Skip to main content
SpringerLink
Log in

Isolation and Analysis of Cold Stress Inducible Genes in Zea mays by Suppression Subtractive Hybridization and cDNA Macroarray

  • Published:
Plant Molecular Biology Reporter Aims and scope Submit manuscript

Abstract

In order to understand the molecular and cellular mechanisms underlying cold stress conditions (4°C) in maize seedlings, a forward subtractive cDNA library was constructed using the suppression subtractive hybridization (SSH) technique. Through the “Virtual” Northern blot analysis, 893 positive clones were screened from a total 1,200 clones in the subtractive cDNA library. After sequencing 528 randomly chosen cDNA clones, 213 uniquely expressed sequence tags (ESTs) were obtained by clustering and blast analysis, which included transcripts that had previously been reported as responsive to stress as well as some functionally unknown transcripts. Based on a list of functional Arabidopsis protein categories, the ESTs with significant protein similarity were sorted into ten functional categories. A cDNA macroarray containing the 213 unique ESTs was used to monitor the spatial and temporal distribution of gene expression in maize seedlings during cold stress. The results showed that 118 ESTs were induced by cold-stress in maize seedlings and 66 ESTs identified in the leaves and 89 ESTs in the roots. Hierarchical cluster analysis indicated that the expression profiles of cold stress inducible ESTs in the leaves were different from that observed in the roots. Moreover, some induced genes were related to sugar synthesis and reestablishment of high rates of photosynthesis. In addition, Northern blot analysis validated well the cDNA macroarray data.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Chen W, Provart NJ, Glazebrook J, et al. Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. Plant Cell 2002;14(3):559–74. doi:10.1105/tpc.010410.

    Article  PubMed  CAS  Google Scholar 

  • Chinnusamy V, Zhu J, Zhu JK. Gene regulation during cold acclimation in plants. Physiol Plant 2006;126:52–61. doi:10.1111/j.1399-3054.2006.00596.x.

    Article  CAS  Google Scholar 

  • Cook D, Fowler S, Fiehn O, Thomashow MF. A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis. Proc Natl Acad Sci USA 2004;101(42):15243–8. doi:10.1073/pnas.0406069101.

    Article  PubMed  CAS  Google Scholar 

  • Delauney AJ, Verma DPS. Proline biosynthesis and osmoregulation in plants. Plant J 1993;4:215–23. doi:10.1046/j.1365-313X.1993.04020215.x.

    Article  CAS  Google Scholar 

  • De los Reyes BG, McGrath JM. Cultivar-specific seedling vigor and expression of a putative oxalate oxidase germin-like protein in sugar beet (Beta vulgaris L.). Theor Appl Genet 2003;107(1):54–61.

    Google Scholar 

  • Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, et al. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 1996;93(12):6025–30. doi:10.1073/pnas.93.12.6025.

    Article  PubMed  CAS  Google Scholar 

  • Fowler S, Thomashow MF. Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 2002;14(8):1675–90. doi:10.1105/tpc.003483.

    Article  PubMed  CAS  Google Scholar 

  • Hazen SP, Wu Y, Kreps JA. Gene expression profiling of plant responses to abiotic stress. Funct Integr Genomics 2003;3(3):105–11. doi:10.1007/s10142-003-0088-4.

    Article  PubMed  CAS  Google Scholar 

  • Hurry VM, Malmberg G, Gardestrom P, Oquist G. Effects of a short-term shift to low temperature and of long-term cold hardening on photosynthesis and ribulose-1,5-bisphosphate carboxylase/oxygenase and sucrose phosphate synthase activity in leaves of winter rye (Secale cereale L.). Plant Physiol 1994;106(3):983–90.

    PubMed  CAS  Google Scholar 

  • Hurry VM, Strand A, Tobiaeson M, Gardestrom P, Oquist G. Cold hardening of spring and winter wheat and rape results in differential effects on growth, carbon metabolism, and carbohydrate content. Plant Physiol 1995;109(2):697–706.

    PubMed  CAS  Google Scholar 

  • Kaplan F, Kopka J, Haskell DW, Zhao W, Schiller KC, Gatzke N, et al. Exploring the temperature-stress metabolome of Arabidopsis. Plant Physiol 2004;136(4):4159–68. doi:10.1104/pp.104.052142.

    Article  PubMed  CAS  Google Scholar 

  • Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, et al. Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 2001;13(4):889–905.

    Article  PubMed  CAS  Google Scholar 

  • Kay R, Chan A, Daly M, Mcpherson J. Duplication of CaMV 35S promoter sequences creates a strong enhancer for plant genes. Science 1987;236:1299–302. doi:10.1126/science.236.4806.1299.

    Article  PubMed  CAS  Google Scholar 

  • Kishitani S, Watanabe K, Yasuda S, Arakawa K, Takabe T. Accumulation of glycinebetaine during cold acclimation and freezing tolerance in leaves of winter and spring barley plants. Plant Cell Environ 1994;17:89–95. doi:10.1111/j.1365-3040.1994.tb00269.x.

    Article  CAS  Google Scholar 

  • Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, Harper JF. Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 2002;130(4):2129–41. doi:10.1104/pp.008532.

    Article  PubMed  CAS  Google Scholar 

  • Lee DG, Ahsan N, Lee SH, Kang KY, Lee JJ, Lee BH. An approach to identify cold- induced low-abundant proteins in rice leaf. C R Biol 2007;330(3):215–25. doi:10.1016/j.crvi.2007.01.001.

    Article  PubMed  CAS  Google Scholar 

  • Levitt J. Responses of plants to environmental stresses, 2nd edn. New York: Academic Press; 1980.

    Google Scholar 

  • Nakashima K, Yamaguchi-Shinozaki K. Regulons involved in osmotic stress-responsive and cold stress-responsive gene expression in plants. Physiol Plant 2006;126:62–71. doi:10.1111/j.1399-3054.2005.00592.x.

    Article  CAS  Google Scholar 

  • Oh SJ, Song SI, Kim YS, Jang HJ, Kim SY, Kim M, et al. Arabidopsis CBF3/DREB1A and ABF3 in transgenic rice increased tolerance to abiotic stress without stunting growth. Plant Physiol 2005;138(1):341–51. doi:10.1104/pp.104.059147.

    Article  PubMed  CAS  Google Scholar 

  • Oztur ZN, Talame V, Deyholos M, Michalowski CB, Galbraith DW, Gozukirmizi N, et al. Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley. Plant Mol Biol 2002;48(5–6):551–73. doi:10.1023/A:1014875215580.

    Article  PubMed  Google Scholar 

  • Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, et al. 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 2003;133(4):1755–67. doi:10.1104/pp.103.025742.

    Article  PubMed  CAS  Google Scholar 

  • Rishi AS, Munir S, Kapur V, Nelson ND, Goyal A. Identification and analysis of safener-inducible expressed sequence tags in Populus using a cDNA microarray. Planta 2004;220(2):296–306. doi:10.1007/s00425-004-1356-9.

    Article  PubMed  CAS  Google Scholar 

  • Rolland F, Baena-Gonzalez E, Sheen J. Sugar sensing and signaling in plants: conserved and novel mechanisms. Annu Rev Plant Biol 2006;57:675–709. doi:10.1146/annurev.arplant.57.032905.105441.

    Article  PubMed  CAS  Google Scholar 

  • Saijo Y, Hata S, Kyozuka J, Shimamoto K, Izui K. Over-expression of a single Ca2+-dependent protein kinase confers both cold and salt/drought tolerance on rice plants. Plant J 2000;23(3):319–27. doi:10.1046/j.1365-313x.2000.00787.x.

    Article  PubMed  CAS  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T. Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 1989.

    Google Scholar 

  • Seki M, Narusaka M, Abe H, Kasuga M, Yamaguchi-Shinozaki K, Carninci P, et al. Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 2001;13(1):61–72.

    Article  PubMed  CAS  Google Scholar 

  • Seki M, Narusaka M, Ishida J, et al. Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 2002;31(3):279–92. doi:10.1046/j.1365-313X.2002.01359.x.

    Article  PubMed  CAS  Google Scholar 

  • Shi C, Thümmler F, Melchinger AE, Wenzel G, Lübberstedt T. Comparison of transcript profiles between near-isogenic maize lines in association with SCMV resistance based on unigene-microarrays. Plant Sci 2006;170:159–69. doi:10.1016/j.plantsci.2005.08.016.

    Article  CAS  Google Scholar 

  • Shinozaki K, Yamaguchi-Shinozaki K. Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways. Curr Opin Plant Biol 2000;3(3):217–23.

    PubMed  CAS  Google Scholar 

  • Sreenivasulu N, Radchuk V, Strickert M, Miersch O, Weschke W, Wobus U. Gene expression patterns reveal tissue-specific signaling networks controlling programmed cell death and ABA- regulated maturation in developing barley seeds. Plant J 2006;47(2):310–27. Erratum in: Plant J 47(6):987. doi:10.1111/j.1365-313X.2006.02789.x

    Article  PubMed  CAS  Google Scholar 

  • Sreenivasulu N, Sopory SK, Kavi Kishor PB. Deciphering the regulatory mechanisms of abiotic stress tolerance in plants by genomic approaches. Gene 2007;388(1–2):1–13. doi:10.1016/j.gene.2006.10.009.

    Article  PubMed  CAS  Google Scholar 

  • Steponkus PL. Role of plasma membrane in freezing injury and cold acclimation. Annu Rev Plant Physiol 1984;35:543–84. doi:10.1146/annurev.pp.35.060184.002551.

    Article  CAS  Google Scholar 

  • Stitt M, Hurry V. A plant for all seasons: alterations in photosynthetic carbon metabolism during cold acclimation in Arabidopsis. Curr Opin Plant Biol 2002;5(3):199–206. doi:10.1016/S1369-5266(02)00258-3.

    Article  PubMed  CAS  Google Scholar 

  • Thomashow MF. Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu Rev Plant Physiol Plant Mol Biol 1999;50:571–99. doi:10.1146/annurev.arplant.50.1.571.

    Article  PubMed  CAS  Google Scholar 

  • Thomashow MF. So what’s new in the field of plant cold acclimation? Lots! Plant Physiol 2001;125(1):89–93. doi:10.1104/pp.125.1.89.

    Article  CAS  Google Scholar 

  • Van Buskirk HA, Thomashow MF. Arabidopsis transcription factors regulating cold acclimation. Physiol Plant 2006;126:72–80. doi:10.1111/j.1399-3054.2006.00625.x.

    Article  Google Scholar 

  • Wang Y, Mi GH, Chen FJ, Zhang FS. Genotypic difference in nitrogen efficiency of five maize inbred lines as affected by nitrate levels. Chin J Appl Environ Biol 2002;8(4):361–5.

    CAS  Google Scholar 

  • Wanner LA, Junttila O. Cold-induced freezing tolerance in Arabidopsis. Plant Physiol 1999;120(2):391–400. doi:10.1104/pp.120.2.391.

    Article  PubMed  CAS  Google Scholar 

  • Xin Z, Browse J. Cold comfort farm: the acclimation of plants to freezing temperatures. Plant Cell Environ 2000;23:893–902. doi:10.1046/j.1365-3040.2000.00611.x.

    Article  Google Scholar 

  • Yang GP, Ross DT, Kuang WW, Brown PO, Weigel RJ. Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes. Nucleic Acids Res 1999;27(6):1517–23. doi:10.1093/nar/27.6.1517.

    Article  PubMed  CAS  Google Scholar 

  • Yang TW, Xie XD, Zhang LJ, Zhang TG, Zhang H, Xu SJ, et al. Transcriptional regulation network of cold-responsive genes in higher plants. Plant Sci 2005;169(6):987–95. doi:10.1016/j.plantsci.2005.07.005.

    Article  CAS  Google Scholar 

  • Zheng J, Zhao J, Tao Y, Wang J, Liu Y, Fu J, et al. Isolation and analysis of water stress induced genes in maize seedlings by subtractive PCR and cDNA macroarray. Plant Mol Biol 2004;55(6):807–23.

    PubMed  CAS  Google Scholar 

  • Zheng J, Zhao JF, Zhang JP, Fu JJ, Gou MY, Dong ZG, et al. Comparative expression profiles in maize genes from a water stress-specific cDNA macroarray in response to high-salinity, cold or abscisic acid. Plant Sci 2006;170:1125–32. doi:10.1016/j.plantsci.2006.01.019.

    Article  CAS  Google Scholar 

  • Zhu J, Dong CH, Zhu JK. Interplay between cold-responsive gene regulation, metabolism and RNA processing during plant cold acclimation. Curr Opin Plant Biol 2007;10(3):290–5. doi:10.1016/j.pbi.2007.04.010.

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank Dr. Hongya Gu (Peking University, China) for her kind help in the preparation of the cDNA macroarray. This work was supported by the National High-tech Program (2006AA10A106) and a key project foundation from the Ministry of Education in China.

Author information

Authors and Affiliations

  1. Department of Seed Sciences and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100094, China

    Ying Zhang, Junjie Fu, Riliang Gu, Jianhua Wang, Xiaoping Chen & Jinping Jia

  2. Institute of Crop Sciences and National Plant Research Center (Beijing), Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Jinpeng Zhang & Guoying Wang

Authors
  1. Ying Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Junjie Fu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Riliang Gu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jianhua Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xiaoping Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jinping Jia
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jinpeng Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Guoying Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Guoying Wang.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhang, Y., Fu, J., Gu, R. et al. Isolation and Analysis of Cold Stress Inducible Genes in Zea mays by Suppression Subtractive Hybridization and cDNA Macroarray. Plant Mol Biol Rep 27, 38–49 (2009). https://doi.org/10.1007/s11105-008-0055-2

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11105-008-0055-2

Keywords

Search

Navigation