Molecular Biology Reports

, 37:875 | Cite as

Analysis of genome expression in the response of Oryza granulata to Xanthomonas oryzae pv oryzae

  • Yu Luo
  • Guang-Lei Lv
  • Wen-Ting Wu
  • Shan-Na Chen
  • Zai-Quan Cheng


In order to understand the mechanism of the strong resistance of Oryza granulata to Xanthomonas oryzae pv oryzae (Xoo), cDNA microarrays containing 2,436 cDNA clones of Oryza granulata derived from Suppression subtractive library and cDNA library were constructed and genome expression patterns after inoculating Xoo were investigated. Three hundred and 83 clones were up-regulated, 836 clones were down-regulated after pathogen infection. Approximately 800 clones were sequenced and BLAST search were carried out. There are no homologous sequences for 35 clones of them. The functions of the homologous sequences for most clones are unknown. The known functions of the homologous sequences involved in photosynthesis, respiration, material transport, signal transduction, pathogenesis-related proteins, transcription factors, the active oxygen scavenging system and so on. The putative functions of them in responding to Xoo were discussed.


Microarray Oryza granulata Xanthomonas oryzae pv oryzae (XooDefense Disease resistance 



This research was funded by the National Science Foundation of China (No. 30460019 and 30660090), and Key Project of Natural Science Foundation of Yunnan Province (No. 2008C004).


  1. 1.
    Peng SQ, Wei ZS, Mao CX (1981) Identification of wild rice resistance: O. granulata with a highly resistant to Xoo. Hunan Agr Sci 5:47–48Google Scholar
  2. 2.
    Zhang Q, Wang CL, Shi AN et al (1994) Evaluation of resistance to bacterial blight (Xanthomonas oryzae pv. oryzae) in wild rice species. Sci Agr Sin 27:1–9Google Scholar
  3. 3.
    Cheng ZQ, Yan HJ, Geng XS, Yin FY, Sun YD, Zhang C, Huang XQ (2008) Identification of Oryza granulata for resistance to Xanthomonas oryzae pv. oryzae and observation of leaf tissue. Acta Phytopathol Sin 38:582–591Google Scholar
  4. 4.
    HuangPu WG, Ying CB, Qiu RJ et al (2001) Studies on 4th generation character of wild rice and cultivated rice somatic hybridization. J Henan Vocat Coll 29:12–14Google Scholar
  5. 5.
    Zhu YS, Chen BT, Yu SW (2004) Transferring the resistance of O. granulata to Xoo by asymmetric somatic hybrids. Chin Sci Bull 49:1395–1398Google Scholar
  6. 6.
    Song WY, Wang GL, Chen LL, Kim HS et al (1995) A receptor kinase-like protein encoded by the rice disease resistance gene Xa21. Science 270:1772–1804CrossRefGoogle Scholar
  7. 7.
    Yoshimura S, Yamanouchi U, Kayayose Y et al (1998) Expression of Xa1, a bacterial blight-resistance gene in rice is induced by bacterial inoculation. Proc Natl Acad Sci USA 95:1663–1668CrossRefPubMedGoogle Scholar
  8. 8.
    Sun X, Cao Y, Yang Z, Xu C, Li X, Wang S, Zhang Q (2004) Xa26 a gene conferring resistance to Xanthomouas oryzae Pv. oryzae in rice, encodes an LRR receptor kinase-like protein. Plant J 37:517–527CrossRefPubMedGoogle Scholar
  9. 9.
    Iyer AS, Mccouch SR (2004) The rice bacterial blight resistance gene Xa5 encodes a novel form of disease resistance. Mol Plant Microbe Interact 17:1348–1354CrossRefPubMedGoogle Scholar
  10. 10.
    Gu K, Tian D, Yang F et al (2004) High-resolution genetic mapping of Xa27(t) a new bacterial blight resistance gene in rice Oryza Sativa L. Theor Appl Genet 108:800–807CrossRefPubMedGoogle Scholar
  11. 11.
    Chu ZH, Fu BY, Yang H et al (2006) Targeting xa13, a recessive gene for bacterial blight resistance in rice. Theor Appl Genet 112:455–461CrossRefPubMedGoogle Scholar
  12. 12.
    Qian J, Cheng ZQ, Yang MZ, Liu JM, Wu CJ, Huang XQ (2005) Isolation and sequence analysis of the Xa21 gene exon II homologs from different species of wild rice in Yunnan. Hereditas 27:382–386PubMedGoogle Scholar
  13. 13.
    Xiong ZY, Tan GX, You AQ (2004) Comparative physical mapping of rice BAC clones linked to resistance genes Glh, Bph-3 and xa-5 in Oryza sativa and O. granulate. Chin Sci Bull 49:252–257Google Scholar
  14. 14.
    Kottapalli KR, Rakwal R, Satoh K et al (2007) Transcriptional profiling of indica rice cultivar IET8585 (Ajaya) infected with bacterial leaf blight pathogen Xanthomonas oryzae pv oryzae. Plant Physiol Biochem 45:834–850CrossRefPubMedGoogle Scholar
  15. 15.
    Lia Q, Chena F, Sun L et al (2006) Expression profiling of rice genes in early defense responses to blast and bacterial blight pathogens using cDNA microarray. Physiol Mol Plant Pathol 68:51–60CrossRefGoogle Scholar
  16. 16.
    Zhou B, Peng KM, Chu ZH (2002) The defense-responsive genes showing enhanced and repressed expression after pathogen infection in rice (Oryza sativa L.). Sci Chin (Series C) 45(44):9–467Google Scholar
  17. 17.
    Qian J, Zhang S, Ji G (2003) Evaluation of resistance to bacterial blight (Xanthomonas oryzae pv. oryzae) in Yunnan rice cultivars. J Yunnan Agric Univ 18:239–245Google Scholar
  18. 18.
    Chu ZH, Peng KM, Zhang LD et al (2002) Construction and characterization of a normalized cDNA library of rice all life. Chin Sci Bull 47:1656–1662CrossRefGoogle Scholar
  19. 19.
    Lan WZ, He GC, Wu SJ, Qin R (2006) Comparative analysis of Oryza sativa, O. officinalis and O. meyeriana genome with C0t–1 DNA and genomic DNA. Chin J Agric Sci 39:1083–1090Google Scholar
  20. 20.
    Wang HH, Cao CS, Kang J, Zeng FH (2002) Systemic resistance of rice to bacterial blight induced by salicylic acid and changes in activities of some enzymes in untreated leaves. Chin J Rice Sci 16:252–256Google Scholar
  21. 21.
    Gagne JM, Smalle J, Gingerich DJ, Walker JM, Yoo S-D, Yanagisawa S, Vierstra RD (2004) Arabidopsis EIN3-binding F-box and form ubiquitin-protein ligases that repress ethylene action and promote growth by directing EIN3 degradation. Proc Natl Acad Sci USA 101:6803–6808CrossRefPubMedGoogle Scholar
  22. 22.
    Gagne JM, Downes BP, Shiu S-H, Durski AM, Vierstra RD (2002) The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proc Natl Acad Sci USA 99:11519–11524CrossRefPubMedGoogle Scholar
  23. 23.
    Gray WM, Kepinski S, Rouse D et al (2001) Auxin regulates SCFTIR1-dependent degradation of AUX/IAA proteins. Nature 414:271–276CrossRefPubMedGoogle Scholar
  24. 24.
    Gray WM et al (2002) Role of the Arabidopsis RING2H2 protein RBX1 in RUB modification and SCF function. Plant Cell 14:2137–2144CrossRefPubMedGoogle Scholar
  25. 25.
    Dharmasiri N, Dharmasiri S, Estelle M (2005) The F-box protein TIR1 is an auxin receptor. Nature 435:441–445CrossRefPubMedGoogle Scholar
  26. 26.
    Kitagawa K, Hieter P (2001) Evolutionary conservation between budding yeast and human kinetochores. Nat Rev Mol Cell Biol 2:678–687CrossRefPubMedGoogle Scholar
  27. 27.
    Austin MJ, Muskett P, Kahn K, Feys BJ, Jones JDG, Parker JE (2002) Regulatory role of SGT1 in early R gene-mediated plant defenses. Science 295:2077–2080CrossRefPubMedGoogle Scholar
  28. 28.
    Azevedo C, Sadanandom A, Kitagawa K, Freialdenhoven A, Shirasu K, Schulze-Lefert P (2002) The RAR1 interactor SGT1, an essential component of R gene-triggered disease resistance. Science 295:2073–2076CrossRefPubMedGoogle Scholar
  29. 29.
    Liu Y, Schiff M, Serino G, Deng X-W, Dinesh-Kumar SP (2002) Role of SCF ubiquitin-ligase and the COP9 signalosome in the N gene-mediated resistance response to tobacco mosaic virus. Plant Cell 14:1483–1496CrossRefPubMedGoogle Scholar
  30. 30.
    Tor M, Gordon P, Cuzick A, Eulgem T, Sinapidou E, Mert F, Can C, Dangl JL, Holub EB (2002) Arabidopsis SGT1b is required for defense signaling conferred by several downy mildew (Peronospora parasitica) resistance genes. Plant Cell 14:993–1003CrossRefPubMedGoogle Scholar
  31. 31.
    Schwechheimer C, Deng X-W (2001) COP9 signalosome revisited: a novel mediator of protein degradation. Trends Cell Biol 11:420–426CrossRefPubMedGoogle Scholar
  32. 32.
    Kim HS, Delaney TP (2002) Arabidopsis SON1 is an F-box protein that regulates a novel induced defense response independent of both salicylic acid and systemic acquired resistance. Plant Cell 14:1469–1482CrossRefPubMedGoogle Scholar
  33. 33.
    Boyes DC, Nam J, Dangl JL (1998) The Arabidopsis thaliana RPM1 disease resistance gene product is a peripheral plasma membrane protein that is degraded coincident with the hypersensitive response. Proc Natl Acad Sci USA 95:15849–15854CrossRefPubMedGoogle Scholar
  34. 34.
    Schwechheimer C, Serino G, Deng X-W (2002) Multiple ubiquitin ligase-mediated processes require COP9 signalosome and AXR1 function. Plant Cell 14:2553–2563CrossRefPubMedGoogle Scholar
  35. 35.
    Gonzalez-Lamothe R, Tsitsigiannis DI, Ludwig AA, Panicot M, Shirasu K, Jones JDG (2006) The U-Box protein CMPG1 is required for efficient activation of defense mechanisms triggered by multiple resis-tance genes in tobacco and tomato. Plant Cell 18:1067–1083CrossRefPubMedGoogle Scholar
  36. 36.
    Yang CW, Gonzalez-Lamothe R, Ewan RA, Rowland O, Yoshioka H, Shenton M, Ye H (2006) A. Sadanan-dom, The E3 ubiquitin ligase activity of Arabidopsis PLANTU-BOX17 and its functional tobacco homolog ACRE276 are required for cell death and defense. Plant Cell 18:1084–1098CrossRefPubMedGoogle Scholar
  37. 37.
    Shirasu K, Schulze-Lefert P (2003) Complex formation, promiscuity and multi-functionality: protein interactions in disease-resistance pathways. Trends Plant Sci 8:252–258CrossRefPubMedGoogle Scholar
  38. 38.
    Dubacq C, Guerois R, Courbeyrette R, Kitagawa K, Mann C (2002) Sgt1p contributes to cyclic AMP pathway activity and physically interacts with the adenylyl cyclase Cyr1p/Cdc35p in budding yeast. Eukaryot Cell 1:568–582CrossRefPubMedGoogle Scholar
  39. 39.
    Garcia-Hernandez M, Murphy A, Taiz L (1998) Metallothioneins 1 and 2 have distinct but overlapping expression patterns in Arabidopsis. Plant Physiol 118:387–397CrossRefPubMedGoogle Scholar
  40. 40.
    Molina A, Garcia OF (1997) Enhanced tolerance to bacterial pathogens caused by the transgenic expression of barley lipid transfer protein LTP2. Plant J 12:669–675CrossRefPubMedGoogle Scholar
  41. 41.
    Chassot C, Nawrath C, Metraux JP (2007) Cuticular defects lead to full immunity to a major plant pathogen. Plant J 49:972–980CrossRefPubMedGoogle Scholar
  42. 42.
    Maldonado AM, Doerner P, Dixon RA, Lamb CJ, Cameron RK (2002) A putative lipid transfer protein involved in systemic resistance signalling in Arabidopsis. Nature 419:399–403CrossRefPubMedGoogle Scholar
  43. 43.
    Buhot N, Douliez JP, Jacquemard A et al (2001) A lipid transfer protein binds to a receptor involved in the control of plant defenses. FEBS Lett 509:27–30CrossRefPubMedGoogle Scholar
  44. 44.
    Sonnewald U, Sturm A, Chrispeels MJ, Willmitzer L (1989) Targeting and glycosylation of patatin, the major potato tuber protein in leaves of transgenic tobacco. Planta 179:171–180CrossRefGoogle Scholar
  45. 45.
    Twell D, Ooms G (1988) Structural diversity of the patatin gene family in potato cv. Desiree. Mol Gen Genet 212:325–336CrossRefPubMedGoogle Scholar
  46. 46.
    Koda Y, Kikuta Y (1994) Wound-induced accumulation of jasmolic acid in tissues of potato tubers. Plant Cell Physiol 35:751–756Google Scholar
  47. 47.
    Sembder G, Parthier B (1993) The biochemistry and the physiological and molecular action of jasmonates. Plant Mol Biol 44:569–589CrossRefGoogle Scholar
  48. 48.
    Si HJ, Liu J, Xie CH (2004) Transformation of potato using an antisense class I patatin genes and its effect on microtuber formation. J Agric Biotechnol 12:147–151Google Scholar
  49. 49.
    Romeis T, Ludwig AA, Martin R, Jones JD (2001) Calcium-dependent protein kinases play an essential role in a plant defence response. EMBO J 20:5556–5567CrossRefPubMedGoogle Scholar
  50. 50.
    Romeis T, Piedras P, Jones JD (2000) Resistance gene-dependent activation of a calcium-dependent protein kinase in the plant defense response. Plant Cell 12:803–816CrossRefPubMedGoogle Scholar
  51. 51.
    Romeis T, Piedras P, Zhang S, Klessig DF, Hirt H, Jones JD (1999) Rapid Avr9-and Cf-9-dependent activation of MAP kinases in tobacco cell cultures and leaves: convergence of resistance gene, elicitor, wound, and salicylate responses. Plant Cell 11:273–287CrossRefPubMedGoogle Scholar
  52. 52.
    Zhang S, Klessig DF (1998) Resistance gene N-mediated de novo synthesis and activation of a tobacco mitogen-activated protein kinase by tobacco mosaic virus infection. Proc Natl Acad Sci USA 95:7433–7438CrossRefPubMedGoogle Scholar
  53. 53.
    Zhang S, Liu Y (2001) Activation of salicylic acid-induced protein kinase, a mitogen-activated protein kinase, induces multiple defense responses in tobacco. Plant Cell 13:1877–1889CrossRefPubMedGoogle Scholar
  54. 54.
    Yang KY, Liu Y, Zhang S (2001) Activation of a mitogen-activated protein kinase pathway is involved in disease resistance in tobacco. Proc Natl Acad Sci USA 98:741–746CrossRefPubMedGoogle Scholar
  55. 55.
    Petersen M, Brodersen P, Naested H, Andreasson E, Lindhart U, Johansen B, Nielsen HB, Lacy M, Austin MJ, Parker JE, Sharma SB, Klessig DF, Martienssen R, Mattsson O, Jensen AB, Mundy J (2000) Arabidopsis map kinase 4 negatively regulates systemic acquired resistance. Cell 103:1111–1120CrossRefPubMedGoogle Scholar
  56. 56.
    Wiermer M, Feys BJ, Parker JE (2005) Plant immunity: the EDS1 regulatory node. Curr Opin Plant Biol 8:383–389CrossRefPubMedGoogle Scholar
  57. 57.
    Thomma BPHJ, Penninckx IAMA, Broekaert WF, Cammue BPA (2001) The complexity of disease signaling in Arabidopsis. Curr Opin Immunol 13:63–68CrossRefPubMedGoogle Scholar
  58. 58.
    Thomma BPHJ, Nelissen L, Eggermont K et al (1999) Deficiency in phytoalexin production causes enhanced susceptibility of Arabidopsis thaliana to fungal Alternaria brassicicola. Plant J 19:163–171CrossRefPubMedGoogle Scholar
  59. 59.
    Glazebrook J, Zook M, Mert F et al (1997) Phytoalexin deficient mutants of Arabidopsis reveal that PAD4 encodes a regulatory factor and that four PAD genes contribute to downy mildew resistance. Genetics 146:381–392PubMedGoogle Scholar
  60. 60.
    Kim YC, Kim SY, Paek KH et al (2006) Suppression of CaCYP1, a novel cytochrome P450 gene, compromises the basal pathogen defense response of pepper plants. Biochem Biophys Res 345:638–645CrossRefGoogle Scholar
  61. 61.
    Schenk H, Klein M, Erdbrügger W et al (1994) Distinct effects of thioredoxin and antioxidants on the activation of transcription factors NF-kappa B and AP-1. Proc Natl Acad Sci USA 91:1672–1676Google Scholar
  62. 62.
    Saitoh M, Nishitoh H, Fujii M et al (1998) Mammalian thioredox in is a direct inhibitor of apoptosis signal regulating kinase (ASK) l. EMBO J 17:2596–2606CrossRefPubMedGoogle Scholar
  63. 63.
    Cosgrove DJ (2000) New genes and new biological roles for expansins. Curr Opin Plant Biol 3:73–78CrossRefPubMedGoogle Scholar
  64. 64.
    Bouzareloua D, Billinia M, Roumeliotia K, Sophianopoulou V (2008) EglD, a putative endoglucanase, with an expansin like domain is localized in the conidial cell wall of Aspergillus nidulans. Fungal Genet Biol 45:839–850CrossRefGoogle Scholar
  65. 65.
    Liu QP, Feng Y, Dong H (2005) Insilico cloning of mSHMT gene from rice (Oryza sativa L.). Chin J Bioinformatics 3:5–9Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Yu Luo
    • 1
  • Guang-Lei Lv
    • 2
  • Wen-Ting Wu
    • 2
  • Shan-Na Chen
    • 1
  • Zai-Quan Cheng
    • 2
  1. 1.College of Life ScienceYunnan UniversityKunmingChina
  2. 2.Biotechnology Research InstituteYunnan Academy of Agricultural SciencesKunmingChina

Personalised recommendations