Skip to main content
SpringerLink
Log in

Analysis of the transcriptional response to Rice Yellow Mottle Virus infection in Oryza sativa indica and japonica cultivars

  • Original Paper
  • Published:
Molecular Genetics and Genomics Aims and scope Submit manuscript

Abstract

Several cDNA libraries were constructed using mRNA isolated from roots, panicles, cell suspensions and leaves of non-stressed Oryza sativa indica (IR64) and japonica (Azucena) plants, from wounded leaves, and from leaves of both cultivars inoculated with Rice Yellow Mottle Virus (RYMV). A total of 5549 cleaned expressed sequence tags (ESTs) were generated from these libraries. They were classified into functional categories on the basis of homology, and analyzed for redundancy within each library. The expression profiles represented by each library revealed great differences between indica and japonica backgrounds. EST frequencies during the early stages of RYMV infection indicated that changes in the expression of genes involved in energy metabolism and photosynthesis are differentially accentuated in susceptible and partially resistant cultivars. Mapping of these ESTs revealed that several co-localize with previously described resistance gene analogs and QTLs (quantitative trait loci).

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. 4A, B.
Fig. 5.

Similar content being viewed by others

References

  • Ahn S, Tanksley SD (1993) Comparative linkage maps of the rice and maize genomes. Proc Nat Acad Sci USA 90:7980–7984

    CAS  PubMed  Google Scholar 

  • Albar L, Lorieux M, Ahmadi N, Rimbault I, Pinel A, Sy AA, Fargette D, Ghesquière A (1998) Genetic basis and mapping of the resistance to rice yellow mottle virus. I. QTLs identification and relationship between resistance and plant morphology. Theor Appl Genet 97:1145–1154

    Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman D (1990) Basic local alignment search tool. J Mol Biol 215:402–410

    Article  Google Scholar 

  • Bakker W (1974) Characterisation and ecological aspects of rice yellow mottle virus in Kenya. PhD Thesis, Agricultural University, Wageningen, Netherlands

  • Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SE, Second G, McCouch SR, Tanksley SD (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138:1251–1274

    CAS  PubMed  Google Scholar 

  • Chen L, Zhang S, Beachy RN, Fauquet CM (1998) A protocol for consistent, large scale production of fertile transgenic rice plants. Plant Cell Rep 18:25–31

    Google Scholar 

  • Cook MG, Evans LT (1983) Some physiological aspects of the domestication and improvement of rice ( Oryza spp.). Field Crops Res 19:219–238

    Article  Google Scholar 

  • Cooke R, et al (1996) Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs. Plant J 9:101–124

    CAS  PubMed  Google Scholar 

  • Cushman JC, Bohnert HJ (2000) Genomic approaches to plant stress tolerance. Curr Opin Plant Biol 3:117–124

    CAS  PubMed  Google Scholar 

  • Delseny M (2003) Towards an accurate sequence of the rice genome. Curr Opin Plant Biol 6:101–105

    Article  CAS  PubMed  Google Scholar 

  • Ewing G, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research 8:186–194

    CAS  PubMed  Google Scholar 

  • Feng Q, et al (2002) Sequence and analysis of rice chromosome 4. Nature 420:316–320

    Article  CAS  PubMed  Google Scholar 

  • Goff SA, et al (2002) A draft sequence of the rice genome ( Oryza sativa L. ssp. japonica). Science 296:92–100

    Article  CAS  Google Scholar 

  • Good AG, Muench DG (1992) Purification and characterization of an anaerobically induced alanine aminotransferase from barley roots. Plant Physiol 99:1520–1525

    CAS  Google Scholar 

  • Ioannidou D, Lett JM, Pinel A, Assigbétse K, Brugidou C, Ghesquière A, Nicole M, Fargette D (2000) Responses of Oryza sativa japonica sub-species to infection with Rice Yellow Mottle Virus. Physiol Mol Plant Pathol 57:177–188

    Article  CAS  Google Scholar 

  • Jeong SW, Choi SM, Lee DS, Ahn SN, Hur Y, Chow WS, Park YI (2002) Differential susceptibility of photosynthesis to light-chilling stress in rice ( Oryza sativa L.) depends on the capacity for photochemical dissipation of light. Molecules Cells 13:419–428

    CAS  Google Scholar 

  • McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS, Coffman WR, Tanksley SD (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76:815–829

    CAS  Google Scholar 

  • Moore G, Devos KM, Wang Z, Gale MD (1995) Grasses, line up and form a circle. Curr Biol 5:737–739

    CAS  PubMed  Google Scholar 

  • Ndjiondjop MN, Albar L, Fargette D, Fauquet C, Ghesquière A (1999) The genetic basis oh high resistance to the rice yellow mottle virus (RYMV) in cultivars of two cultivated rice species. Plant Dis 83:931–935

    Google Scholar 

  • Ramalingam J, Vera Cruz CM, Kukreja K, Chittoor JM, Wu JL, Lee SW, Baraoidan M, George ML, Cohen MB, Hulbert SH, Leach JE, Leung H (2003) Candidate defense genes from rice, barley and maize and their association with qualitative and quantitative resistance in rice. Mol Plant Microbe Interact 16:14–24

    CAS  PubMed  Google Scholar 

  • Reddy AR, Ramakrishnan 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

    PubMed  Google Scholar 

  • Reymond P, Weber H, Damond M, Farmer EE (2000) Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis. Plant Cell 12:707–719

    CAS  PubMed  Google Scholar 

  • Sasaki T, Burr B (2000) International rice genome sequencing project: the effort to completely sequence the rice genome. Curr Opin Plant Biol 3:138–141

    CAS  PubMed  Google Scholar 

  • Sasaki T, et al (2002) The genome sequence and structure of rice chromosome 1. Nature 420:312–316.

    Article  CAS  PubMed  Google Scholar 

  • Schoof H, Zaccaria P, Gundlach H, Lemcke K, Rudd S, Kolesov G, Arnold R, Mewes HW, Mayer KF (2002) MIPS Arabidopsis thaliana database (MatDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res 30:91–93

    Article  CAS  PubMed  Google Scholar 

  • Stekel DJ, Git Y, Falciani F (2000) The comparison of gene expression from multiple cDNA libraries. Genome Res 10:2055–2061

    Article  CAS  PubMed  Google Scholar 

  • Temnykh S, Park WD, Ayres NM, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice ( Oryza sativa L.). Theor Appl Genet 100:697–712

    CAS  Google Scholar 

  • Theodoulou FL (2000) Plant ABC transporters. Biochim Biophys Acta 1465:79–103

    CAS  PubMed  Google Scholar 

  • Thottapilly G, Rossel HW (1993) Evaluation of resistance to rice yellow mottle virus in Oryza species. Indian J Virol 9:65–73

    Google Scholar 

  • Ventelon-Debout M, Delalande F, Brizard JP, Diemer H, Van Dorsselaer A, Brugidou C (2004) Proteome analysis of cultivar-specific deregulations of Oryza sativa indica and O. sativa japonica cellular suspensions undergoing Rice Yellow Mottle Virus infection. Mol Cell Proteomics, in press

  • Xiong L, Lee M-W, Qi M, Yang Y (2001) Identification of defense-related rice genes by suppression subtractive hybridization and differential screening. Mol Plant Microbe Interact 14:685–692

    CAS  PubMed  Google Scholar 

  • Yamamoto K, Sasaki T (1997) Large-scale EST sequencing in rice. Plant Mol Biol 35:135–144

    CAS  PubMed  Google Scholar 

  • Yu J, et al (2002) A draft sequence of the rice genome ( Oryza sativa L. ssp. indica). Science 296:79–92

    Google Scholar 

Download references

Acknowledgements

This work was supported in part by Genoplante program and by Montpellier-Languedoc Roussillon Genopole for sequencing. We would like to thank S. Hearne, A. Barakat and L. Albar for their helpful advice. We acknowledge G. Debout for his help with statistical analysis

Author information

Authors and Affiliations

  1. UMR 5096, Institut de Recherche pour le Développement, BP 64501, 34394, Montpellier, France

    M. Ventelon-Debout, T.-T. -H. Nguyen, A. Wissocq, A. Ghesquière & C. Brugidou

  2. UMR 5096, Université de Perpignan, 52, Avenue de Villeneuve, 66860, Perpignan, France

    C. Berger, M. Laudie, B. Piégu, R. Cooke & M. Delseny

Authors
  1. M. Ventelon-Debout
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. T.-T. -H. Nguyen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. A. Wissocq
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. C. Berger
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. M. Laudie
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. B. Piégu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. R. Cooke
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. A. Ghesquière
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. M. Delseny
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. C. Brugidou
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to M. Ventelon-Debout or C. Brugidou.

Additional information

Communicated by M.-A. Grandbastien

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ventelon-Debout, M., Nguyen, TT.H., Wissocq, A. et al. Analysis of the transcriptional response to Rice Yellow Mottle Virus infection in Oryza sativa indica and japonica cultivars. Mol Genet Genomics 270, 253–262 (2003). https://doi.org/10.1007/s00438-003-0903-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00438-003-0903-6

Keywords

Search

Navigation