R. L. 2005. A gibberellin-regulated calcineurin B in rice localizes to the tonoplast and is implicated in vacuole function. Plant Physiol. 138: 1347–1358.
  • Innan, H., and Kondrashov, F. 2010. The evolution of gene duplications: classifying and distinguishing between models. Nat. Rev. Genet. 11: 97–108.
  • Ishiguro, S., Ogasawara, K., Fujino, K., Sato, Y., and Kishima, Y. 2014. Low temperature-responsive changes in the anther transcriptome's repeat sequences are indicative of stress sensitivity and pollen sterility in rice strains. Plant Physiol. 164: 671–682.
  • Ito, Y., Katsura, K., Maruyama, K., Taji, T., Kobayashi, M., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. 2006. Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant Cell Physiol. 47: 141–153.
  • Itoh, T., Tanaka, T., Barrero, RA., Yamasaki, C., Fujii, Y., Hilton, P. B., Antonio, B. A., Aono, H., Apweiler, R., Bruskiewich, R., et al. 2007. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res. 17: 175–183.
  • Iyer, L. M., Koonin, E. V., and Aravind, L. 2003. Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases. BMC Struct. Biol. 3: 1.
  • Izawa, T., Foster, R., and Chua, N. H. 1993. Plant bZIP protein DNA binding specificity. J. Mol. Biol. 230: 1131–1144.
  • Jabnoune, M., Espeout, S., Mieulet, D., Fizames, C., Verdeil, J. L., Conejero, G., Rodriguez-Navarro, A., Sentenac, H., Guiderdoni, E., Abdelly, C., et al. 2009. Diversity in expression patterns and functional properties in the rice HKT transporter family. Plant Physiol. 150: 1955–1971.
  • Jacquemin, J., Ammiraju, J. S. S., Haberer, G., Billheimer, D. D., Yu, Y., Liu, L. C., Rivera, L. F., Mayer, K., Chend, M., and Wing, R. A. 2014. Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion. Mol. Plant 4: 642–656.
  • Jain, M., Tyagi, A. K. and Khurana, J. P. 2008. Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice. FEBS J. 275: 2845–2861.
  • Jami, S. K., Roux, S. J. and Kirti, P. B. 2012. Identification and characterization of annexin gene family in rice. Plant Cell Rep. 31: 813–825.
  • Jan, A., Maruyama, K., Todaka, D., Kidokoro, S., Abo, M., Yoshimura, E., Shinozaki, K., Nakashima, K. and Yamaguchi-Shinozaki, K. 2013. OsTZF1, a CCCH-tandem zinc finger protein, confers delayed senescence and stress tolerance in rice by regulating stress-related genes. Plant Physiol. 161: 1202–1216.
  • Jenkins, T. H., Li, J., Scutt, C. P., and Gilmartin, P. M. 2005. Analysis of members of the Silene latifolia Cys2/His2 zinc-finger transcription factor family during dioecious flower development and in a novel stamen-defective mutant ssf1. Planta 220: 559–571.
  • Jeon, J., Kim, NY., Kim, S., Kang, N. Y., Novak, O., Ku, S. J., Cho, C., Lee, D. J., Lee, E. J., Strnad, M., et al. 2010. A subset of cytokinin two-component signaling system plays a role in cold temperature stress response in Arabidopsis. J. Biol. Chem. 285: 23371–23386.
  • Jeong, J. S., Kim, Y. S., Baek, K. H., Jung, H., Ha, S. H., Choi, Y. D., Kim, M., Reuzeau, C., and Kim, J. K. 2010. Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought condition. Plant Physiol. 153: 185–197.
  • Ji, H., Pardo, J. M., Batelli, G., Van Oosten, M. J., Bressan, R. A., and Li, X. 2013. The Salt Overly Sensitive SOS pathway: established and emerging roles. Mol. Plant 6: 275–286.
  • Jin, J. P., Zhang, H., Kong, L., Gao, G., and Luo, J. C. 2014. PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucl. Acids Res. 42: D1182–D1187.
  • Jin, X., Xue, Y., Wang, R., Xu, R., Bian, L., Zhu, B., Han, H., Peng, R., and Yao, Q. 2013b. Transcription factor OsAP21 gene increases salt/drought tolerance in transgenic Arabidopsis thaliana. Mol. Biol. Rep. 40: 1743–1752.
  • Jin, X. F., Xiong, A. S., Peng, R. H., Liu, J. G., Gao, F., Chen, J. M., and Yao, Q. H. 2010. OsAREB1, an ABRE-binding protein responding to ABA and glucose, has multiple functions in Arabidopsis. BMB Rep. 43: 34–39.
  • Jin, Y., Yang, H., Wei, Z., Ma, H., and Ge, X. 2013a. Rice male development under drought stress: phenotypic changes and stage-dependent transcriptomic reprogramming. Mol. Plant 6: 1630–1645.
  • Jisha, V., Dampanaboina, L., Vadassery, J., Mithöfer, A., Kappara, S., and Ramanan, R. 2015. Overexpression of an AP2/ERF type transcription factor OsEREBP1 confers biotic and abiotic stress tolerance in rice. PLoS One 10: e0127831.
  • Jung, C., Seo, J. S., Han, S. W., Koo, Y. J., Kim, C. H., Song, S. I., Nahm, B. H., Choi, Y. D., and Cheong, J. J. 2008. Overexpression of AtMYB44 enhances stomatal closure to confer abiotic stress tolerance in transgenic Arabidopsis. Plant Physiol. 146: 623–635.
  • Jurani´c, M., and Dresselhaus, T. 2014. Phylogenetic analysis of the expansion of the MATH-BTB gene family in the grasses. Plant Signal. Behav. 9: e28242.
  • Kagaya, Y., Ohmiya, K., and Hattori, T. 1999. RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucl. Acids Res. 27: 470–478.
  • Kajava, A. V. 1998. Structural diversity of leucine-rich repeat proteins. J. Mol. Biol. 277: 519–527.
  • Kakimoto, T. 2003. Perception and signal transduction of cytokinins. Annu. Rev. Plant Biol. 54: 605–627.
  • Kamthan, A., Chaudhuri, A., Kamthan, M., and Datta, A. 2015. Small RNAs in plants: recent development and application for crop improvement. Front. Plant Sci. 6: 208.
  • Kang, B., Zhang, Z., Wang, L., Zheng, L., Mao, W., Li, M., Wu, Y., Wu, P., and Mo, X. 2013b. OsCYP2, a chaperone involved in degradation of auxin-responsive proteins, plays crucial roles in rice lateral root initiation. Plant J. 74: 86–97.
  • Kang, M., Addelmageed, H., Lee, S., Reichert, A., Mysore, K. S., and Allen, R. D. 2013a. AtMBP-1, an alternative translation product of LOS2, affects abscisic acid responses and is modulated by the E3 ubiquitin ligase AtSAP5. Plant J. 76: 481–493.
  • Kang, M., Fokar, M., Abdelmageed, H., and Allen, R. D. 2011. Arabidopsis SAP5 functions as a positive regulator of stress responses and exhibits E3 ubiquitin ligase activity. Plant Mol. Biol. 75: 451–466.
  • Kanneganti, V. and Gupta A.K. 2008. Overexpression of OsiSAP8, a member of stress associated protein (SAP) gene family of rice confers tolerance to salt, drought and cold stress in transgenic tobacco and rice. Plant Mol. Biol. 66: 445–462.
  • Kansal, S., Mutum, R. D., Balyan, S. C., Arora, M. K., Singh, A. K., Mathur, S., and Raghuvanshi, S. 2015. Unique miRNome during anthesis in drought-tolerant indica rice var. Nagina 22. Planta 241: 1543–1559.
  • Kanwar, P., Sanyal, S. K., Tokas, I., Yadav, A. K., Pandey, A., Kapoor, S., and Pandey, G. K. 2014. Comprehensive structural, interaction and expression analysis of CBL and CIPK complement during abiotic stresses and development in rice. Cell Calcium 56: 81–95.
  • Kapoor, M., Arora, R., Lama, T., Nijhawan, A., Khurana, J. P., Tyagi, A. K., and Kapoor, S. 2008. Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analysis during reproductive development and stress in rice. BMC Genomics 9: 451.
  • Kasuga, M., Liu, Q., Miura, S., Yamaguchi-Shinozaki, K., and Shinozaki, K. 1999. Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nat. Biotechnol. 17: 287–291.
  • Katiyar, A., Smita, S., Lenka, S. K., Rajwanshi, R., Chinnusamy, V., and Bansal, K. C. 2012. Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC Genomics 13: 544.
  • Katiyar-Agarwal, S., Agarwal, M., and Grover, A. 2003. Heat-tolerant basmati rice engineered by over-expression of hsp101. Plant Mol.Biol. 51: 677–686.
  • Kaupp, U. B., and Seifert, R. 2002. Cyclic nucleotide-gated ion channels. Physiol. Rev. 82: 769–824.
  • Kaur, C., Ghosh, A., Pareek, A., Sopory, S. K., and Singla-Pareek, S. L. 2014a. Glyoxalases and stress tolerance in plants. Biochem. Soc. Trans. 42: 485–490.
  • Kaur, C., Kushwaha, H. R., Mustafiz, A., Pareek, A., Sopory, S. K., and Singla-Pareek, S. L. 2015a. Analysis of global gene expression profile of rice in response to methylglyoxal indicates its possible role as a stress signal molecule. Front. Plant Sci. 6: 682.
  • Kaur, C., Singla-Pareek, S. L., and Sopory, S. K. 2014b. Glyoxalase and methylglyoxal as biomarkers for plant stress tolerance. Crit. Rev. Plant Sci. 33: 429–456.
  • Kaur, H., Petla, B. P., Kamble, N. U., Singh, A., Rao, V., Salvi, P., Ghosh, S., and Majee, M. 2015b. Differentially expressed seed aging responsive heat shock protein OsHSP18.2 implicates in seed vigor., longevity and improves germination and seedling establishment under abiotic stress. Front. Plant Sci. 6: 713.
  • Kenrick, P., and Crane, P. R. 1997. The origin and early evolution of plants on land. Nature 389: 33–39.
  • Khong, G. N., Richaud, F., Coudert, Y., Pati, P. K., Santi, C., Perin, C., Breitler, J. C., and Meynard, D. 2008. Modulating rice stress tolerance by transcription factors. Biotechnol. Genet. Eng. Rev. 25: 381–404.
  • Kim, H. R., Chae, K. S., Han, K. H., and Han, D. M. 2009. The nsdC gene encoding a putative C2H2-type transcription factor is a key activator of sexual development in Aspergillus nidulans. Genetics 182: 771–783.
  • Kim, J. Y., Kim, W. Y., Kwak, K. J., Oh, S. H., Han, Y. S., and Kang, H. 2010. Zinc finger-containing glycine-rich RNA-binding protein in Oryza sativa has an RNA chaperone activity under cold stress conditions. Plant Cell Environ. 33: 759–768.
  • Kim, K. H., Alam, I., Kim, Y. G., Sharmin, S. A., Lee, K. W., Lee, S. H. and Lee, B. H. 2012b. Overexpression of a chloroplast-localized small heat shock protein OsHSP26 confers enhanced tolerance against oxidative and heat stresses in tall fescue. Biotechnol. Lett. 34: 371–377.
  • Kim, K. N., Cheong, Y. H., Gupta, R., and Luan, S. 2000. Interaction specificity of Arabidopsis calcineurin B-like calcium sensors and their target kinases. Plant Physiol. 124: 1844–1853.
  • Kim, S. K., You, Y. N., Park, J. C., Joung, Y., Kim, B. G., Ahn, J. C., and Cho, H. S. 2012a. The rice thylakoid lumenalcyclophilin OsCYP20-2 confers enhanced environmental stress tolerance in tobacco and Arabidopsis. Plant Cell Rep. 31: 417–426.
  • Kim, S. R., and An, G. 2013. Rice chloroplast-localized heat shock protein 70, OsHsp70CP1, is essential for chloroplast development under high-temperature conditions. J. Plant Physiol. 170: 854–863.
  • Klug, A., Schwabe, J. W. 1995. Protein motifs 5. Zinc fingers. FASEB J. 9: 597–604.
  • Knizewski, L., Ginalski, K., and Jerzmanowski, A. 2008. Snf2 proteins in plants: gene silencing and beyond. Trends Plant Sci. 13: 557–565.
  • Koch, A., and Kogel, K. H. 2014. New wind in the sails: improving the agronomic value of crop plants through RNAi-mediated gene silencing. Plant Biotechnol. J. 12: 821–831.
  • Kolukisaoglu, U., Weinl, S., Blazevic, D., Batistic, O., and Kudla, J. 2004. Calcium sensors and their interacting protein kinases: genomics of the Arabidopsis and rice CBL-CIPK signaling networks. Plant Physiol. 134: 43–58.
  • Komatsu, S., Yang, G., Khan, M., Onodera, H., Toki, S., and Yamaguchi, M. 2007. Over-expression of calcium-dependent protein kinase 13 and calreticulin interacting protein 1 confers cold tolerance on rice plants. Mol. Genet. Genomics 277: 713–723.
  • Kosugi, S., and Ohashi, Y. 1997. PCF1 and PCF2 specifically bind to cis elements in the rice proliferating cell nuclear antigen gene. Plant Cell 9: 1607–1619.
  • Kosugi, S., and Ohashi, Y. 2002. DNA binding and dimerization specificity and potential targets for the TCP protein family. Plant J. 30: 337–348.
  • Kudla, J., Xu, Q., Harter, K., Gruissem, W., and Luan, S. 1999. Genes for calcineurin B-like proteins in Arabidopsis are differentially regulated by stress signals. Proc. Natl. Acad. Sci. U S A 96: 4718–4723.
  • Kumar, S., Singla-Pareek, S. L., Reddy, M. K., and Sopory, S. K. 2003. Glutathione: biosynthesis, homeostasis and its role in abiotic stresses. J. Plant Biol. 30: 179–187.
  • Kumari, S., Joshi, R., Singh, K., Roy, S., Tripathi, A. K., Singh, P., Singla-Pareek, S. L., and Pareek, A. 2014. Expression of a cyclophilin OsCyp2-P isolated from a salt-tolerant landrace of rice in tobacco alleviates stress via ion homeostasis and limiting ROS accumulation. Funct. Integr. Genomics 15: 395–412.
  • Kumari, S., Sabharwal, V. P., Kushwaha, H. R., Sopory, S. K., Singla-Pareek, S. L., and Pareek, A. 2009. Transcriptome map for seedling stage specific salinity stress response indicates a specific set of genes as candidate for saline tolerance in Oryza sativa L. Funct. Integr. Genomics 9: 109–123.
  • Kushwaha, H. R., Joshi, R., Pareek, A., and Singla-Pareek, S. L. 2016. MATH-Domain family shows response toward abiotic stress in Arabidopsis and rice. Front. Plant Sci. 7: 923.
  • Lademann, U., Kallunki, T., and Jaattela, M. 2001. A20 zinc finger protein inhibits TNF-induced apoptosis and stress response early in the signaling cascades and independently of binding to TRAF2 or 14-3-3 proteins. Cell Death Differ. 8: 265–272.
  • Lakra, N., Nutan, K. K., Das, P., Anwar, K., Singla-Pareek, S. L., and Pareek, A. 2015. A nuclear-localized histone-gene binding protein from rice OsHBP1b functions in salinity and drought stress tolerance by maintaining chlorophyll content and improving the antioxidant machinery. J. Plant Physiol. 176: 36–46.
  • Lan, L., Li, M., Lai, Y., Xu, W., Kong, Z., Ying, K., Han, B. and Xue, Y. 2005. Microarray analysis reveals similarities and variations in genetic programs controlling pollination/fertilization and stress responses in rice Oryza sativa L. Plant Mol. Biol. 59: 151–164.
  • Laohavisit, A. and Davies, J. M. 2011. Annexins. New Phytol. 189: 40–53.
  • Lee, G. J. and Vierling, E. 2000. A small heat shock protein cooperates with heat shock protein 70 systems to reactivate a heat-denatured protein. Plant Physiol. 122: 189–198.
  • Lee, S. S., Park, H. J., Jung, W. Y., Lee, A., Yoon, D. H., You, Y. N., Kim, H. S., Kim, B. G., Ahn, J. C., and Cho, H. S. 2015. OsCYP21–4, a novel Golgi-resident cyclophilin, increases oxidative stress tolerance in rice. Front. Plant Sci. 6: 797.
  • Lenka, S. K., Katiyar, A., Chinnusamy, V., and Bansal, K. C. 2011. Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance. Plant Biotechnol. J. 9: 315–327.
  • Li, F., Guo, S., Zhao, Y., Chen, D., Chong, K., and Xu, Y. 2010. Overexpression of a homopeptide repeat-containing bHLH protein gene OrbHLH001 from Dongxiang Wild Rice confers freezing and salt tolerance in transgenic Arabidopsis. Plant Cell Rep. 29: 977–986.
  • Li, L., Yu, X., Thompson, A., Guo, M., Yoshida, S., Asami, T., Chory, J., and Yin, Y. 2009. Arabidopsis MYB30 is a direct target of BES1 and cooperates with BES1 to regulate brassinosteroid-induced gene expression. Plant J. 58: 275–286.
  • Li, X., Duan, X., Jiang, H., Sun, Y., Tang, Y., Yuan, Z., Guo, J., Liang, W., Chen, L., Yin, J., et al. 2006. Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Plant Physiol. 141: 1167–1184.
  • Lim, S. D., Cho, H. Y., Park, Y. C., Ham, D. J., Lee, J. K., and Jang, C. S. 2013a. The rice RING finger E3 ligase, OsHCI1, drives nuclear export of multiple substrate proteins and its heterogeneous overexpression enhances acquired thermotolerance. J. Exp. Bot. 64: 2899–2914.
  • Lim, S. D., Hwang, J. G., Jung, C. G., Hwang, S. G., Moon, J. C., and Jang, C. S. 2013b. Comprehensive analysis of the rice RING E3 ligase family reveals their functional diversity in response to abiotic stress. DNA Res. 20: 299–314.
  • Lim, S. D., Yim, W. C., Moon, J. C., Kim, D. S., Lee, B. M., and Jang, C. S. 2010. A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes. Plant Mol. Biol. 72: 369–380.
  • Lindroth, A. M., Shultis, D., Jasencakova, Z., Fuchs, J., Johnson, L., Schubert, D., Patnaik, D., Pradhan, S., Goodrich, J., and Schubert, I. 2004. Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J. 23: 4286–4296.
  • Liu, A. L., Zou, J., Liu, C. F., Zhou, X. Y., Zhang, X. W., Luo, G. Y., and Chen, X. B. 2013. Over-expression of OsHsfA7 enhanced salt and drought tolerance in transgenic rice. BMB Rep. 46: 31–36.
  • Liu, C., Mao, B., Ou, S., Wang, W., Liu, L., Wu, Y., Chu, C., and Wang, X. 2014a. OsbZIP71, a bZIP transcription factor, confers salinity and drought tolerance in rice. Plant Mol. Biol. 2: 19–36.
  • Liu, C., Wu, Y., and Wang, X. 2012a. bZIP transcription factor OsbZIP52/RISBZ5: a potential negative regulator of cold and drought stress response in rice. Planta 235: 1157–1169.
  • Liu, C., Lu, F., Cui, X., and Cao, X. 2010. Histone methylation in higher plants. Annu. Rev. Plant Biol. 61: 395–420.
  • Liu, D., Chen, X., Liu, J., Ye, J. and Gao, Z. 2012a. The rice ERF transcription factor OsERF922 negatively regulates resistance to Magnoporthe oryzae and salt tolerance. Plant J. 63: 3899–3912.
  • Liu, G., Li, X., Jin, S., Liu, X., Zhu, L., Nie, Y., and Zhang, X. 2014b. Overexpression of rice NAC gene SNAC1 improves drought and salt tolerance by enhancing root development and reducing transpiration rate in transgenic cotton. PLoS One 9: e86895.
  • Liu, H., Ma, Y., Chen, N., Guo, S., Liu, H., Guo, X., Chong, K., and Xu, Y. 2014c. Overexpression of stress-inducible OsBURP16, the beta subunit of polygalacturonase 1, decreases pectin content and cell adhesion and increases abiotic stress sensitivity in rice. Plant Cell Environ. 37: 1144–1158.
  • Liu, H., Zhang, H., Yang, Y., Li, G., Yang, Y., Wang, X., Basnayake, B. M., Li, D., and Song, F. 2008. Functional analysis reveals pleiotropic effects of rice RING-H2 finger protein gene OsBIRF1 on regulation of growth and defense responses against abiotic and biotic stresses. Plant Mol. Biol. 68: 17–30.
  • Liu, J. G., Qin, Q. L., Zhang, Z., Peng, R. H., Xiong, A. S., Chen, J. M., Yao, Q. H. 2009. OsHSF7 gene in rice, Oryza sativa L, encodes a transcription factor that functions as a high temperature receptive and responsive factor. BMB Rep. 42: 16–21.
  • Liu, J. G., Yao, Q. H., Zhang, Z., Peng, R. H., Xiong, A. S., Xu, F., Zhu, H. 2005. Isolation and characterization of a cDNA encoding two novel heat-shock factor OsHSF6 and OsHSF12 in Oryza sativa L. J. Biochem. Mol. Biol. 38: 602–608.
  • Liu, Q., Kasuga, M., Sakuma, Y., Abe, H., Miura, S., Yamaguchi-Shinozaki, K. and Shinozaki, K. 1998. Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 10: 1391–1406.
  • Liu, X., Luo, M., Zhang, W., Zhao, J., Zhang, J., Wu, K., Tian, L., and Duan, J. 2012c. Histone acetyltransferases in rice Oryza sativa L.: phylogenetic analysis, subcellular localization and expression. BMC Plant Biol. 12: 145.
  • Lockton, S., and Gaut, B. S. 2005. Plant conserved non-coding sequences and paralogue evolution. Trends Genet. 21: 60–65.
  • Lorkovic, Z. J. 2009. Role of plant RNA-binding proteins in development, stress response and genome organization. Trends Plant Sci. 14: 229–236.
  • Lorkovic, Z. J., and Barta, A. 2002. Genome analysis: RNA recognition motif RRM and K homology KH domain RNA-binding proteins from the flowering plant Arabidopsis thaliana. Nucl. Acids Res. 30: 623–635.
  • Lovering, R., Hanson, I. M., Borden, K. L., Martin, S., O'Reilly, N. J., Evan, G. I., Rahman, D., Pappin, D. J., Trowsdale, J., and Freemont, P. S. 1993. Identification and preliminary characterization of a protein motif related to the zinc finger. Proc. Natl. Acad. Sci. U S A 90: 2112–2116.
  • Lu, G., Gao, C., Zheng, X., and Han, B. 2009. Identification of OsbZIP72 as a positive regulator of ABA response and drought tolerance in rice. Planta 229: 605–615.
  • Lu, Z., Huang, X., Ouyang, Y., and Yao, J. 2013. Genome-wide identification, phylogenetic and co-expression analysis of OsSET gene family in rice. PLoS One 8: e65426.
  • Luan, S., Kudla, J., Rodriguez-Concepcion, M., Yalovsky, S., and Gruissem, W. 2002. Calmodulins and calcineurin B-like proteins: calcium sensors for specific signal response coupling in plants. Plant Cell 14: S389–S400.
  • Ludvigsen, S., and Poulsen, F. M. 1992. Secondary structure in solution of barwin from barley seed using 1H nuclear magnetic resonance spectroscopy. Biochemistry 31: 8771–8782.
  • Luo, D., Carpenter, R., Vincent, C., Copsey, L., and Coen, E. 1996. Origin of floral asymmetry in Antirrhinum. Nature 383: 794–799.
  • Luo, M., Platten, D., Chaudhury, A., Peacock, W. J., and Dennis, E. S. 2009. Expression, imprinting, and evolution of rice homologs of the polycomb group genes. Mol Plant. 2: 711–723.
  • Lv, D. K., Bai, X., Li, Y., Ding, X. D., Ge, Y., Cai, H., Ji, W., Wu, N., and Zhu, Y. M. 2010. Profiling of cold-stress-responsive miRNAs in rice by microarrays. Gene. 459: 39–47.
  • Lynch, M., and Conery, J. S. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151–1155.
  • Ma, Q., Dai, X., Xu, Y., Guo, J., Liu, Y., Chen, N., Xiao, J., Zhang, D.,Xu, Z., Zhang, X., et al. 2009. Enhanced tolerance to chilling stress in OsMYB3R-2 transgenic rice is mediated by alteration in cell cycle and ectopic expression of stress genes. Plant Physiol. 150: 244–256.
  • Ma, X., Lv, S., Zhang, C., Yang, C. 2013. Histone deacetylases and their functions in plants. Plant Cell Rep. 32: 465–478.
  • Maathuis, F. J. 2006. The role of monovalent cation transporters in plant responses to salinity. J. Exp. Bot. 57: 1137–1147.
  • Mackay, J. P., and Crossley, M. 1998. Zinc fingers are sticking together. Trends Biochem. Sci. 23: 1–4.
  • Mahajan, S., and Tuteja, N. 2005. Cold, salinity and drought stresses: an overview. Arch. Biochem. Biophys. 444: 139–158.
  • Maris, C., Dominguez, C., and Allain, F. H. 2005. The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J. 272: 2118–2131.
  • Martin, C., and Paz-Ares, J. 1997. MYB transcription factors in plants. Trends Genet. 13: 67–73.
  • Martıín-Trillo, M., and Cubas, P. 2010. TCP genes: a family snapshot ten years later. Trends Plant Sci. 15: 31–39.
  • Maruyama, K., Urano, K., Yoshiwara, K., Morishita, Y., Sakurai, N., Suzuki, H., Kojima, M., Sakakibara, H., Shibata, D., Saito, K., et al. 2014. Integrated analysis of the effects of cold and dehydration on rice metabolites, phytohormones, and gene transcripts. Plant Physiol. 164: 1759–1771.
  • Mäser, P., Eckelman, B., Vaidyanathan, R., Horie, T., Fairbairn, DJ., Kubo, M., Yamagami, M., Yamaguchi, K., Nishimura, M., Uozumi, N., et al. 2002. Altered shoot/root Na+ distribution and bifurcating salt sensitivity in Arabidopsis by genetic disruption of the Na+ transporter AtHKT1. FEBS Lett. 531: 157–161.
  • Mäser, P., Thomine, S., Schroeder, J. I., Ward, J. M., Hirschi, K., Sze, H., Talke, I. N., Amtmann, A., Maathuis, F. J., Sanders, D., et al. 2001. Phylogenetic relationships within cation transporter families of Arabidopsis. Plant Physiol. 126: 1646–1667.
  • Matzke, M. A., and Birchler, J. A. 2005. RNAi-mediated pathways in the nucleus. Nat. Rev. Genet. 6: 24–35.
  • McCormack, E., and Braam, J. 2003. Calmodulins and related potential calcium sensors of Arabidopsis. New Phytol. 159: 585–598.
  • Mehrotra, P. V., Ahel, D., Ryan, D. P., Weston, R., Wiechens, N., Kraehenbuehl, R., Owen-Hughes, T., Ahel, I. 2011. DNA repair factor APLF is a histone chaperone. Mol. Cell 41: 46–55.
  • Milla, M. A., Townsend, J., Chang, I. F., Cushman, J. C. 2006. The Arabidopsis AtDi19 gene family encodes a novel type of Cys2/His2 zinc-finger protein implicated in ABA-independent dehydration, high-salinity stress and light signaling pathways. Plant Mol. Biol. 61: 13–30.
  • Mittal, D., Chakrabarti, S., Sarkar, A., Singh, A., Grover, A. 2009. Heat shock factor gene family in rice: genomic organization and transcript expression profiling in response to high temperature, low temperature and oxidative stresses. Plant Physiol. Biochem. 47: 785–795.
  • Mittal, D., Madhyastha, D., Grover, A. 2012. Gene expression analysis in response to low and high temperature and oxidative stresses in rice: combination of stresses evokes different transcriptional changes as against stresses applied individually. Plant Sci. 197: 102–113.
  • Mizoi, J., Shinozaki, K., Yamaguchi-Shinozaki, K. 2012. AP2/ERF family transcription factors in plant abiotic stress responses. Biochim. Biophys. Acta 1819: 86–96.
  • Moeder, W., Uequhart, W., Ung, H., Yoshioka, K. 2011. The role of cyclic nucleotide-gated ion channels in plant immunity. Mol. Plant 4: 442–452.
  • Mohanty, B., Kitazumi, A., Cheung, C. Y., Lakshmanan, M., de los Reyes, B. G., Jang, I. C., and Lee, D. Y. 2016. Identification of candidate network hubs involved in metabolic adjustments of rice under drought stress by integrating transcriptome data and genome-scale metabolic network. Plant Sci. 242: 224–239.
  • Morello, L., Frattini, M., Gianì, S., Christou, P., and Breviario, D. 2000. Overexpression of the calcium-dependent protein kinase OsCDPK2 in transgenic rice is repressed by light in leaves and disrupts seed development. Transgenic Res. 9: 453–462.
  • Morillo, S. A., and Tax, F. E. 2006. Functional analysis of receptor-like kinases in monocots and dicots. Curr. Opin. Plant Biol. 9: 460–469.
  • Mortimer, J. C., Laohavisit, A., Macpherson, N., Webb, A., Brownlee, C., Battey, N. H., and Davies, J. M. 2008. Annexins: multifunctional components of growth and adaptation. J. Exp. Bot. 59: 533–544.
  • Moss, S. E., and Morgan, R. O. 2004. The annexins. Genome Biol. 5: 219.
  • Moumeni, A., Satoh, K., Venuprasad, R., Serraj, R., Kumar, A., Leung, H., and Kikuchi, S. 2015. Transcriptional profiling of the leaves of near-isogenic rice lines with contrasting drought tolerance at the reproductive stage in response to water deficit. BMC Genomics 16: 1110.
  • Mourrain, P., Beclin, C., Elmayan, T., Feuerbach, F., Godon, C., Morel, J. B., Jouette, D., Lacombe, A. M., Nikic, S., Picault, N., et al. 2000. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101: 533–542.
  • Mukherjee, K., and Burglin, T. R. 2006. MEKHLA, a novel domain with similarity to PAS domains, is fused to plant homeodomain-leucine zipper III proteins. Plant Physiol. 140: 1142–1150.
  • Mukhopadhyay, A., Vij, S., and Tyagi, A. K. 2004. Overexpression of a zinc-finger protein gene from rice confers tolerance to cold, dehydration, and salt stress in transgenic tobacco. Proc. Natl. Acad. Sci. U S A 101: 6309–6314.
  • Mukhopadhyay, P., and Tyagi, A. K. 2015. OsTCP19 influences developmental and abiotic stress signaling by modulating ABI4-mediated pathways. Sci. Rep. 5: 12381.
  • Murakami, T., Matsuba, S., Funatsuki, H., Kawaguchi, K., Saruyama, H., Tanida, M., and Sato, Y. 2004. Over-expression of a small heat shock protein, sHSP17.7, confers both heat tolerance and UV B resistance to rice plants. Mol. Breed. 13: 165–175.
  • Mustafiz, A., Singh, A. K., Pareek, A., Sopory, S. K., and Singla-Pareek, S. L. 2011. Genome-wide analysis of rice and Arabidopsis identifies two glyoxalase genes that are highly expressed in abiotic stresses. Funct. Integr. Genomics 11: 293–305.
  • Mutum, R. D., Balyan, S. C., Kansal, S., Agarwal, P., Kumar, S., Kumar, M., and Raghuvanshi, S. 2013. Evolution of variety-specific regulatory schema for expression of osa-miR408 in indica rice varieties under drought stress. FEBS J. 280: 1717–1730.
  • Nakagawa, H., Ohmiya, K., and Hattori, T. 1996. A rice bZIP protein, designated OSBZ8, is rapidly induced by abscisic acid. Plant J. 9: 217–227.
  • Nakano, T., Suzuki, K., Fujimura, T., and Shinshi, H. 2006. Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol. 140: 411–432.
  • Nakashima, K., Ito, Y., and Yamaguchi-Shinozaki, K. 2009. Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant Physiol. 149: 88–95.
  • Nakashima, K., Tran, L.S., Van Nguyen, D., Fujita, M., Maruyama, K., Todaka, D., Ito, Y., Hayashi, N., Shinozaki, K., and Yamaguchi-Shinozaki, K. 2007. Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J. 51: 617–630.
  • Nardmann, J., and Werr, W. 2006. The shoot stem cell niche in angiosperms: expression patterns of WUS orthologues in rice and maize imply major modifications in the course of mono- and dicot evolution. Mol. Biol. Evol. 23: 2492–2504.
  • Navarro-Gochicoa, M. T., Camut, S., Timmers, A. C., Niebel, A., Herve, C., Boutet, E., Bono, JJ., Imberty, A., and Cullimore, J. V. 2003. Characterization of four lectin-like receptor kinases expressed in roots of Medicago truncatula. Structure, location, regulation of expression, and potential role in the symbiosis with Sinorhizo biummeliloti. Plant Physiol. 133: 1893–1910.
  • Nawaz, Z., Kakar, K. U., Saand, M. A., and Shu, Q. Y. 2014. Cyclic nucleotide-gated ion channel gene family in rice, identification, characterization and experimental analysis of expression response to plant hormones, biotic and abiotic stresses. BMC Genomics 15: 853.
  • Nijhawan, A., Jain, M., Tyagi, A. K., and Khurana, J. P. 2008. Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice. Plant Physiol. 146: 333–350.
  • Ning, Y., Jantasuriyarat, C., Zhao, Q., Zhang, H., Chen, S., Liu, J., Liu, L., Tang, S., Park, C. H., Wang, X., et al. 2011. The SINA E3 ligase OsDIS1 negatively regulates drought response in rice. Plant Physiol. 157: 242–255.
  • Nishiyama, R., Watanabe, Y., Leyva-Gonzalez, M. A., Ha, CV., Fujita, Y., Tanaka, M., Seki, M., Yamaguchi-Shinozaki, K., Shinozaki, K., Herrera-Estrella, L., et al. 2013. Arabidopsis AHP2,AHP3, and AHP5 histidine phosphotransfer proteins function as redundant negative regulators of drought stress response. Proc. Natl. Acad. Sci. U S A 110: 4840–4845.
  • Nover, L., Bharti, K., Doring, P., Mishra, SK., Ganguli, A., Scharf, K. D. 2001. Arabidopsis and the heat stress transcription factor world: how many heat stress transcription factors do we need? Cell Stress Chaperones 6: 177–189.
  • Nuruzzaman, M., Manimekalai, R., Sharoni, A. M., Satoh, K., Kondoh, H., Ooka, H., and Kikuchi, S. 2010. Genome-wide analysis of NAC transcription factor family in rice. Gene 465: 30–44.
  • Olsen, A. N., Ernst, H. A., Leggio, L. L., Skriver, K. 2005. NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci. 10: 79–87.
  • Oono, Y., Yazawa,T., Kawahara, Y., Kanamori, H., Kobayashi, F., Sasaki, H., Mori, S., Wu, J., Handa, H., Itoh, T., et al. 2014. Genome-wide transcriptome analysis reveals that cadmium stress signaling controls the expression of genes in drought stress signal pathways in rice. PLoS One 9: e96946.
  • Otting, G., Qian, YQ., Billeter, M., Muller, M., Affolter, M., Gehring, WJ., and Wuthrich, K. 1990. Protein-DNA contacts in the structure of a homeodomain-DNA complex determined by nuclear magnetic resonance spectroscopy in solution. EMBO J. 9: 3085–3092.
  • Ouyang, S. Q., Liu, Y. F., Liu, P., Lei, G., He, S. J., Ma, B., Zhang, W. K., Zhang, J. S., Chen, S. Y. 2010. Receptor-like kinase OsSIK1 improves drought and salt stress tolerance in rice Oryza sativa plants. Plant J. 62: 316–329.
  • Owttrim, G. W. 2006. RNA helicases and abiotic stress. Nucl. Acids Res. 34: 3220–3230.
  • Palatnik, J. F., Allen, E., Wu, X., Schommer, C., Schwab, R., Carrington, J. C., and Weigel, D. 2003. Control of leaf morphogenesis by microRNAs. Nature 425: 257–263.
  • Pandey, S. P., and Somssich, I. E. 2009. The role of WRKY transcription factors in plant immunity. Plant Physiol. 150: 1648–1655.
  • Pareek, A., Singh, A., Kumar, M., Kushwaha, H. R., Lynn, A. M., and Singla-Pareek, S. L. 2006. Whole-genome analysis of Oryza sativa reveals similar architecture of two-component signaling machinery with Arabidopsis. Plant Physiol. 142: 380–397.
  • Park, G. G., Park, J. J., Yoon, J., Yu, S. N., and An, G. 2010. A RING finger E3 ligase gene, Oryza sativa Delayed Seed Germination 1 (OsDSG1), controls seed germination and stress responses in rice. Plant Mol. Biol. 74: 467–478.
  • Park, H. Y., Kang, I. S., Han, J. S., Lee, C. H., An, G., and Moon, Y. H. 2009. OsDEG10 encoding a small RNA-binding protein is involved in abiotic stress signaling. Biochem. Biophys. Res. Commun. 380: 597–602.
  • Park, S., Moon, J. C., Park, Y. C., Kim, J. H., Kim, D. S., and Jang, C. S. 2014. Molecular dissection of the response of a rice leucine-rich repeat receptor-like kinase (LRR-RLK) gene to abiotic stresses. J. Plant Physiol. 171: 1645–1653.
  • Pasquali, G., Biricolti, S., Locatelli, F., Baldoni, E., and Mattana, M. 2008. Osmyb4 expression improves adaptive responses to drought and cold stress in transgenic apples. Plant Cell Rep. 27: 1677–1686.
  • Paterson, A. H., Bowers, J. E., and Chapman, B. A. 2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc. Natl. Acad. Sci. U S A 101: 9903–9908.
  • Pelham, H. R. 1982. A regulatory upstream promoter element in the Drosophila hsp 70 heat-shock gene. Cell 30: 517–528.
  • Peña-Castro, J. M., Zanten, M. V., Lee, S. C., Patel, M. R., Voesenek, L. A. J. C., Fukao, T., and Bailey-Serres, J. 2011. Expression of rice SUB1A and SUB1C transcription factors in Arabidopsis uncovers flowering inhibition as a submergence tolerance mechanism. Plant J. 67: 434–446.
  • Peškan-Berghöfer, T., Shahollari, B., Giong, P. H., Hehl, S., Markert, C., Blanke, V., Kost, G., Varma, A., Oelmuller, R. 2004. Association of Piriformospora indica with Arabidopsis thaliana roots represents a novel system to study beneficial plant-microbe interactions and involves early plant protein modifications in the endoplasmic reticulum and at the plasma membrane. Physiol. Plant. 122: 465–477.
  • Piao, H. L., Xuan, Y. H., Park, S. H., Je, B. I., Park, S. J., Kim, C. M., Huang, J., Wang, G. K., Kim, M. J., Kang, S. M., et al. 2010. OsCIPK31, a CBL-interacting protein kinase is involved in germination and seedling growth under abiotic stress conditions in rice plants. Mol. Cells 30: 19–27.
  • Pillitteri, L. J., and Torii, K. U. 2007. Breaking the silence: three bHLH proteins direct cell-fate decisions during stomatal development. Bioessays 29: 861–870.
  • Platten, J. D., Cotsaftis, O., Berthomieu, P., Bohnert, H., Davenport, R. J., Fairbairn, D. J., Horie, T., Leigh, R. A., Lin, H. X., Luan, S., et al. 2006. Nomenclature for HKT transporters, key determinants of plant salinity tolerance. Trends Plant Sci. 11: 372–374.
  • Ponger, L., Li, and W. H. 2005. Evolutionary diversification of DNA methyltransferases in eukaryotic genomes. Mol. Biol. Evol. 22: 1119–1128.
  • Popescu, S. C., Popescu, G. V., Bachan, S., Zhang, Z., Gerstein, M., Snyder, M., and Dinesh-Kumar, S. P. 2009. MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev. 23: 80–92.
  • Price, E. R., Jin, M., Lim, D., Pati, S., Walsh, C. T., and McKeon, F. D. 1994. Cyclophilin B trafficking through the secretory pathway is altered by binding of cyclosporin A. Proc. Natl. Acad. Sci. U S A 91: 3931–3935.
  • Priya, P., and Jain, M. 2013. RiceSRTFDB: a database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis. Database 2013:bat027.
  • Qiao, B., Zhang, Q., Liu, D., Wang, H., Yin, J., Wang, R., He, M., Cui, M., Shang, Z., Wang, D., et al. 2015. Calcium-binding protein, rice annexin OsANN1, enhances heat stress tolerance by modulating the production of H2O2. J. Exp. Bot. 66: 5853–5866.
  • Qin, F., Shinozaki, K., and Yamaguchi-Shinozaki, K. 2011. Achievements and challenges in understanding plant abiotic stress responses and tolerance. Plant Cell Physiol. 52: 1569–1582.
  • Qin, Y., Ye, H., Tang, N., and Xiong, L. 2009. Systematic identification of X1-homologous genes reveals a family involved in stress responses in rice. Plant Mol. Biol. 71: 483–496.
  • Qiu, Y. P., and Yu, D. Q. 2009. Over-expression of the stress-induced OsWRKY45 enhances disease resistance and drought tolerance in Arabidopsis. Environ. Exp. Bot. 65: 35–47.
  • Qu, A. L., Ding, Y. F., Jiang, Q., and Zhu, C. 2013. Molecular mechanisms of the plant heat stress response. Biochem. Biophys. Res. Commun. 432: 203–207.
  • Quirk, S., Maciver, S. K., Ampe, C., Doberstein, S. K., Kaiser, D. A., VanDamme, J., Vandekerckhove, J. S., and Pollard, T. D. 1993. Primary structure of and studies on Acanthamoeba actophorin. Biochemistry 32: 8525–8533.
  • Rabbani, M. A., Maruyama, K., Abe, H., Khan, M. A., Katsura, K., Ito, Y., Yoshiwara, K., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. 2003. Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol. 133: 1755–1767.
  • Rabbani, N., and Thornalley, P. J. 2011. Glyoxalase in diabetes, obesity and related disorders. Semin. Cell Dev. Biol. 22: 309–317.
  • Rabinowicz, P. D., Braun, E. L., Wolfe, A. D., Bowen, B., and Grotewold, E. 1999. Maize R2R3 Myb genes: sequence analysis reveals amplification in the higher plants. Genetics 153: 427–444.
  • Ramamoorthy, R., Jiang, S. Y., Kumar, N., Venkatesh, P. N., and Ramachandran, S. 2008. A comprehensive transcriptional profiling of the WRKY gene family in rice under various abiotic and phytohormone treatments. Plant Cell Physiol. 49: 865–879.
  • Rana, R. M., Dong, S., Tang, H., Ahmad, F., and Zhang, H. 2012. Functional analysis of OsHSBP1 and OsHSBP2 revealed their involvement in the heat shock response in rice (Oryza sativa L.). J. Exp. Bot. 63: 6003–6016.
  • Ransom, M., Dennehey, B. K., and Tyler, J. K. 2010. Chaperoning histones during DNA replication and repair. Cell 140: 183–195.
  • Ray, S., Agarwal, P., Arora, R., Kapoor, S., and Tyagi, A. K. 2007. Expression analysis of calcium-dependent protein kinase gene family during reproductive development and abiotic stress conditions in rice (Oryza sativa L. ssp. indica). Mol. Genet. Genomics 278: 493–505.
  • Ray, S., Dansana, P. K., Giri, J., Deveshwar, P., Arora, R., Agarwal, P., Khurana, J. P., Kapoor, S., and Tyagi, A. K. 2011. Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice.Funct.Integr. Genomics 11: 157–178.
  • Redillas, M. C. R. F., Jeong, J. S., Kim, Y. S., Jung, H., Bang, S. W., Choi, Y. D., Ha, S. W., Reuzeau, C., and Kim, J. K. 2012. The overexpression of OsNAC9 alters the root architecture of rice plants enhancing drought resistance and grain yield under field conditions. Plant Biotechnol. J. 10: 792–805.
  • Ren, Z. H., Gao, J. P., Li, L. G., Cai, X. L., Huang, W., Chao, D. Y., Zhu, M. Z., Wang, Z. Y., Luan, S., and Lin, H. X. 2005. A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat. Genet. 37: 1141–1146.
  • Rhoades, M. W., Reinhart, B. J., Lim, L. P., Burge, C. B., Bartel, B., and Bartel, D. P. 2002. Prediction of plant microRNA targets. Cell 110: 513–520.
  • Riechmann, J. L., Heard, J., Martin, G., Reuber, L., Jiang, C., Keddie, J., Adam, L., Pineda, O., Ratcliffe, O. J., Samaha, R. R., et al. 2000. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290: 2105–2110.
  • Riechmann, J. L., and Meyerowitz, E. M. 1998. The AP2/EREBP family of plant transcription factors. Biol. Chem. 379: 633–646.
  • Rossberg, M., Theres, K., Acarkan, A., Herrero, R., Schmitt, T., Schumacher, K., Schmitz, G., Schmidt, R. 2001. Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and Capsella genomes. Plant Cell 13: 979–988.
  • Ruan, S. L., Ma, H. S., Wang, S. H., Fu, Y. P., Xin, Y., Liu, W. Z., Wang, F., Tong, J. X., Wang, S. Z., and Chen, H. Z. 2011. Proteomic identification of OsCYP2, a rice cyclophilin that confers salt tolerance in rice (Oryza sativa L.) seedlings when overexpressed. BMC Plant Biol. 11: 34.
  • Rushton, P. J., Macdonald, H., Huttly, A. K., Lazarus, C. M., Hooley, R. 1995. Members of a new family of DNA-binding proteins bind to a conserved cis-element in the promoters of alpha-Amy2 genes. Plant Mol. Biol. 29: 691–702.
  • Rushton, P. J., Somssich, I. E., Ringler, P., Xi, Q., and Shen, J. 2010. WRKY transcription factors. Trends Plant Sci. 15: 247–248.
  • Saad, A. S. I., Li, X., Li, H. P., Huang, T., Gao, C. S., Guo, W., Cheng, W., Zhao, G. Y., Liao, Y. C. 2013. A rice stress-responsive NAC gene enhances tolerance of transgenic wheat to drought and salt stresses. Plant Sci. 203: 33–40.
  • Sahi, C., Agarwal, M., Singh, A., and Grover, A. 2007. Molecular characterization of a novel isoform of rice (Oryza sativa L.) glycine rich-RNA binding protein and evidence for its involvement in high temperature stress response. Plant Sci. 173: 144–155.
  • Saijo, Y., Hata, S., Kyozuka, J., Shimamoto, K., and Izui, K. 2000. Over-expression of a single Ca2+-dependent protein kinase confers both cold and salt/drought tolerance on rice plants. Plant J. 23: 319–327.
  • Saijo, Y., Kinoshita, N., Ishiyama, K., Hata, S., Kyozuka, J., Hayakawa, T., Nakamura, T., Shimamoto, K., Yamaya, T., and Izui, K. 2001. A Ca2+-dependent protein kinase that endows rice plants with cold- and salt stress tolerance functions in vascular bundles. Plant Cell Physiol. 42: 1228–1233.
  • Sanchez-Garcia, I., and Rabbitts, T. H. 1994. The LIM domain: a new structural motif found in zinc-finger-like proteins. Trends Genet. 10: 315–320.
  • Sanders, D., Pelloux, J., Brownlee, C., and Harper, J. F. 2002. Calcium at the crossroads of signaling. Plant Cell 14: S401–S417.
  • Sarkar, N. K., Kim, Y. K., and Grover, A. 2009. Rice sHsp genes: genomic organization and expression profiling under stress and development. BMC Genomics 10: 393.
  • Sato, Y., and Yokoya, S. 2008. Enhanced tolerance to drought stress in transgenic rice plants overexpressing a small heat-shock protein, sHSP17.7. Plant Cell Rep. 27: 329–334.
  • Saurin, A. J., Borden, K. L., Boddy, M. N., and Freemont, P. S. 1996. Does this have a familiar RING? Trends Biochem. Sci. 21: 208–214.
  • Sawa, S., Ohgishi, M., Goda, H., Higuchi, K., Shimada, Y., Yoshida, S., and Koshiba, T. 2002. The HAT2 gene, a member of the HD-Zip gene family, isolated as an auxin inducible gene by DNA microarray screening, affect auxin response in Arabidopsis. Plant J. 36: 1011–1022.
  • Saxena, M., Roy, S. B., Singla-Pareek, S. L., Sopory, S. K., and Bhalla-Sarin, N. 2011. Overexpression of the glyoxalase II gene leads to enhanced salinity tolerance in Brassica juncea. Open Plant Sci. J. 5: 23–28.
  • Scharf, K. D., Siddique, M., and Vierling, E. 2001. The expanding family of Arabidopsis thaliana small heat stress proteins and a new family of proteins containing alpha-crystallin domains Acd proteins. Cell Stress Chaperones 6: 225–237.
  • Schmid, F. X. 1993. Prolyl isomerase: enzymatic catalysis of slow protein-folding reactions. Annu. Rev. Biophys. Biomol. Struct. 22: 123–142.
  • Schmidt, R., Schippers, J. H., Welker, A., Mieulet, D., Guiderdoni, E., and Mueller-Roeber, B. 2012. Transcription factor OsHsfC1b regulates salt tolerance and development in Oryza sativa ssp. Japonica. AoB Plants: pls011.
  • Schreiber, S. L. 1991. Chemistry and biology of the immunophilins and their immunosuppressive ligands. Science 251: 283–287.
  • Schrick, K., Nguyen, D., Karlowski, W. M., and Mayer, K. F. 2004. START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors. Genome Biol. 5: R41.
  • Schuettengruber, B., and Cavalli, G. 2009. Recruitment of polycomb group complexes and their role in the dynamic regulation of cell fate choice. Development 136: 3531–3542.
  • Schuurink, R. C., Shartzer, S. F., Fath, A., and Jones, R. L. 1998. Characterization of a calmodulin-binding transporter from the plasma membrane of barley aleurone. Proc. Natl. Acad. Sci. U S A 95: 1944–1949.
  • Sehnke, P. C., DeLille, J. M., and Ferl, R. J. 2002a. Consummating signal transduction: the role of 14-3-3 proteins in the completion of signal-induced transitions in protein activity. Plant Cell 14: S339–S354.
  • Sehnke, P. C., Rosenquist, M., Alsterfjord, M., DeLille, J., Sommarin, M., Larsson, C., and Ferl, R. J. 2002b. Evolution and isoform specificity of plant 14-3-3 proteins. Plant Mol. Biol. 50: 1011–1018.
  • Seo, J. S., Joo, J., Kim, M. J., Kim, Y. K., Nahm, B. H., Song, S. I., Cheong, J. J., Lee, J. S., Kim, J. K., and Choi, Y. D. 2011. OsbHLH148, a basic helix-loop-helix protein, interacts with OsJAZ proteins in a jasmonate signaling pathway leading to drought tolerance in rice. Plant J. 65: 907–921.
  • Shahollari, B., Varma, A., and Oelmuller, R. 2005. Expression of a receptor kinase in Arabidopsisroots is stimulated by the basidiomycete Piriformospora indica and the protein accumulates in Triton X-100 insoluble plasma membrane microdomains. J. Plant Physiol. 162: 945–958.
  • Shaik, R., and Ramakrishna, W. 2012. Bioinformatic analysis of epigenetic and microRNA mediated regulation of drought responsive genes in rice. PLoS One 7: e49331.
  • Shankar, R., Bhattacharjee, A., and Jain, M. 2016. Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses. Sci. Rep. 6: 23719.
  • Sharma, G., Giri, J., and Tyagi, A. K. 2015. Rice OsiSAP7 negatively regulates ABA stress signalling and imparts sensitivity to water-deficit stress in Arabidopsis. Plant Sci. 237: 80–92.
  • Sharma, R., Kapoor, M., Tyagi, A. K., and Kapoor, S. 2010. Comparative transcript profiling of TCP family genes provide insight into gene functions and diversification in rice and Arabidopsis. J. Plant Mol. Biol. Biotechnol. 1: 24–38.
  • Sharma, R., Mohan, S. R. K., Malik, G., Deveshwar, P., Tyagi, A. K., Kapoor, S., Kapoor, M. 2009. Rice cytosine DNA methyltransferases-gene expression profiling during reproductive development and abiotic stress. FEBS J. 276: 6301–6311.
  • Sharoni, A. M., Nuruzzaman, M., Satoh, K., Shimizu, T., Kondoh, H., Sasaya, T., Choi, I. R., Omura, T., Kikuchi, S. 2011. Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. Plant Cell Physiol. 52: 344–360.
  • Shaw, P. E. 2002. Peptidyl-prolyl isomerases: a new twist to transcription. EMBO Rep. 3: 521–526.
  • Shen, H., Liu, C., Zhang, Y., Meng, X., Zhou, X., Chu, C., Wang, X. 2012. OsWRKY30 is activated by MAP kinases to confer drought tolerance in rice. Plant Mol. Biol. 80: 241–253.
  • Shen, Y., Shen, L., Shen, Z., Jing, W., Ge, H., Zhao, J., Zhang, W. 2015. The potassium transporter OsHAK21 functions in the maintenance of ion homeostasis and tolerance to salt stress in rice. Plant Cell Environ. 38: 2766–2779.
  • Shi, J., Kim, K. N., Ritz, O., Albrecht, V., Gupta, R., Harter, K., Luan, S., Kudla, J. 1999. Novel protein kinases associated with calcineurin B-like calcium sensors in Arabidopsis. Plant Cell 11: 2393–2405.
  • Shi, J., Dong, A., and Shen, W. H. 2015. Epigenetic regulation of rice flowering and reproduction. Front. Plant Sci. 5: 803.
  • Shimizu, H., Sato, K., Berberich, T., Miyazaki, A., Ozaki, R., Imai, R., Kusano, T. 2005. LIP19, a basic region leucine zipper protein, is a Fos-like molecular switch in the cold signaling of rice plants. Plant Cell Physiol. 46: 1623–1634.
  • Shinozaki, K., and Yamaguchi-Shinozaki, K. 2007. Gene networks involved in drought stress response and tolerance. J. Exp. Bot. 58: 221–227.
  • Shiu, S. H., and Bleecker, A. B. 2001. Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc. Natl. Acad. Sci. U S A 98: 10763–10768.
  • Shiu, S. H., and Bleecker, A. B. 2003. Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis. Plant Physiol. 132: 530–543.
  • Shiu, S. H., Karlowski, W. M., Pan, R., Tzeng, Y. H., Mayer, K. F., and Li, W. H. 2004. Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell 16: 1220–1234.
  • Shiu, S. H., Shih, M. C., and Li, W. H. 2005. Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiol. 139: 18–26.
  • Singh, A., Kushwaha, H. R., Soni, P., Gupta, H., Singla-Pareek, S. L., Pareek, A. 2015a. Tissue specific and abiotic stress regulated transcription of histidine kinases in plants is also influenced by diurnal rhythm. Front. Plant Sci. 6: 711.
  • Singh, A., Mittal, D., Lavania, D., Agarwal, M., Mishra, R. C., and Grover, A. 2012. OsHsfA2c and OsHsfB4b are involved in the transcriptional regulation of cytoplasmic OsClpB Hsp100 gene in rice Oryza sativa L. Cell Stress Chaperones 17: 243–254.
  • Singh, A. K., Ansari, M. W., Pareek, A., and Singla-Pareek, S. L. 2008. Raising salinity tolerant rice: recent progress and future perspectives. Physiol. Mol. Biol. Plants 14: 137–154.
  • Singh, A. K., Kumar, R., Tripathi, A. K., Gupta, B. K., Pareek, A., and Singla-Pareek, S. L. 2015b. Genome-wide investigation and expression analysis of sodium/calcium exchanger gene family in rice and Arabidopsis. Rice N Y. 8: 54.
  • Singh, R., and Jwa, N. S. 2013. Understanding the responses of rice to environmental stress using proteomics. J. Proteome Res. 12: 4652–4669.
  • Singla-Pareek, S. L., Reddy, M. K., and Sopory, S. K. 2003. Genetic engineering of the glyoxalase pathway in tobacco leads to enhanced salinity tolerance. Proc. Natl. Acad. Sci. U S A 100: 14672–14677.
  • Singla-Pareek, S. L., Yadav, S. K., Pareek, A., Reddy, M. K., and Sopory, S. K. 2006. Transgenic tobacco overexpressing glyoxalase pathway enzymes grow and set viable seeds in zinc-spiked soils. Plant Physiol. 140: 613–623.
  • Singla-Pareek, S. L., Yadav, S. K., Pareek, A., Reddy, M. K., and Sopory, S. K. 2008. Enhancing salt tolerance in a crop plant by overexpression of glyoxalase II. Transgenic Res. 17: 171–180.
  • Smertenko, A. P., Jiang, C. J., Simmons, N. J., Weeds, A. G., Davies, D. R., and Hussey, P. J. 1998. Ser6 in the maize actin-depolymerizing factor, ZmADF3, is phosphorylated by a calcium-stimulated protein kinase and is essential for the control of functional activity. Plant J. 14: 187–193.
  • Smita, S., Katiyar, A., Chinnusamy, V., Pandey, D. M., and Bansal, K. C. 2015. Transcriptional regulatory network analysis of MYB transcription factor family genes in rice. Front. Plant Sci. 6: 1157.
  • Smita, S., Katiyar, A., Pandey, D. M., Chinnusamy, V., Archak, S., Bansal, K. C. 2013. Identification of conserved drought stress responsive gene-network across tissues and developmental stages in rice. Bioinformation 9: 72–78.
  • Soltis, P. S., Soltis, D. E., Savolainen, V., Crane, P. R., and Barraclough, T. G. 2002. Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils. Proc. Natl. Acad. Sci. U S A 99: 4430–4435.
  • Song, J. J., Liu, J., Tolia, N. H., Schneiderman, J., Smith, S. K., Martienssen, R. A., Hannon, G. J., and Joshua-Tor, L. 2003. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat. Struct. Biol. 10: 1026–1032.
  • Song, S. Y., Chen, Y., Chen, J., Dai, X. Y., and Zhang, W. H. 2011. Physiological mechanisms underlying OsNAC5-dependent tolerance of rice plants to abiotic stress. Planta 234: 331–345.
  • Staiger, C. J., Gibbon, B. C., Kovar, D. R., and Zonia, L. E. 1997. Profilin and actin-depolymerizing factor: modulators of actin organization in plants. Trends Plant Sci. 2: 275–281.
  • Stone, S. L., Hauksdottir, H., Troy, A., Herschleb, J., Kraft, E., and Callis, J. 2005. Functional analysis of the RING-type ubiquitin ligase family of Arabidopsis. Plant Physiol. 137: 13–30.
  • Ströher, E., Wang, X. J., Roloff, N., Klein, P., Husemann, A., and Dietz, K. J. 2009. Redox-dependent regulation of the stress-induced zinc-finger protein SAP12 in Arabidopsis thaliana. Mol. Plant 2: 357–367.
  • Su, C. F., Wang, Y. C., Hsieh, T. H., Lu, C. A., Tseng, T. H., and Yu, S. M. 2010. A novel MYBS3-dependent pathway confers cold tolerance in rice. Plant Physiol. 153: 145–158.
  • Suckow, M., von Wilcken-Bergmann, B., and Muller-Hill, B. 1993. Identification of three residues in the basic regions of the bZIP proteins GCN4, C/EBP and TAF-1 that are involved in specific DNA binding. EMBO J. 12: 1193–1200.
  • Sun, L., Zhang, Q., Wu, J., Zhang, L., Jiao, X., Zhang, S., Zhang, Z., Sun, D., Lu, T., and Sun, Y. 2014. Two rice authentic histidine phosphotransfer proteins, OsAHP1 and OsAHP2, mediate cytokinin signaling and stress responses in rice. Plant Physiol. 165: 335–345.
  • Sun, S. J., Guo, S. Q., Yang, X., Bao, Y. M., Tang, H. J., Sun, H., Huang, J., and Zhang, H. S. 2010. Functional analysis of a novel Cys2/His2-type zinc finger protein involved in salt tolerance in rice. J. Exp. Bot. 61: 2807–2818.
  • Sunkar, R., Chinnusamy, V., Zhu, J., and Zhu, J. K. 2007. Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci. 12: 301–309.
  • Sunkar, R., and Zhu, J. K. 2004. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16: 2001–2019.
  • Sunnerhagen, M., Pursglove, S., and Fladvad, M. 2002. The new MATH: homology suggests shared binding surfaces in meprin etramers and TRAF trimers. FEBS Lett. 530: 1–3.
  • Suzuki, K., Yamaji, N., Costa, A., Okuma, E., Kobayashi, N. I., Kashiwagi, T., Katsuhara, M., Wang, C., Tanoi, K., Murata, Y., et al. 2016. OsHKT1;4-mediated Na+. transport in stems contributes to Na+. exclusion from leaf blades of rice at the reproductive growth stage upon salt stress. BMC Plant Biol. 16: 22.
  • Takasaki, H., Maruyama, K., Kidokoro, S., Ito, Y., Fujita, Y., Shinozaki, K., Yamaguchi-Shinozaki, K., and Nakashima, K. 2010. The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. Mol. Genet. Genomics 284: 173–183.
  • Takatsuji, H. 1999. Zinc-finger proteins: the classical zinc finger emerges in contemporary plant science. Plant Mol. Biol. 39: 1073–1078.
  • Talke, I. N., Blaudez, D., Maathuis, F. J., and Sanders, D. 2003. CNGCs: prime targets of plant cyclic nucleotide signalling? Trends Plant Sci. 8: 286–293.
  • Tam, P. P., Barrette-Ng, I. H., Simon, D. M., Tam, M. W., Ang, A. L., and Muench, D. G. 2010. The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization. BMC Plant Biol. 10: 44.
  • Tang, N., Zhang, H., Li, X., Xiao, J., and Xiong, L. 2012. Constitutive activation of transcription factor OsbZIP46 improves drought tolerance in rice. Plant Physiol. 158: 1755–1765.
  • Ten Hove, C. A., and Heidstra, R. 2008. Who begets whom? Plant cell fate determination by asymmetric cell division. Curr.Opin. Plant Biol. 11: 34–41.
  • Tian, C., Zuo, Z., and Qiu, J. L. 2015. Identification and characterization of ABA-responsive microRNAs in rice. J. Genet. Genomics 42: 393–402.
  • Tiwari, M., Sharma, D., and Trivedi, P. K. 2014. Artificial microRNA mediated gene silencing in plants: progress and perspectives. Plant Mol. Biol. 86: 1–18.
  • To, J. P., Haberer, G., Ferreira, F. J., Deruere, J., Mason, M. G., Schaller, G. E., Alonso, J. M., Ecker, J. R., Kieber, J. J. 2004. Type-A Arabidopsis response regulators are partially redundant negative regulators of cytokinin signaling. Plant Cell 16: 658–671.
  • To, J. P., and Kieber, J. J. 2008. Cytokinin signaling: two-components and more. Trends Plant Sci. 13: 85–92.
  • Todaka, D., Nakashima, K., Shinozaki, K., and Yamaguchi-Shinozaki, K. 2012. Toward understanding transcriptional regulatory networks in abiotic stress responses and tolerance in rice. Rice 5: 6.
  • Tran, L. S., Urao, T., Qin, F., Maruyama, K., Kakimoto, T., Shinozaki, K., and Yamaguchi-Shinozaki, K. 2007. Functional analysis of AHK1/ATHK1 and cytokinin receptor histidine kinases in response to abscisic acid, drought, and salt stress in Arabidopsis. Proc. Natl. Acad. Sci. U S A 104: 20623–20628.
  • Tripathi, A. K., Pareek, A., Sopory, S. K., and Singla-Pareek, S. L. 2012. Narrowing down the targets for yield improvement in rice under normal and abiotic stress conditions via expression profiling of yield-related genes. Rice 5: 37.
  • Tripathi, A. K., Singh, K., Pareek, A., and Singla-Pareek, S. L. 2015. Histone chaperones in Arabidopsis and rice: genome-wide identification, phylogeny, architecture and transcriptional regulation. BMC Plant Biol. 15: 42.
  • Trivedi, D. K., Yadav, S., Vaid, N., and Tuteja, N. 2012. Genome wide analysis of Cyclophilin gene family from rice and Arabidopsis and its comparison with yeast. Plant Signal. Behav. 7: 1653–1666.
  • Tsukada, Y., Fang, J., Erdjument-Bromage, H., Warren, M. E., Borchers, C. H., Tempst, P., and Zhang, Y. 2006. Histone demethylation by a family of JmjC domain-containing proteins. Nature 439: 811–816.
  • Urao, T., Yamaguchi-Shinozaki, K., Urao, S., and Shinozaki, K. 1993. An Arabidopsis myb homolog is induced by dehydration stress and its gene product binds to the conserved MYB recognition sequence. Plant Cell 5: 1529–1539.
  • Vaid, N., Pandey, P. K., and Tuteja, N. 2012. Genome-wide analysis of lectin receptor-like kinase family from Arabidopsis and rice. Plant Mol. Biol. 80: 365–388.
  • Van Der Graaff, E., Laux, T., and Rensing, S. A. 2009. The WUS homeobox-containing WOX protein family. Genome Biol. 10: 248.
  • van Loon, L. C., Rep, M., and Pieterse, C. M. 2006. Significance of inducible defense-related proteins in infected plants. Annu. Rev. Phytopathol. 44: 135–162.
  • Vanholme, B., Grunewald, W., Bateman, A., Kohchi, T., and Gheysen, G. 2007. The tify family previously known as ZIM. Trends Plant Sci. 12: 239–244.
  • Vannini, C., Locatelli, F., Bracale, M., Magnani, E., Marsoni, M., Osnato, M., Mattana, M., Baldoni, E., and Coraggio, I. 2004. Overexpression of the rice Osmyb4 gene increases chilling and freezing tolerance of Arabidopsis thaliana plants. Plant J. 37: 115–127.
  • Vantard, M., and Blanchoin, L. 2002. Actin polymerization processes in plant cells. Curr. Opin. Plant Biol. 5: 502–506.
  • Vanyushin, B. F., and Ashapkin, V. V. 2011. DNA methylation in higher plants: past, present and future. Biochim. Biophys. Acta 1809: 360–368.
  • Vanyushin, B. F., Kadyrova, D. K. H., Karimov, KhKh, and Belozersky, A. N. 1971. Minor bases in the DNA of higher plants. Biokhimiya Moscow 36: 1251–1258.
  • Verma, M., Verma, D., Jain, R. K., Sopory, S. K., and Wu, R. 2005. Overexpression of glyoxalase I gene confers salinity tolerance in transgenic japonica and indica rice plants. Rice Genet. Newslett. 2(2): 58–62.
  • Vij, S., Giri, J., Dansana, P. K., Kapoor, S., and Tyagi, A. K. 2008. The receptor-like cytoplasmic kinase OsRLCK gene family in rice: organization, phylogenetic relationship, and expression during development and stress. Mol. Plant 1: 732–750.
  • Vij, S., and Tyagi, A. K. 2006. Genome-wide analysis of the stress associated protein SAP gene family containing A20/AN1 zinc-fingers in rice and their phylogenetic relationship with Arabidopsis. Mol. Genet. Genomics 276: 565–575.
  • Vij, S., and Tyagi, A. K. 2008. A20/AN1 zinc-finger domain-containing proteins in plants and animals represent common elements in stress response. Funct. Integr. Genomics 8: 301–307.
  • Voinnet, O. 2009. Origin, biogenesis, and activity of plant microRNAs. Cell 136: 669–687.
  • Volpe, T. A., Kidner, C., Hall, I. M., Teng, G., Grewal, S. I., and Martienssen, R. A. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297: 1833–1837.
  • von Koskull-Doring, P., Scharf, K. D., and Nover, L. 2007. The diversity of plant heat stress transcription factors. Trends Plant Sci. 12: 452–457.
  • Wakasa, Y., Oono, Y., Yazawa, T., Hayashi, S., Ozawa, K., Handa, H., Matsumoto, T., and Takaiwa, F. 2014. RNA sequencing-mediated transcriptome analysis of rice plants in endoplasmic reticulum stress conditions. BMC Plant Biol. 14: 101.
  • Wang, D., Guo, Y., Wu, G., Yang, G., Li, Y., and Zheng, C. 2008. Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice. BMC Genomics 9: 44.
  • Wang, H., Zhang, H., Gao, F., Li, J., and Li, Z. 2007. Comparison of gene expression between upland and lowland rice cultivars under water stress using cDNA microarray. Theor. Appl. Genet. 115: 1109–1126.
  • Wang, L., Yu, C., Chen, C., He, C., Zhu, Y., and Huang, W. 2014b. Identification of rice Di19 family reveals OsDi19-4 involved in drought resistance. Plant Cell Rep. 33: 2047–2062.
  • Wang, N., Xiao, B., and Xiong, L. 2011. Identification of a cluster of PR4-like genes involved in stress responses in rice. J. Plant Physiol. 168: 2212–2224.
  • Wang, P., and Heitman, J. 2005. The cyclophilins. Genome Biol. 6: 226.
  • Wang, P., Li, Z., Wei, J., Zhao, Z., Sun, D., and Cui, S. 2012. A Na+/Ca2+ exchanger-like protein AtNCL. involved in salt stress in Arabidopsis. J. Biol. Chem. 287: 44062–44070.
  • Wang, R., Jing, W., Xiao, L., Jin, Y., Shen, L., and Zhang, W. 2015b. The rice high-affinity potassium transporter1;1 is involved in salt tolerance and regulated by an MYB-type transcription factor. Plant Physiol. 168: 1076–1090.
  • Wang, W., Li, G., Zhao, J., Chu, H., Lin, W., Zhang, D., Wang, Z., and Liang, W. 2014a. DWARF TILLER1, a WUSCHEL-related homeobox transcription factor, is required for tiller growth in rice. PLoS Genetics 10: e1004154.
  • Wang, W., Liu, B., Xu, M., Jamil, M., and Wang, G. 2015a. ABA-induced CCCH tandem zinc finger protein OsC3H47 decreases ABA sensitivity and promotes drought tolerance in Oryza sativa. Biochem. Biophys. Res. Commun. 464: 33–37.
  • Wang, Y., Dou, D., Wang, X., Li, A., Sheng, Y., Hua, C., Cheng, B., Chen, X., Zheng, X., and Wang, Y. 2009. The PsCZF1 gene encoding a C2H2 zinc finger protein is required for growth, development and pathogenesis in Phytophthora sojae. Microb. Pathog. 47: 78–86.
  • Wani, S. H., and Gosal, S. S. 2011. Introduction of OsglyII gene into Oryza sativa for increasing salinity tolerance. Biol. Plant. 55: 536–540.
  • Wassenegger, M., Heimes, S., Riedel, L., and Sanger, H. L. 1994. RNA-directed de novo methylation of genomic sequences in plants. Cell 76: 567–576.
  • Wei, S., Hu, W., Deng, X., Zhang, Y., Liu, X., Zhao, X., Luo, Q., Jin, Z., Li, Y., Zhou, S., et al. 2014. Rice calcium-dependent protein kinase OsCPK9 positively regulates drought stress tolerance and spikelet fertility. BMC Plant Biol. 14: 133.
  • Weisman, R., Creanor, J., and Fantes, P. 1996. A multicopy suppressor of a cell cycle defect in S. pombe encodes a heat shock-inducible 40 kDa cyclophilin-like protein. EMBO J. 15: 447–456.
  • Windhövel, A., Hein, I., Dabrowa, R., and Stockhaus, J. 2001. Characterization of a novel class of plant homeodomain proteins that bind to the C4 phosphoenolpyruvate carboxylase gene of Flaveria trinervia. Plant Mol. Biol. 45: 201–214.
  • Wohlbach, D. J., Quirino, B. F., and Sussman, M. R. 2008. Analysis of the Arabidopsis histidine kinase ATHK1 reveals a connection between vegetative osmotic stress sensing and seed maturation. Plant Cell 20: 1101–1117.
  • Wolf, J. A., Stys, P. K., Lusardi, T., Meaney, D., Smith, D. H. 2001. Traumatic axonal injury induces calcium influx modulated by tetrodotoxin-sensitive sodium channels. J. Neurosci. 21: 1923–1930.
  • Wu, F., Sheng, P., Tan, J., Chen, X., Lu, G., Ma, W., Heng, Y., Lin, Q., Zhu, S., Wang, J., et al. 2015c. Plasma membrane receptor-like kinase leaf panicle 2 acts downstream of the DROUGHT AND SALT TOLERANCE transcription factor to regulate drought sensitivity in rice. J. Exp. Bot. 66: 271–281.
  • Wu, H., Ye, H., Yao, R., Zhang, T., and Xiong, L. 2015b. OsJAZ9 acts as a transcriptional regulator in jasmonate signaling and modulates salt stress tolerance in rice. Plant Sci. 232: 1–12.
  • Wu, L., Taohua, Z., Gui, W., Xu, L., Li, J., and Ding, Y. 2015a. Five pectinase gene expressions highly responding to heat stress in rice floral organs revealed by RNA-seq analysis. Biochem. Biophys. Res. Commun. 463: 407–413.
  • Wu, L., Zhou, H., Zhang, Q., Zhang, J., Ni, F., Liu, C., and Qi, Y. 2010. DNA methylation mediated by a microRNA pathway. Mol. Cell 38: 465–475.
  • Wu, L. J., Zhang, Z., Peng, R. H., Xiong, A. S., Liu, J. G., Fu, X. Y., Gao, F., and Yao. Q. H. 2007. Cloning and bioinformatic analysis of the cDNA encoding a novel heat-shock factor OsHSF13 in Oryza sativa L. Fen Zi Xi Bao Sheng Wu Xue Bao 40: 251–257.
  • Wu, X., Shiroto, Y., Kishitani, S., Ito, Y., and Toriyama, K. 2009. Enhanced heat and drought tolerance in transgenic rice seedlings overexpressing OsWRKY11 under the control of HSP101 promoter. Plant Cell Rep. 28: 21–30.
  • Wyatt, G.R. 1950. Occurrence of 5-methylcytosine in nucleic acids. Nature 166: 237–238.
  • Xiang, J., Ran, J., Zou, J., Zhou, X., Liu, A., Zhang, X., Peng, Y., Tang, N., Luo, G., and Chen, X. 2013. Heat shock factor OsHsfB2b negatively regulates drought and salt tolerance in rice. Plant Cell Rep. 32: 1795–1806.
  • Xiang, Y., Huang, Y., and Xiong, L. 2007. Characterization of stress-responsive CIPK genes in rice for stress tolerance improvement. Plant Physiol. 144: 1416–1428.
  • Xiang, Y., Tang, N., Du, H., Ye, H., and Xiong, L. 2008. Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. Plant Physiol. 148: 1938–1952.
  • Xiao, H., Tang, J., Li, Y., Wang, W., Li, X., Jin, L., Xie, R., Luo, H., Zhao, X., and Meng, Z., et al. 2009. STAMENLESS 1, encoding a single C2H2 zinc finger protein, regulates floral organ identity in rice. Plant J. 59: 789–801.
  • Xie, Z., Johansen, L. K., Gustafson, A. M., Kasschau, K. D., Lellis, A. D., Zilberman, D., Jacobsen, S. E., and Carrington, J. C. 2004. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2: e104.
  • Xie, Z., Zhang, Z. L., Zou, X., Huang, J., Ruas, P., Thompson, D., and Shen, Q. J. 2005. Annotations and functional analyses of the rice WRKY gene superfamily reveal positive and negative regulators of abscisic acid signaling in aleurone cells. Plant Physiol. 137: 176–189.
  • Xu, D. Q., Huang, J., Guo, S. Q., Yang, X., Bao, Y. M., Tang, H. J., and Zhang, H. S. 2008. Overexpression of a TFIIIA-type zinc finger protein gene ZFP252 enhances drought and salt tolerance in rice Oryza sativa L. FEBS Lett. 582: 1037–1043.
  • Xu, G. Y., Rocha, P. S., Wang, M. L., Xu, M. L., Cui, Y. C., Li, L. Y., Zhu, Y. X., and Xia, X. 2011. A novel rice calmodulin-like gene, OsMSR2, enhances drought and salt tolerance and increases ABA sensitivity in Arabidopsis. Planta 234: 47–59.
  • Xu, K., Xu, X., Fukao, T., Canlas, P., Maghirang-Rodriguez, R., Hwuer, S., Ismail, A. M., Bailey-Serres, J., Ronald, P. C., and Mackill, D. J. 2006. Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442: 705–708.
  • Xue, Y. M., Kowalska, A. K., Grabowska, K., Przybyt, K., Cichewicz, M. A., Del Rosario, B. C., and Pemberton, LF. 2013. Histone chaperones Nap1 and Vps75 regulate histone acetylation during transcription elongation. Mol. Cell Biol. 33: 1645–1656.
  • Yadav, S. K., Singla-Pareek, SL., Kumar, M., Pareek, A., Saxena, M., Sarin, N. B., and Sopory, S. K. 2007. Characterization and functional validation of glyoxalase II from rice. Protein Expr. Purif. 51: 126–132.
  • Yadav, S. K., Singla-Pareek, S. L., Ray, M., Reddy, M. K., and Sopory, S. K. 2005a. Methylglyoxal levels in plants under salinity stress are dependent on glyoxalase I and glutathione. Biochem. Biophys. Res. Commun. 337: 61–67.
  • Yadav, S. K., Singla-Pareek, SL., Reddy, M. K., and Sopory, S. K. 2005b. Methylglyoxal detoxifcation by glyoxalase system: a survival strategy during environmental stresses. Physiol. Mol. Biol. Plants 11: 1–11.
  • Yadav, S. K., Singla-Pareek, S. L., Reddy, M. K., and Sopory, S. K. 2005c. Transgenic tobacco plants overexpressing glyoxalase enzymes resist an increase in methylglyoxal and maintain higher reduced glutathione levels under salinity stress. FEBS Lett. 579: 6265–6271.
  • Yamaguchi-Shinozaki, K., Koizumi, M., Urao, S., and Shinozaki, K. 1992. Molecular cloning and characterization of 9 cDNAs for genes that are responsive to desiccation in Arabidopsis thaliana: sequence analysis of one cDNA clone that encodes a putative transmembrane channel protein. Plant Cell Physiol. 33: 217–224.
  • Yamaguchi-Shinozaki, K., and Shinozaki, K. 1994. A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 6: 251–264.
  • Yamaguchi-Shinozaki, K., and Shinozaki, K. 2005. Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters. Trends Plant Sci. 10: 88–94.
  • Yang, A., Dai, X., and Zhang, W. H. 2012. A R2R3-type MYB gene, OsMYB2, is involved in salt, cold, and dehydration tolerance in rice. J. Exp. Bot. 63: 2541–2556.
  • Yang, D. H., Kwak, K. J., Kim, M. K., Park, S. J., Yang, K. Y., and Kang, H. 2014b. Expression of Arabidopsis glycine-rich RNA-binding protein AtGRP2 or AtGRP7 improves grain yield of rice Oryza sativa. under drought stress conditions. Plant Sci. 214: 106–112.
  • Yang, T., and Poovaiah, B. W. 2003. Calcium/calmodulin-mediated signal network in plants. Trends Plant Sci. 8: 505–512.
  • Yang, T., Zhang, S., Hu, Y., Wu, F., Hu, Q., Chen, G., Cai, J., Wu, T., Moran, N., Yu, L., et al. 2014a. The role of a potassium transporter OsHAK5 in potassium acquisition and transport from roots to shoots in rice at low potassium supply levels. Plant Physiol. 166: 945–959.
  • Yang, W., Kong, Z., Omo-Ikerodah, E., Xu, W., Li, Q., and Xue, Y. 2008. Calcineurin B-like interacting protein kinase OsCIPK23 functions in pollination and drought stress responses in rice Oryza sativa L. J. Genet. Genomics 35: 531–543.
  • Yang, X., Yang, Y. N., Xue, L. J., Zou, M. J., Liu, J. Y., Chen, F., and Xue, H. W. 2011. Rice ABI5-like1 regulates abscisic acid and auxin responses by affecting the expression of ABRE-containing genes. Plant Physiol. 156: 1397–1409.
  • Yang, Y., Zhong, J., Ouyang, Y. D., and Yao, J. 2013. The integrative expression and co-expression analysis of the AGO gene family in rice. Gene 528: 221–235.
  • Yang, Z., Gao, Q., Sun, C., Li, W., Gu, S., and Xu, C. 2009. Molecular evolution and functional divergence of HAK potassium transporter gene family in rice Oryza sativa L. J. Genet. Genomics 36: 161–172.
  • Yao, X., and Shen, W. 2011. Crucial function of histone lysine methylation in plant reproduction. Chin. Sci. Bull. 56: 3493–3499.
  • Ye, H., Du, H., Tang, N., Li, X., and Xiong, L. 2009. Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice. Plant Mol. Biol. 71: 291–305.
  • Yeh, CH., Chang, PF., Yeh, K. W., Lin, W. C., Chen, Y. M., and Lin, C. Y. 1997. Expression of a gene encoding a 16.9-kDa heat-shock protein, Oshsp16.9, in Escherichia coli enhances thermotolerance. Proc. Natl. Acad. Sci. U S A 94: 10967–10972.
  • Yim, W. C., Lee, BM., and Jang, C. S. 2009. Expression diversity and evolutionary dynamics of rice duplicate genes. Mol. Genet. Genomics 281: 483–493.
  • Yokotani, N., Ichikawa, T., Kondou, Y., Iwabuchi, M., Matsui, M., Hirochika, H., and Oda, K. 2013a. Role of the rice transcription factor JAmyb in abiotic stress response. J. Plant Res. 126: 131–139.
  • Yokotani, N., Ichikawa, T., Kondou, Y., Matsui, M., Hirochika, H., Iwabuchi, M., and Oda, K. 2009. Tolerance to various environmental stresses conferred by the salt-responsive rice gene ONAC063 in transgenic Arabidopsis. Planta 229: 1065–1075.
  • Yokotani, N., Ichikawa, T., Kondou, Y., Matsui, M., Hirochika, H., Iwabuchi, M., and Oda, K. 2008. Expression of rice heat stress transcription factor OsHsfA2e enhances tolerance to environmental stresses in transgenic Arabidopsis. Planta 227: 957–967.
  • Yokotani, N., Sato, Y., Tanabe, S., Chujo, T., Shimizu, T., Okada, K., Yamane, H., Shimono, M., Sugano, S., Takatsuji, H., et al. 2013b. WRKY76 is a rice transcriptional repressor playing opposite roles in blast disease resistance and cold stress tolerance. J. Exp. Bot. 64: 5085–5097.
  • You, J., Zong, W., Li, X., Ning, J., Hu, H., Li, X., Xiao, J., and Xiong, L. 2013. The SNAC1-targeted gene OsSRO1c modulates stomatal closure and oxidative stress tolerance by regulating hydrogen peroxide in rice. J. Exp. Bot. 64: 569–583.
  • Young, J. C., Barral, J. M., and Ulrich Hartl, F. 2003. More than folding: localized functions of cytosolic chaperones. Trends Biochem. Sci. 28: 541–547.
  • Yu, J., Hu, S., Wang, J., Wong, G. K., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., et al. 2002. A draft sequence of the rice genome Oryza sativa L. ssp. indica. Science 296: 79–92.
  • Yu, Q., An, L., and Li, W. 2014. The CBL-CIPK network mediates different signaling pathways in plants. Plant Cell Rep. 33: 203–214.
  • Yu, S. P., and Choi, D. W. 1997. Na+.-Ca2+ exchange currents in cortical neurons: concomitant forward and reverse operation and effect of glutamate. Eur. J. Neurosci. 9: 1273–1281.
  • Yu, Y., Bu, Z., Shen, W. H., and Dong, A. 2009. An update on histone lysine methylation in plants. Progr. Nat. Sci. 19: 407–413.
  • Yu, Y., Yang, D., Zhou, S., Gu, J., Wang, F., Dong, J., and Huang, R. 2016. The ethylene response factor OsERF109 negatively affects ethylene biosynthesis and drought tolerance in rice. Protoplasma. doi: 10.1007/s00709-016-0960-4.
  • Zahur, M., Maqbool, A., Irfan, M., Jamal, A., Shahid, N., Aftab, B., and Husnain, T. 2012. Identification and characterization of a novel gene encoding myb-box binding zinc finger protein in Gossypium arboretum. Biol. Plant. 56: 641–647.
  • Zelman, A. K., Dawe, A., Gehring, C., and Berkowitz, GA. 2012. Evolutionary and structural perspectives of plant cyclic nucleotide-gated cation channels. Front. Plant Sci. 3: 95.
  • Zeng, Z., Xiong, F., Yu, X., Gong, X., Luo, J., Jiang, Y., Kuang, H., Gao, B., Niu, X., and Liu, Y. 2016. Overexpression of a glyoxalase gene, OsGly I, improves abiotic stress tolerance and grain yield in rice Oryza sativa L. Plant Physiol. Biochem. 109: 62–71.
  • Zhang, H., Liu, Y., Wen, F., Yao, D., Wang, L., Guo, J., Ni, L., Zhang, A., Tan, M., and Jiang, M. 2014. A novel rice C2H2-type zinc finger protein, ZFP36, is a key player involved in abscisic acid-induced antioxidant defence and oxidative stress tolerance in rice. J. Exp. Bot. 65: 5795–5809.
  • Zhang, L., Vision, T. J., and Gaut, B. S. 2002. Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Mol. Biol. Evol. 19: 1464–1473.
  • Zhang, S., Haider, I., Kohlen, W., Jiang, L., Bouwmeester, H., Meijer, AH., Schluepmann, H., and Liu, CM., Ouwerkerk, PB. 2012b. Function of the HD-Zip I gene Oshox22 in ABA-mediated drought and salt tolerances in rice. Plant Mol. Biol. 80: 571–585.
  • Zhang, X., Li, J., Liu, A., Zou, J., Zhou, X., Xiang, J., Rerksiri, W., Peng, Y., Xiong, X., and Chen, X. 2012a. Expression profile in rice panicle: insights into heat response mechanism at reproductive stage. PLoS One 7: e49652.
  • Zhang, X., Rerksiri, W., Liu, A., Zhou, X., Xiong, H., Xiang, J., Chen, X., and Xiong, X. 2013. Transcriptome profile reveals heat response mechanism at molecular and metabolic levels in rice flag leaf. Gene 530: 185–192.
  • Zhang, X., Zong, J., Liu, J., Yin, J., and Zhang, D. 2010b. Genome-wide analysis of WOX gene family in rice, sorghum, maize, Arabidopsis and poplar. J. Integr. Plant Biol. 52: 1016–1026.
  • Zhang, Y., Lan, H., Shao, Q., Wang, R., Chen, H., Tang, H., Zhang, H., and Huang, J. 2016. An A20/AN1-type zinc finger protein modulates gibberellins and abscisic acid contents and increases sensitivity to abiotic stress in rice Oryza sativa. J. Exp. Bot. 67: 315–326.
  • Zhang, Z., Li, F., Li, D., Zhang, H., and Huang, R. 2010a. Expression of ethylene response factor JERF1 in rice improves tolerance to drought. Planta 232: 765–774.
  • Zhang, Y., and Wang, L. 2005. The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol. Biol. 5: 1.
  • Zhao, B., Ge, L., Liang, R., Li, W., Ruan, K., Lin, H., and Jin, Y. 2009. Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor. BMC Mol. Biol. 10: 29.
  • Zhao, J., Li, M., Gu, D., Liu, X., Zhang, J., Wu, K., Zhang, X., Teixeira da Silva, J. A., and Duan, J. 2016. Involvement of rice histone deacetylase HDA705 in seed germination and in response to ABA and abiotic stresses. Biochem. Biophys. Res. Commun. 470: 439–444.
  • 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.
  • Zhao, M., Morohashi, K., Hatlestad, G., Grotewold, E., and Lloyd, A. 2008. The TTG1-bHLH-MYB complex controls trichome cell fate and patterning through direct targeting of regulatory loci. Development 135: 1991–1999.
  • Zheng, X., Chen, B., Lu, G., and Han, B. 2009. Overexpression of a NAC transcription factor enhances rice drought and salt tolerance. Biochem. Biophys. Res. Commun. 379: 985–989.
  • Zhou, J., Lia, F., Wang, J., Maa, Y., Chong, K., and Xu, Y. 2009. Basic helix-loop-helix transcription factor from wild rice OrbHLH2. improves tolerance to salt and osmotic stress in Arabidopsis. J. Plant. Physiol. 166: 1296–1306.
  • Zhou, J., Wang, X., Jiao, Y., Qin, Y., Liu, X., He, K., Chen, C., Ma, L., Wang, J., Xiong, L., et al. 2007. Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. Plant Mol. Biol. 63: 591–608.
  • Zhou, L., Liu, Y., Liu, Z., Kong, D., Duan, M., and Luo, L. 2010. Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. J. Exp. Bot. 61: 4157–4168.
  • Zhu, D., Li, R., Liu, X., Sun, M., Wu, J., Zhang, N., and Zhu, Y. 2014. The positive regulatory roles of the TIFY10 proteins in plant responses to alkaline stress. PLoS One 9: e111984.
  • Zhu, J. K. 2000. Genetic analysis of plant salt tolerance using Arabidopsis. Plant Physiol. 124: 941–948.
  • Zhu, J. K. 2003. Regulation of ion homeostasis under salt stress. Curr. Opin. Plant Biol. 6: 441–445.
  • Zhu, JK., Liu, J. P., and Xiong, L. M. 1998. Genetic analysis of salt tolerance in Arabidopsis: evidence for a critical role of potassium nutrition. Plant Cell 10: 1181–1191.
  • Zhu, N., Cheng, S., Liu, X., Du, H., Dai, M., Zhou, D. X., Yang, W., and Zhao, Y. 2015. The R2R3-type MYB gene OsMYB91 has a function in coordinating plant growth and salt stress tolerance in rice. Plant Sci. 236: 146–156.
  • Zhu, Y., Dong, A., and Shen, W. H. 2012. Histone variants and chromatin assembly in plant abiotic stress responses. Biochim. Biophys. Acta 1819: 343–348.
  • Ziolkowski, P. A., Blanc, G., and Sadowski, J. 2003. Structural divergence of chromosomal segments that arose from successive duplication events in the Arabidopsis genome. Nucl. Acids Res. 31: 1339–1350.
  • Zou, M., Guan, Y., Ren, H., Zhang, F., and Chen, F. 2007. Characterization of alternative splicing products of bZIP transcription factors OsABI5. Biochem. Biophys. Res. Commun. 360: 307–313.
  • Zou, M., Guan, Y., Ren, H., Zhang, F., and Chen, F. 2008. A bZIP transcription factor, OsABI5, is involved in rice fertility and stress tolerance. Plant Mol. Biol. 6: 675–683.

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