Plant Molecular Biology

, Volume 48, Issue 5–6, pp 551–573 | Cite as

Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley

  • Z. Neslihan Ozturk
  • Valentina Talamé
  • Michael Deyholos
  • Christine B. Michalowski
  • David W. Galbraith
  • Nermin Gozukirmizi
  • Roberto Tuberosa
  • Hans J. Bohnert


Responses to drought and salinity in barley (Hordeum vulgare L. cv. Tokak) were monitored by microarray hybridization of 1463 DNA elements derived from cDNA libraries of 6 and 10 h drought-stressed plants. Functional identities indicated that many cDNAs in these libraries were associated with drought stress. About 38% of the transcripts were novel and functionally unknown. Hybridization experiments were analyzed for drought- and salinity-regulated sequences, with significant changes defined as a deviation from the control exceeding 2.5-fold. Responses of transcripts showed stress-dependent expression patterns and time courses. Nearly 15% of all transcripts were either up- or down-regulated under drought stress, while NaCl led to a change in 5% of the transcripts (24 h, 150 mM NaCl). Transcripts that showed significant up-regulation under drought stress are exemplified by jasmonate-responsive, metallothionein-like, late-embryogenesis-abundant (LEA) and ABA-responsive proteins. Most drastic down-regulation in a category was observed for photosynthesis-related functions. Up-regulation under both drought and salt stress was restricted to ESTs for metallothionein-like and LEA proteins, while increases in ubiquitin-related transcripts characterized salt stress. A number of functionally unknown transcripts from cDNA libraries of drought-stressed plants showed up-regulation by drought but down-regulation by salt stress, documenting how precisely transcript profiles report different growth conditions and environments.

drought stress Hordeum vulgare microarray hybridization salinity stress stress-regulated transcripts 


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  1. Acevedo, E. 1987. Gas exchange of barley and wheat genotypes under drought. In: Cereal Improvement Program Annual Report 1987. ICARDA, Aleppo, Syria, pp. 101-116.Google Scholar
  2. Altinkut, A., Kazan, K., Ipekci, Z. and Gozukirmizi, N. 2001. Tolerance to paraquat is correlated with the traits associated with water stress tolerance in segregating F2 populations of barley and wheat. Euphytica, 121: 81-86.Google Scholar
  3. Amtmann, A. and Sanders, D. 1999. Mechanisms of Na+ uptake by plant cells. Adv. Bot. Res. 29: 75-112.Google Scholar
  4. Apse, M.P., Aharon, G.S., Snedden, W.A. and Blumwald, E. 1999. Salt tolerance conferred by overexpression of a vacuolar Na+/H+-antiport in Arabidopsis. Science 285: 1256-1258.Google Scholar
  5. Bajaj, S., Targolli, J., Liu-Lifei, Ho, T.H.D. and Wu, R. 2000. Transgenic approaches to increase dehydration-stress tolerance in plants. Mol. Breed. 5: 493-503.Google Scholar
  6. Blum, A. 1988. Plant Breeding for Stress Environments, CRC Press, Boca Raton, FL.Google Scholar
  7. Bohnert, H.J. and Bressan, R.A. 2001. Abiotic stresses, plant reactions, and approaches towards improving stress tolerance. In: J. Nössberger (Ed.) Crop Science: Progress and Prospects, CABI International, Wallingford, UK, pp. 81-100.Google Scholar
  8. Borel, C., Simonneau, T., This, D. and Tardieu, F. 1997. Stomatal conductance and ABA concentration in the xylem sap of barley lines of contrasting genetic origins. Aust. J. Plant Physiol. 24: 607-615.Google Scholar
  9. Bray, E. 1997. Plant responses to water deficit. Trends Plant Sci. 2: 48-54.Google Scholar
  10. Ceccarelli, S. and Grando, S. 1996. Drought as a challenge for the plant breeder. Plant Growth Regul. 20: 149-155.Google Scholar
  11. Ceccarelli, S., Grando, S. and Impiglia, A. 1998. Choice of selection strategy in breeding barley for stress enviroments. Euphytica 103: 307-318.Google Scholar
  12. Close, T.J. 1997. Dehydrins: a commonality in the response of plants to dehydration and low temperature. Physiol. Plant. 100: 291-296.Google Scholar
  13. Close, T.J., Kortt, A.A. and Chandler, P.M. 1989. A cDNAbased comparison of dehydration-induced proteins (dehydrins) in barley and corn. Plant Mol. Biol. 13: 95-108.Google Scholar
  14. Close, T.J., Fenton, R.D. and Moonan, F. 1993. A view of plant dehydrins using antibodies specific to the carboxy-terminal peptide. Plant Mol. Biol. 23: 279-286.Google Scholar
  15. Conti, S., Landi, P., Sanguineti, M.C., Stefanelli, S. and Tuberosa, R. 1994. Genetic and environmental effects on abscisic acid accumulation in leaves of field-grown maize. Euphytica 78: 81-89.Google Scholar
  16. Delauney, A.J. and Verma, D.P.S. 1993. Proline biosynthesis and osmoregulation in plants. Plant J. 4: 215-223.Google Scholar
  17. Deyholos, M. and Galbraith, D.W. 2001. High-density microarrays for gene expression analysis. Cytometry 43: 229-238.Google Scholar
  18. Forster, B.P., Ellis, R.P., Thomas, W.T., Newton, A.C., Tuberosa, R., This, D., el-Enein, R.A., Bahri, M.H. and Ben Salem, M. 2000. The development and application of molecular markers for abiotic stress tolerance in barley. J. Exp. Bot. 51: 18-27.Google Scholar
  19. Girke, T., Todd, J., Ruuska, S., White, J., Benning, C. and Ohlrogge, J. 2000. Microarray analysis of developing Arabidopsis seeds. Plant Physiol. 124: 1570-1581.Google Scholar
  20. Greenway, H., 1962. Plant response to saline substrates. Growth and ion uptake of several varieties of Hordeum during and after sodium chloride treatment. Aust. J. Biol. Sci. 15: 16-38.Google Scholar
  21. Greenway, H. and Munns, R., 1980. Mechanisms of salt tolerance in non-halophytes. Annu. Rev. Plant Physiol. 31: 149-190.Google Scholar
  22. Grover, A. 1999. A novel approach for raising salt tolerant transgenic plants based on altering stress signalling through Ca++/calmodulin-dependent protein phosphatase calcineurin. Curr. Sci. 76: 136-137.Google Scholar
  23. Grumet, R., Albrechtensen, R.S. and Hanson, A.D. 1987. Growth and yield of barley isopopulations differing in solute potential. Crop Sci. 27: 119-130.Google Scholar
  24. Hasegawa, P.M., Bressan, R.A., Zhu, J.-K. and Bohnert, H.J. 2000. Molecular biology of salinity stress responses in higher plants. Annu. Rev. Plant Physiol Plant Mol. Biol. 51: 463-499.Google Scholar
  25. Hsieh, H.M., Liu, W.K., Cheng, A. and Huang, P.C. 1996. RNA expression patterns of a type 2 metallothionein-like gene from rice. Plant Mol. Biol. 32: 525-529.Google Scholar
  26. Hsieh, H.M., Liu, W.K. and Huang, P.C. 1995. A novel stressinducible metallothionein-like gene from rice. Plant Mol. Biol. 28: 381-389.Google Scholar
  27. Jaglo-Ottosen, K.R., Gilmour, S.J., Zarka, D.G., Schabenberger, O. and Thomashow, M.F. 1998. Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance. Science 280: 104-106.Google Scholar
  28. Kamalay, J.C. and Goldberg, R.B. 1980. Regulation of structural gene expression in tobacco. Cell 19: 935-946.Google Scholar
  29. 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. Nature Biotechnol. 17: 287-291.Google Scholar
  30. Kawasaki, S., Deyholos, M., Borchert, C., Brazille, S., Kawai, K., Galbraith, D.W. and Bohnert, H.J. 2001. Temporal succession of salt stress responses in rice by microarray analysis. Plant Cell 12: 889-905.Google Scholar
  31. Lane, B.G., Cuming, A.C., Fregeau, J., Carpita, N.C., Hurkman, W.J., Bernier, F., Dratweka-Kas, E. and Kennedy, T.D. 1992. Germin isoforms are discrete temporal markers of wheat development. Eur. J. Biochem. 209: 961-969.Google Scholar
  32. Levitt, J. 1980. Responses of Plants to Environmental Stress, 2nd ed. Academic Press, New York.Google Scholar
  33. Livak, K.J., Flood, S.J., Marmaro, J., Giusti,W. and Deetz, K. 1995. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe useful for detecting PCR product and nucleic acid hybridization. PCR Meth. Appl. 4: 357-362.Google Scholar
  34. Maleck, K., Levine, A., Eulgem, T., Morgan, A., Schmid, J., Lawton, K.A., Dangl, J.L. and Dietrich, R.A. 2000. The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nature Genet. 26: 403-410.Google Scholar
  35. Masgrau, C., Altabella, T., Farras, R., Flores, D., Thompson, A.J., Besford, R.T. and Tiburcio, A.F. 1997. Inducible overexpression of oat arginine decarboxylase in transgenic tobacco. Plant J. 11: 465-473.Google Scholar
  36. Matin, M.A., Brown, J.H. and Ferguson, H., 1989. Leaf water potential, relative water content, and diffusive resistance as screening techniques for drought resistance in barley. Agron. J. 81: 100-105.Google Scholar
  37. Munns, R. 1993. Physiological processes limiting plant-growth in saline soils: some dogmas and hypotheses. Plant Cell Envir. 16: 15-24.Google Scholar
  38. Munns, R., Passioura, J.B., Guo, J., Chazen, O. and Cramer, G.R. 2000. Water elations and leaf expansion: importance of timing. J. Exp. Bot. 51: 1495-1504.Google Scholar
  39. Nakashima, K., Kiyosue, T., Yamaguchi-Shinozaki, K. and Shinozaki, K. 1997. A nuclear gene, erd1, encoding a chloroplasttargeted Clp protease regulatory subunit homolog is not only induced by water stress but also developmentally up-regulated during senescence in Arabidopsis thaliana. Plant J. 12: 851-861.Google Scholar
  40. Powell, W., Caligari, P.D.S., Phillips, M.S. and Jinks, J. 1986. The measurement and interpretation of genotype by environment interaction in spring barley (Hordeum vulgare). Heredity 56: 255-262.Google Scholar
  41. Reymond, P. and Farmer, E.E. 1999. Jasmonate and salicylate as global signals for defense gene expression. Curr. Opin. Plant Biol. 1: 404-411.Google Scholar
  42. Reymond, P., Weber, H., Damond, M. and Farmer, E.E. 2000. Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis. Plant Cell 12: 707-719.Google Scholar
  43. Richards, R.A., Dennet, C.W., Qualset, C.O., Epstein, E., Norlyn, J.D. and Winslow, M.D. 1987. Variation in yield of grain and biomass in wheat, barley, and triticale in a salt-affected field. Field Crops Res. 15: 277-287.Google Scholar
  44. Richmond, T. and Somerville, S. 2000. Chasing the dream: plant EST microarrays. Curr. Opin. Plant Biol. 3: 108-116.Google Scholar
  45. Ruan, Y., Gilmore, J. and Conner, T. 1998. Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays. Plant J. 15: 821-833.Google Scholar
  46. Rus, A., Yokoi, S., Sharkhuu, A., Reddy, M., Lee, B.-H., Damsz, B., Sokolchik, I., Matsumoto, T., Barb, A.W., Koiwa, H., Zhu, J.-K., Bressan, R.A. and Hasegawa, P.M. 2001. AtHKT1 is a salt tolerance determinant that controls sodium entry into plant roots. Submitted for publication.Google Scholar
  47. Sanguineti, M.C., Tuberosa, R., Stefanelli, S., Noli, E., Blake, T.K. and Hayes, P.M. 1994. Utilization of a recombinant inbred population to localize QTLs for abscisic acid content in leaves of drought-stressed barley (Hordeum vulgare L.). Russ. J. Plant Physiol. 41: 572-576.Google Scholar
  48. Schachtman, D. and Liu,W. 1999. Molecular pieces to the puzzle of the interaction between potassium and sodium uptake in plants. Trends Plant Sci. 4: 281-287.Google Scholar
  49. Schenk, P.M., Kazan, K., Wilson, I., Anderson, J.P., Richmond.,T., Somerville, S.C. and Manners, J.M. 2000. Coordinated plant defense responses in Arabidopsis revealed by microarray analysis. Proc. Natl. Acad. Sci. USA 97: 21: 11655-11660.Google Scholar
  50. Schuchardt, J., Beule, D., Malik, A., Wolski, E., Eickhoff, H., Lehrach, H. and Herzel, H. 2000. Normalization strategies for cDNA microarrays. Nucl. Acids Res. 28: E47.Google Scholar
  51. Slavich, P.G., Read, B.J. and Cullis, B.R. 1990. Yield response of barley germplasm to field variation in salinity quantified using the EM-38. Aust. J. Exp. Agric. 30: 551-556.Google Scholar
  52. Smirnoff, N. and Bryant, J.A. 1999. DREB takes the stress out of growing up. Nature Biotechnol. 17: 229-230.Google Scholar
  53. Soyka, S. and Heyer, A.G. 1999. Arabidopsis knockout mutation of ADC2 gene reveals inducibility by osmotic stress. FEBS Lett. 458: 219-223.Google Scholar
  54. Stewart, C.R. and Voetberg, G. 1985. Relationship between stressinduced ABA and proline accumulations and ABA-induced proline accumulation in excised barley leaves. Plant Physiol. 79: 2-27.Google Scholar
  55. Stewart, C.R., Voetberg, G. and Rayapati, P.J. 1986. The effects of benzyladenine, cycloheximide, and cardycepin on wiltinginduced abscisic acid and proline accumulations and abscisic acid-and salt-induced proline accumulation in barley leaves. Plant Physiol. 82: 707.Google Scholar
  56. Teulat, B., Monneveux P., Wery, J., Borries, C., Souyris, I., Charrier, A. and This, D. 1997. Relationships between relative water content and growth parameters under water stress in barley: A QTL study. New Phytol. 137: 99-107.Google Scholar
  57. Thomas, J.C., DeArmond, R.L. and Bohnert, H.J. 1992. Influence of NaCl on growth, proline and phosphoenolpyruvate carboxylase levels in Mesembryanthenum crystallinum suspension cultures. Plant Physiol. 98: 626-631.Google Scholar
  58. Tuberosa, R., Sanguineti, M.C., Landi, P., Salvi, S., Casarini, E. and Conti, S. 1998. RFLP mapping of quantitative trait loci controlling abscisic acid concentration in leaves of drought-stressed maize (Zea mays L.). Theor. Appl. Genet. 97: 744-755.Google Scholar
  59. van Buuren, M., Salvi, S., Morgante, M., Serhani, B. and Tuberosa, R. 2002. Comparative genomic mapping between a 754 kb region flanking DREB1A in Arabidopsis thaliana and maize. Plant Mol. Biol., 48: 741-750.Google Scholar
  60. Voros, K., Feussner, I., Kuhn, H., Lee, J., Graner, A., Lobler, M., Parthier, B. and Wasternak, C. 1998. Characterization of a methyljasmonate-inducible lipoxygenase from barley. Eur. J. Biochem. 251: 36-44.Google Scholar
  61. Wang, R.C., Guegler, K., LaBrie, S.T., Crawford, N.M. and Wang, R.C. 2000. Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate. Plant Cell 12: 8: 1491-1509.Google Scholar
  62. Wierstra, I. and Kloppstech, K. 2000. Differential effects of methyljasmonate on the expression of the early light-inducible proteins and other light-related genes in barley. Plant Physiol. 124: 833-844.Google Scholar
  63. Xu, DP., Duan, X.L., Wang, B.Y., Hong, B.M., Ho, T.H.D., Wu, R., Xu, D.P., Duan, X.L., Wang, B.Y. and Hong, B.M. 1996. Expression of a late embryogenesis abundant protein gene, HVA1, from barley confers tolerance to water deficit and salt stress in transgenic rice. Plant Physiol. 110: 249-257.Google Scholar
  64. Yale, J. and Bohnert, H.J. 2001. Changes in gene expression in the yeast genome in response to salinity, temperature and oxidative stresses. J. Biol. Chem. 276: 15996-16007.Google Scholar
  65. 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.Google Scholar
  66. Yoshiba, Y., Kiyosue, T., Nakashima, K., Yamaguchi-Shinozaki, K. and Shinozaki, K. 1997. Regulation of levels of proline as an osmolyte in plants under water stress. Plant Cell Physiol. 38: 1095-1102.Google Scholar
  67. Zhang, JX., Klueva, N.Y., Wang, Z., Wu, R., Ho, T.H., Nguyen, H.T. and Ho, T.H.D. 2000. Genetic engineering for abiotic stress resistance in crop plants. In Vitro Cell Devel. Biol. Plant 36: 108-114.Google Scholar

Copyright information

© Kluwer Academic Publishers 2002

Authors and Affiliations

  • Z. Neslihan Ozturk
    • 1
    • 2
  • Valentina Talamé
    • 1
    • 3
  • Michael Deyholos
    • 4
  • Christine B. Michalowski
    • 1
  • David W. Galbraith
    • 4
  • Nermin Gozukirmizi
    • 2
  • Roberto Tuberosa
    • 3
  • Hans J. Bohnert
    • 1
  1. 1.Department of Biochemistry and Molecular BiophysicsUniversity of ArizonaTucsonUSA
  2. 2.TUBITAK, Marmara Research CenterResearch Institute for Genetic EngineeringTurkey
  3. 3.Department of Agroenvironmental Science and TechnologyUniversity of BolognaBolognaItaly
  4. 4.Departments of Plant Biology and of Crop SciencesUniversity of IllinoisUrbanaUSA

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