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Comparison of gene expression between upland and lowland rice cultivars under water stress using cDNA microarray

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Abstract

To elucidate the differences in the regulation of water stress tolerance between two genotypes of rice, upland-rice (UR, resistant to water stress) and lowland-rice (LR, susceptible to water stress), we constructed subtracted cDNA libraries from polyethyleneglycol (PEG)-treated and non-treated rice seedlings (IRAT109, an upland-rice variety) by suppression subtractive hybridization (SSH), from which about 2,000 recombinant colonies were picked and amplified. Then, a cDNA microarray containing these expressed sequence tags (ESTs) was used to analyze the gene expression profiles in UR and LR in response to PEG treatment. Microarray data revealed that the majority of genes expressed in UR and LR are almost identical and Student’s t test showed that 13% of all the ESTs detected in leaves and 7% of that in roots expressed differentially in transcripts abundance between the two genotypes. After sequencing, it was found that 64 and 79 unique ESTs expressed at higher levels in UR and LR, respectively. Many of the ESTs that showed higher expression in UR upon PEG treatment represented genes for transcription factors, genes playing roles in detoxification or protection against oxidative stress, and genes that help in maintaining cell turgor. In contrast, some ESTs that showed higher expression in LR were genes functioning in the degradation of cellular components. Based on data from this study and previous reports, we suggest that overexpression of some genes that expressed at higher level in UR may improve water stress tolerance in LR and other plant species.

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References

  • Akashi K, Nishimura N, Ishida Y, Yokota A (2004) Potent hydroxyl radical-scavenging activity of drought-induced type-2 metallothionein in wild watermelon. Biochem Biophys Res Commun 323:72–78

    Article  PubMed  CAS  Google Scholar 

  • Asakura Y, Hagino T, Ohta Y, Aoki K, Yonekura-Sakakibara K, Deji A, Yamaya T, Sugiyama T, Sakakibara H (2003) Molecular characterization of His-Asp phosphorelay signaling factors in maize leaves: implications of the signal divergence by cytokinin-inducible response regulators in the cytosol and the nuclei. Plant Mol Biol 52:331–341

    Article  PubMed  CAS  Google Scholar 

  • Bohnert HJ, Jensen RG (1996) Strategies for engineering water-stress tolerance in plants. Trends Biotechnol 14:89–97

    Article  CAS  Google Scholar 

  • Boxall SF, Foster JM, Bohnert HJ, Cushman JC, Nimmo HG, Hartwell J (2005) Conservation and divergence of circadian clock operation in a stress-inducible Crassulacean acid metabolism species reveals clock compensation against stress. Plant Physiol 137:969–982

    Article  PubMed  CAS  Google Scholar 

  • Boyer JS (1976) Leaf water potential measured with a pressure chamber. Plant Physiol 42:133–137

    Google Scholar 

  • Bray EA (1997) Plant responses to water deficit. Trends Plant Sci 2:48–54

    Article  Google Scholar 

  • Chang TT (1972) Agronomic and growth characteristics of upland and wetland rices. In: Rice breeding. International Rice Research Institute Los Banos, Philippines, pp 645–661

  • Chaumont F, Barrieu F, Wojcik E, Chrispeels MJ, Jung R (2001) Aquaporins constitute a large and highly divergent protein family in Maize. Plant Physiol 125:1206–1215

    Article  PubMed  CAS  Google Scholar 

  • Chaves MM, Maroc JP, Pereira JS (2003) Understanding plant responses to drought––from genes to the whole plant. Funct Plant Biol 30:239–264

    Article  CAS  Google Scholar 

  • Chen YH, Yang XY, He K, Liu MH, Li JG, Gao ZF, Lin ZQ, Zhang YF, Wang XX, Qiu XM, Shen YP, Zhang L, Deng XH, Luo JC, Deng XW, Chen ZL, Gu HY, Qu LJ (2006) The MYB transcription factor superfamily of arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Mol Biol 60:107–124

    Article  CAS  Google Scholar 

  • Claes B, Dekeyser R, Villarroel R, Van den Bulcke M, Bauw G, Van Montagu M, Caplan A (1990) Characterization of a rice gene showing organ-specific expression in response to salt stress and drought. Plant Cell 2:19–27

    Article  PubMed  CAS  Google Scholar 

  • Collakova E, DellaPenna D (2003) The Role of homogentisate phytyltransferase and other tocopherol pathway enzymes in the regulation of tocopherol synthesis during abiotic stress. Plant Physiol 133:930–940

    Article  PubMed  CAS  Google Scholar 

  • Cruz de Carvalho MH, d’Arcy-Lameta A, Roy-Macauley H, Gareil M, El Maarouf H, Pham-Thi AT, Zuily-Fodil Y (2001) Aspartic protease in leaves of common bean (Phaseolus vulgaris L.) and cowpea (Vigna unguiculata L. Walp): enzymatic activity, gene expression and relation to drought susceptibility. FEBS Lett 492:242–246

    Article  Google Scholar 

  • Delorme VG, McCabe PF, Kim DJ, Leaver CJ (2000) A matrix metalloproteinase gene is expressed at the boundary of senescence and programmed cell death in cucumber. Plant Physiol 123:917–928

    Article  PubMed  CAS  Google Scholar 

  • Diatchenko L, Chrislau YF, Campbell AP, Chenchik A, Mooadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov E, Siebert PD (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probe. Proc Natl Acad Sci USA 93:6025–6030

    Article  PubMed  CAS  Google Scholar 

  • Dornelas MC, van Lammeren AA, Kreis M (2000) Arabidopsis thaliana SHAGGY-related protein kinases (AtSK11 and 12) function in perianth and gynoecium development. Plant J 21:419–429

    Article  PubMed  CAS  Google Scholar 

  • Espartero J, Sanchez-Aguayo I, Pardo JM (1995) Molecular characterization of glyoxalase-I from a higher plant; upregulation by stress. Plant Mol Biol 29:1223–1233

    Article  PubMed  CAS  Google Scholar 

  • Evers D, Ghislain M, Hoffmann L, Hausman JF, Dommes J (2006) A late blight resistant potato plant overexpresses a gene coding for alpha-galactosidase upon infection by Phytophthora infestans. Biol Plant 50:265–271

    Article  CAS  Google Scholar 

  • Feng JX, Liu D, Pan Y, Gong W, Ma LG, Luo JC, Deng XW, Zhu YX (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

    Article  PubMed  CAS  Google Scholar 

  • Feurtado JA, Banik M, Bewley JD (2001) The cloning and characterization of α-galactosidase present during and following germination of tomato (Lycopersicon esculentum Mill.) seed. J Exp Bot 52:1239–1249

    Article  PubMed  CAS  Google Scholar 

  • Fowler TJ, Bernhardt C, Tierney ML (1999) Characterization and expression of four proline-rich cell wall protein genes in arabidopsis encoding two distinct subsets of multiple domain proteins. Plant Physiol 121:1081–1091

    Article  PubMed  CAS  Google Scholar 

  • Fryer MJ (1992) The antioxidant effects of thylakoid vitamin E (alpha-tocopherol). Plant Cell Environ 15:381–392

    Article  CAS  Google Scholar 

  • Fujimori K, Ohta D (2003) Heavy metal induction of Arabidopsis serine decarboxylase gene expression. Biosci Biotechnol Biochem 67:896–898

    Article  PubMed  CAS  Google Scholar 

  • Fujita M, Fujita Y, Maruyama K, Seki M, Hiratsu K, Ohme-Takagi M, Tran LSP, Yamaguchi-Shinozaki K, Shinozaki K (2004) A dehydration-induced NAC protein, RD26, is involved in a novel ABA-dependent stress-signaling pathway. Plant J 39:863–876

    Article  PubMed  CAS  Google Scholar 

  • Gao SQ, Xu HJ, Cheng XG, Chen M, Xu ZS, Li LC, Ye XG, Du LP, Hao XY, Ma YZ (2005) Improvement of wheat drought and salt tolerance by expression of a stress-inducible transcription factor GmDREB of soybean (Glycine max). Chin Sci Bull 50:2714–2723

    Article  CAS  Google Scholar 

  • Garcia I, Rodgers M, Pepin R, Hsieh TF, Matringe M (1999) Characterization and subcellular compartmentation of recombinant 4-hydroxyphenylpyruvate dioxygenase from Arabidopsis in transgenic tobacco. Plant Physiol 119:1507–1516

    Article  PubMed  CAS  Google Scholar 

  • Ge SL (1992) The comparison and classification of several morphological criteria of root of paddy rice and upland rice in different cultural methods. PhD thesis, Beijing Agricultural University, Beijing

  • Gorantla M, Babu PR, Lachagari VBR, Feltus FA, Paterson AH, Reddy AR (2005) Functional genomics of drought stress response in rice: transcript mapping of annotated unigenes of an indica rice (Oryza sativa L. cv. Nagina 22). Curr Sci 89:496–514

    CAS  Google Scholar 

  • Grasser KD, Grill S, Duroux M, Launholt D, Thomsen MS, Nielsen BV, Nielsen HK, Merkle T (2004) HMGB6 from Arabidopsis thaliana specifies a novel type of plant chromosomal HMGB protein. Biochemistry 43:1309–1314

    Article  PubMed  CAS  Google Scholar 

  • Gu RS, Fonseca S, Puskas LG, Hackler L, Zvara A, Dudits D, Pais MS (2004) Transcript identification and profiling during salt stress and recovery of Populus euphratica. Tree Physiol 24:265–276

    PubMed  CAS  Google Scholar 

  • Guo ZJ, Chen XJ, Wu XL, Ling JQ, Xu P (2004) Overexpression of the AP2/EREBP transcription factor OPBP1 enhances disease resistance and salt tolerance in tobacco. Plant Mol Biol 55:607–618

    Article  PubMed  CAS  Google Scholar 

  • Hewitt MM, Carr JM, Williamson CL, Slocum RD (2005) Effects of phosphate limitation on expression of genes involved in pyrimidine synthesis and salvaging in Arabidopsis. Plant Physiol Biochem 43:91–99

    Article  PubMed  CAS  Google Scholar 

  • Holweg C, Nick P (2004) Arabidopsis myosin XI mutant is defective in organelle movement and polar auxin transport. Proc Natl Acad Sci USA 101:10488–10493

    Article  PubMed  CAS  Google Scholar 

  • Huberman M, Pressman E, Jaffe MJ (1993) Pith autolysis in plants. 4. The activity of polygalacturonase and cellulase during drought stress-induced pith autolysis. Plant Cell Physiol 34:795–801

    CAS  Google Scholar 

  • Ishikawa R, Harata Y, Tuchimine Y, Senda M, Akada S, Harada T, Niizeki M (1997) Complex constitutive nature of Japanese upland rice, Oryza sativa L. Euphytica 98:197–203

    Article  Google Scholar 

  • Ishikawa R, Maeda K, Harada T, Niizeki M, Saito K (1992) Genotypic variation for 17 isozyme genes among Japanese upland varieties in rice. Jpn J Breed 42:737–746

    CAS  Google Scholar 

  • Jang IC, Pahk YM, Song SI, Kwon HJ, Nahm BH, Kim JK (2003) Structure and expression of the rice class-I type histone deacetylase genes OsHDAC1-3: OsHDAC1 overexpression in transgenic plants leads to increased growth rate and altered architecture. Plant J 33:531–541

    Article  PubMed  CAS  Google Scholar 

  • Jantasuriyarat C, Gowda M, Haller K, Hatfield J, Lu G, Stahlberg E, Zhou B, Li H, Kim H, Yu Y, Dean RA, Wing RA, Soderlund C, Wang GL (2005) Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction. Plant Physiol 138:105–115

    Article  PubMed  Google Scholar 

  • Jiang S, Ramachandran S (2004) Identification and molecular characterization of myosin gene family in Oryza sativa genome. Plant Cell Physiol 45:590–599

    Article  PubMed  CAS  Google Scholar 

  • Jousse C, Oyadomari S, Novoa I, Lu P, Zhang Y, Harding HP, Ron D (2003) Inhibition of a constitutive translation initiation factor 2alpha phosphatase, CReP, promotes survival of stressed cells. J Cell Biol 163:767–775

    Article  PubMed  CAS  Google Scholar 

  • Kanter U, Usadel B, Guerineau F, Li Y, Pauly M, Tenhaken R (2005) The inositol oxygenase gene family of Arabidopsis is involved in the biosynthesis of nucleotide sugar precursors for cell-wall matrix polysaccharides. Planta 221:243–254

    Article  PubMed  CAS  Google Scholar 

  • Kastner B, Tenhaken R, Kauss H (1998) Chitinase in cucumber hypocotyls is induced by germinating fungal spores and by fungal elicitor in synergism with inducers of acquired resistance. Plant J 13:447–454

    Article  CAS  Google Scholar 

  • Kathiresan A, Lafitte HR, Chen JX, Mansueto L, Bruskiewich R, Bennett J (2006) Gene expression microarrays and their application in drought stress research. Field Crops Res 97:101–110

    Article  Google Scholar 

  • Kaufmann MR, Eckard AN (1971) Evaluation of water stress control with polyethylene glycol by analysis of guttation. Plant Physiol 47:453–456

    Article  PubMed  CAS  Google Scholar 

  • Kawasaki L, Wysong D, Diamond R, Aguirre J (1997) Two divergent catalase genes are differentially regulated during Aspergillus nidulans development and oxidative stress. J Bacteriol 179:3284–3292

    PubMed  CAS  Google Scholar 

  • Kikuchi S et al (2003) Collection, mapping, and annotation of over 28,000 cDNA Clones from japonica rice: the rice full-length cDNA consortium. Science 301:376–379

    Article  PubMed  Google Scholar 

  • Klein M, Perfus-Barbeoch L, Frelet A, Gaedeke N, Reinhardt D, Mueller-Roeber B, Martinoia E, Forestier C (2003) The plant multidrug resistance ABC transporter AtMRP5 is involved in guard cell hormonal signalling and water use. Plant J 33:119–129

    Article  PubMed  CAS  Google Scholar 

  • Kubo Y, Xue YB, Nakatsuka A, Mathooko FM, Inaba A, Nakamura R (2000) Expression of a water stress-induced polygalacturonase gene in harvested cucumber fruit. J Japan Soc Hortic Sci 69:273–279

    Article  CAS  Google Scholar 

  • Lan LF, Li MN, Lai Y, Xu WY, Kong ZS, Ying K, Han B, Xue YB (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

    Article  PubMed  CAS  Google Scholar 

  • Laskowski MJ, Dreher KA, Gehring MA, Abel S, Gensler AL, Sussex IM (2002) FQR1, a novel primary auxin-response gene, encodes a flavin mononucleotide-binding quinone reductase. Plant Physiol 128:578–590

    Article  PubMed  CAS  Google Scholar 

  • Lee WY, Hong JK, Kim CY, Chun HJ, Park HC, Kim JC, Yun DJ, Chung WS, Lee SH, Lee SY, Cho MJ, Lim CO (2003) Over-expressed rice ADP-ribosylation factor 1 (RARF1) induces pathogenesis-related genes and pathogen resistance in tobacco plants. Physiol Plant 119:573–581

    Article  CAS  Google Scholar 

  • Lei Y, Yina C, Li C (2006) Differences in some morphological, physiological, and biochemical responses to drought stress in two contrasting populations of Populus przewalskii. Physiol Plant 127:182–191

    Article  CAS  Google Scholar 

  • Li ZC, Liu WX, Zhao DL (2001) Comparison of growing tendency during young seedling between paddy rice and upland rice under PEG water stress. J China Agric University 6:16–20

    Google Scholar 

  • Li XP, Tian AG, Luo GZ, Gong ZZ, Zhang JS, Chen SY (2005a) Soybean DRE-binding transcription factors that are responsive to abiotic stresses. Theor Appl Genet 110:1355–1362

    Article  PubMed  CAS  Google Scholar 

  • Li ZC, Mu P, Li CP, Zhang HL, Li ZK, Gao YM, Wang XK (2005b) QTL mapping of root traits in a doubled haploid population from a cross between upland and lowland japonicarice in three environments. Theor Appl Genet 110:1244–1252

    Article  PubMed  CAS  Google Scholar 

  • Lian HL, Yu X, Lane D, Sun WN, Tang ZC, Su WA (2006) Upland rice and lowland rice exhibited different PIP expression under water deficit and ABA treatment. Cell Res 16:651–660

    Article  PubMed  CAS  Google Scholar 

  • Ling ZM, Li ZC, Yu R, Mu P (2002) Agronomic root characters of upland rice and paddy rice (Oryza sativa L.). J China Agric University 7:7–11

    Google Scholar 

  • Lorence A, Chevone BI, Mendes P, Nessler CL (2004) myo-Inositol oxygenase offers a possible entry point into plant ascorbate biosynthesis. Plant Physiol 134:1200–1205

    Article  PubMed  CAS  Google Scholar 

  • Maestri E, Klueva N, Perrotta C, Gulli M, Nguyen HT, Marmiroli N (2002) Molecular genetics of heat tolerance and heat shock proteins in cereals. Plant Mol Biol 48:667–681

    Article  PubMed  CAS  Google Scholar 

  • Mahalingam R, Wang GJ, Knap HT (1999) Polygalacturonase and polygalacturonase inhibitor protein: gene isolation and transcription in Glycine max-Heterodera glycines interactions. Mol Plant Microbe Interact 12:490–498

    Article  PubMed  CAS  Google Scholar 

  • Mariaux JB, Bockel C, Salamini F, Bartels D (1998) Desiccation- and abscisic acid-responsive genes encoding major intrinsic proteins (MIPs) from the resurrection plant Craterostigma plantagineum. Plant Mol Biol 38:1089–1099

    Article  PubMed  CAS  Google Scholar 

  • Maruyama A, Kumagai Y, Morikawa K, Taguchi K, Hayashi H, Ohta T (2003) Oxidative-stress-inducible qorA encodes an NADPH-dependent quinone oxidoreductase catalysing a one-electron reduction in Staphylococcus aureus. Microbiology 149:389–398

    Article  PubMed  CAS  Google Scholar 

  • Mathieu M, Neutelings G, Hawkins S, Grenier E, David H (2003) Cloning of a pine germin-like protein (GLP) gene promoter and analysis of its activity in transgenic tobacco Bright Yellow 2 cells. Physiol Plant 117:425–434

    Article  PubMed  CAS  Google Scholar 

  • Minami E, Kuchitsu K, He DY, Kouchi H, Midoh N, Ohtsuki Y, Shibuya N (1996) Two novel genes rapidly and transiently activated in suspension-cultured rice cells by treatment with N-acetylchitoheptaose, a biotic elicitor for phytoalexin production. Plant Cell Physiol 37:563–567

    PubMed  CAS  Google Scholar 

  • Mohamed EA, Iwaki T, Munir I, Tamoi M, Shigeoka S, Wadano A (2003) Overexpression of bacterial catalase in tomato leaf chloroplasts enhances photo-oxidative stress tolerance. Plant Cell Environ 26:2037–2046

    Article  CAS  Google Scholar 

  • Munne-Bosch S (2005) The role of alpha-tocopherol in plant stress tolerance. J Plant Physiol 162:743–748

    Article  PubMed  CAS  Google Scholar 

  • Noventa-Jordao MA, Couto RM, Goldman MHS, Aguirre J, Iyer S, Caplan A, Terenzi HF, Goldman GH (1999) Catalase activity is necessary for heat-shock recovery in Aspergillus nidulans germlings. Microbiology 145:3229–3234

    PubMed  CAS  Google Scholar 

  • Ohnishi T, Sugahara S, Yamada T, Kikuchi K, Yoshiba Y, Hirano HY, Tsutsumi N (2005) OsNAC6, a member of the NAC gene family, is induced by various stresses in rice. Genes Genet Syst 80:135–139

    Article  PubMed  CAS  Google Scholar 

  • O’Toole JC, Cruz RT (1980) Response of leaf water potential, stomatal resistance, and leaf rolling to water stress. Plant Physiol 65:428–432

    PubMed  Google Scholar 

  • Overbeeke N, Fellinger AJ, Toonen MY, van Wassenaar D, Verrips CT (1989) Cloning and nucleotide sequence of the α-galactosidase cDNA from Cyamopsis tetragonoloba (guar). Plant Mol Biol 13:541–550

    Article  PubMed  CAS  Google Scholar 

  • Ozturk ZN, Talame V, Deyholos M, Michalowski CB, Galbraith DW, Gozukirmizi N, Tuberosa R, Bohnert HJ (2002) Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley. Plant Mol Biol 48:551–573

    Article  CAS  Google Scholar 

  • Pandey GK, Gran JJ, Cheong YH, Kim BG, Li LG, Luan S (2005) ABR1, an APETALA2-domain transcription factor that functions as a repressor of ABA response in Arabidopsis. Plant Physiol 139:1185–1193

    Article  PubMed  CAS  Google Scholar 

  • Passardi F, Longet D, Penel C, Dunand C (2004) The class III peroxidase multigenic family in rice and its evolution in land plants. Phytochemistry 65:1879–1893

    Article  PubMed  CAS  Google Scholar 

  • Pennycooke JC, Jones ML, Stushnoff C (2003) Down-regulating alpha-galactosidase enhances freezing tolerance in transgenic petunia. Plant Physiol 133:901–909

    Article  PubMed  CAS  Google Scholar 

  • Pukacka S, Wojkiewicz E (2002) Carbohydrate metabolism in Norway maple and sycamore seeds in relation to desiccation tolerance. J Plant Physiol 159:273–279

    Article  CAS  Google Scholar 

  • Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, 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

    Article  PubMed  CAS  Google Scholar 

  • Ramanjulu S, Bartels D (2002) Drought- and desiccation-induced modulation of gene expression in plants. Plant Cell Environ 25:141–151

    Article  PubMed  CAS  Google Scholar 

  • Recalcati S, Tacchini L, Alberghini A, Conte D, Cairo G (2003) Oxidative stress-mediated down-regulation of rat hydroxyacid oxidase 1, a liver-specific peroxisomal enzyme. Hepatology 38:1159–1166

    Article  PubMed  CAS  Google Scholar 

  • Reddy AR, Ramakrishna W, Sekhar AC, Ithal N, Babu PR, Bonaldo MF, Soares MB, Bennetzen JL (2002) Novel genes are enriched in normalized cDNA libraries from drought-stressed seedlings of rice (Oryza sativa L. subsp. indica cv. Nagina 22). Genome 45:204–211

    Article  PubMed  CAS  Google Scholar 

  • Rouquie D, Tournaire-Roux C, Szponarski W, Rossignol M, Doumas P (1998) Cloning of the V-ATPase subunit G in plant: functional expression and sub-cellular localization. FEBS Lett 437:287–292

    Article  PubMed  CAS  Google Scholar 

  • Rowland O, Ludwig AA, Merrick CJ, Baillieul F, Tracy FE, Durrant WE, Fritz-Laylin L, Nekrasov V, Sjolander K, Yoshioka H, Jones JD (2005) Functional analysis of Avr9/Cf-9 rapidly elicited genes identifies a protein kinase, ACIK1, that is essential for full Cf-9–dependent disease resistance in tomato. Plant Cell 17:295–310

    Article  PubMed  CAS  Google Scholar 

  • Sawada K, Hasegawa M, Tokuda L, Kameyama J, Kodama O, Kohchi T, Yoshida K, Shinmyo A (2004) Enhanced resistance to blast fungus and bacterial blight in transgenic rice constitutively expressing OsSBP, a rice homologue of mammalian selenium-binding proteins. Biosci Biotechnol Biochem 68:873–880

    Article  PubMed  CAS  Google Scholar 

  • Schindelman G, Morikami A, Jung J, Baskin TI, Carpita NC, Derbyshire P, McCann MC, Benfey PN (2001) COBRA encodes a putative GPI-anchored protein, which is polarly localized and necessary for oriented cell expansion in Arabidopsis. Genes Dev 9:1115–1127

    Article  Google Scholar 

  • Seo HS, Song JT, Cheong JJ, Lee YH, Lee YW, Hwang I, Lee JS, Choi YD (2001) Jasmonic acid carboxyl methyltransferase: a key enzyme for jasmonate-regulated plant responses. Proc Natl Acad Sci USA 98:4788–4793

    Article  PubMed  CAS  Google Scholar 

  • Shao HB, Liang ZS, Shao MA (2005) LEA proteins in higher plants: structure, function, gene expression and regulation. Colloids Surf B Biointerfaces 45:131–135

    Article  CAS  Google Scholar 

  • Sharma P, Dubey RS (2005) Drought induces oxidative stress and enhances the activities of antioxidant enzymes in growing rice seedlings. Plant Growth Regul 46:209–221

    Article  CAS  Google Scholar 

  • Shen SH, Sharma A, Komatsu S (2003a) Characterization of proteins responsive to gibberellin in the leaf-sheath of rice (Oryza sativa L.) seedling using proteome analysis. Biol Pharm Bull 26:129–136

    Article  PubMed  CAS  Google Scholar 

  • Shen YG, Yan DQ, Zhang WK, Du BX, Zhang JS, Liu Q, Chen SY (2003b) Novel halophyte EREBP/AP2-type DNA binding protein improves salt tolerance in transgenic tobacco. Acta Bot Sin 45:82–87

    CAS  Google Scholar 

  • Shigyo M, Hasebe M, Ito M (2006) Molecular evolution of the AP2 subfamily. Gene 366:256–265

    Article  PubMed  CAS  Google Scholar 

  • Skibbe DS, Liu F, Wen TJ, Yandeau MD, Cui X, Cao J, Simmons CR, Schnable PS (2002) Characterization of the aldehyde dehydrogenase gene families of Zea mays and Arabidopsis. Plant Mol Biol 48:751–764

    Article  PubMed  CAS  Google Scholar 

  • Sunkar R, Bartels D, Kirch HH (2003) Overexpression of a stress-inducible aldehyde dehydrogenase gene from Arabidopsis thaliana in transgenic plants improves stress tolerance. Plant J 35:452–464

    Article  PubMed  CAS  Google Scholar 

  • Tang W, Charles TM, Newton RJ (2005) Overexpression of the pepper transcription factor CaPF1 in transgenic virginia pine (Pinus virginiana mill.) confers multiple stress tolerance and enhances organ growth. Plant Mol Biol 59:603–617

    Article  PubMed  CAS  Google Scholar 

  • Tran LSP, Nakashima K, Sakuma Y, Simpson SD, Fujita Y, Maruyama K, Fujita M, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2004) Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. Plant Cell 16:2481–2498

    Article  PubMed  CAS  Google Scholar 

  • Truernit E, Schmid J, Epple P, Illig J, Sauer N (1996) The sink-specific and stress-regulated Arabidopsis STP4 gene: enhanced expression of a gene encoding a monosaccharide transporter by wounding, elicitors, and pathogen challenge. Plant Cell 8:2169–2182

    Article  PubMed  CAS  Google Scholar 

  • Tsuji N, Hirayanagi N, Iwabe O, Namba T, Tagawa M, Miyamoto S, Miyasaka H, Takagi M, Hirata K, Miyamoto K (2003) Regulation of phytochelatin synthesis by zinc and cadmium in marine green alga, Dunaliella tertiolecta. Phytochemistry 62:453–459

    Article  PubMed  CAS  Google Scholar 

  • Van Loon LC, Van Strien EA (1999) The families of pathogenesis-related proteins, their activities, and comparative analysis of PR-1 type proteins. Physiol Mol Plant Pathol 55:85–97

    Article  Google Scholar 

  • Veena Reddy VS, Sopory SK (1999) Glyoxalase I from Brassica juncea: molecular cloning, regulation and its over-expression confer tolerance in transgenic tobacco under stress. Plant J 17:385–396

    Article  Google Scholar 

  • Wang HQ, Bouman BAM, Zhao DL, Wang CG, Moya PF (2002) Aerobic rice in northern China: opportunities and challenges. In: Bouman BAM, Hengsdijk H, Hardy B, Bindraban PS, Tuong TP, Ladha JK (eds) Water-wise rice production. International Rice Research Institute Los Banos, Philippines, pp 143–154

    Google Scholar 

  • Wang H, Huang ZJ, Chen Q, Zhang ZJ, Zhang HB, Wu YM, Huang DF, Huang RF (2004) Ectopic overexpression of tomato JERF3 in tobacco activates downstream gene expression and enhances salt tolerance. Plant Mol Biol 55:183–192

    Article  PubMed  CAS  Google Scholar 

  • Wubben JP, Lawrence CB, deWit P (1996) Differential induction of chitinase and 1,3-beta-glucanase gene expression in tomato by Cladosporium fulvum and its race-specific elicitors. Physiol Mol Plant Pathol 48:105–116

    Article  CAS  Google Scholar 

  • Yi SY, Kim JH, Joung YH, Lee S, Kim WT, Yu SH, Choi D (2004) The pepper transcription factor CaPF1 confers pathogen and freezing tolerance in Arabidopsis. Plant Physiol 136:2862–2874

    Article  PubMed  CAS  Google Scholar 

  • Zheng J, Zhao JF, Tao YZ, Wang JH, Liu YJ, Fu JJ, Jin Y, Gao P, Zhang JP, Bai YF, Wang GY (2004) Isolation and analysis of water stress induced genes in maize seedlings by subtractive PCR and cDNA macroarray. Plant Mol Biol 55:807–823

    PubMed  CAS  Google Scholar 

  • Zhu JK (2000) Genetic analysis of plant salt tolerance using Arabidopsis. Plant Physiol 124:941–948

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

The authors thank Dr. Nanfei Xu (BASF Plant Science, USA) for his kind assistance in the analysis of the cDNA microarray, pre-review and helpful suggestions; This work was supported by the State Key Basic Research and Development Plan of China (2003CB114301), the Specialized Research Fund for the Doctoral Program of Higher Education of ministry of education of China (20030019004) and National Natural Science Foundation of China (30250009).

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  1. Key Lab of Crop Genomics and Genetic Improvement of Ministry of Agriculture, Key Lab of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China

    Haiguang Wang, Hongliang Zhang, Fenghua Gao, Junxia Li & Zichao Li

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  1. Haiguang Wang
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  2. Hongliang Zhang
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  3. Fenghua Gao
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  4. Junxia Li
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  5. Zichao Li
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Correspondence to Zichao Li.

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Communicated by A. Graner.

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Wang, H., Zhang, H., Gao, F. et al. Comparison of gene expression between upland and lowland rice cultivars under water stress using cDNA microarray. Theor Appl Genet 115, 1109–1126 (2007). https://doi.org/10.1007/s00122-007-0637-7

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  • DOI: https://doi.org/10.1007/s00122-007-0637-7

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