Transgenic Expression of the Dicotyledonous Pattern Recognition Receptor EFR in Rice Leads to Ligand-Dependent Activation of Defense Responses

English version České info

Plants possess multi-layered immune recognition systems. Early in the infection process, plants use receptor proteins to recognize pathogen molecules. Some of these receptors are present in only in a subset of plant species. Transfer of these taxonomically restricted immune receptors between plant species by genetic engineering is a promising approach for boosting the plant immune system. Here we show the successful transfer of an immune receptor from a species in the mustard family, called EFR, to rice. Rice plants expressing EFR are able to sense the bacterial ligand of EFR and elicit an immune response. We show that the EFR receptor is able to use components of the rice immune signaling pathway for its function. Under laboratory conditions, this leads to an enhanced resistance response to two weakly virulent isolates of an economically important bacterial disease of rice.

Vyšlo v časopise: Transgenic Expression of the Dicotyledonous Pattern Recognition Receptor EFR in Rice Leads to Ligand-Dependent Activation of Defense Responses. PLoS Pathog 11(3): e32767. doi:10.1371/journal.ppat.1004809
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1004809

Souhrn

Zdroje

1. Schwessinger B, Ronald PC. Plant innate immunity: perception of conserved microbial signatures. Annual review of plant biology. 2012;63 : 451–82. doi: 10.1146/annurev-arplant-042811-105518 22404464

2. Macho AP, Zipfel C. Plant PRRs and the Activation of Innate Immune Signaling. Molecular Cell. 2014;54 : 263–272. doi: 10.1016/j.molcel.2014.03.028 24766890

3. Boller T, Felix G. A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annual Review of Plant Biology. 2009;60 : 379–406. doi: 10.1146/annurev.arplant.57.032905.105346 19400727

4. Spoel SH, Dong X. How do plants achieve immunity? Defence without specialized immune cells. Nat Rev Immunol. 2012;12 : 89–100. doi: 10.1038/nri3141 22273771

5. Schulze-Lefert P, Panstruga R. A molecular evolutionary concept connecting nonhost resistance, pathogen host range, and pathogen speciation. Trends Plant Sci. 2011;16 : 117–25. doi: 10.1016/j.tplants.2011.01.001 21317020

6. Jones JD, Dangl JL. The plant immune system. Nature. 2006;444 : 323–9. 17108957

7. Chisholm ST, Coaker G, Day B, Staskawicz BJ. Host-microbe interactions: shaping the evolution of the plant immune response. Cell. 2006;124 : 803–14. 16497589

8. Maekawa T, Kufer TA, Schulze-Lefert P. NLR functions in plant and animal immune systems: so far and yet so close. Nat Immunol. 2011;12 : 817–826. doi: 10.1038/ni.2083 21852785

9. Boyd LA, Ridout C, O’Sullivan DM, Leach JE, Leung H. Plant-pathogen interactions: disease resistance in modern agriculture. Trends in genetics: TIG. 2013;29 : 233–40. doi: 10.1016/j.tig.2012.10.011 23153595

10. Lacombe S, Rougon-Cardoso A, Sherwood E, Peeters N, Dahlbeck D, van Esse HP, et al. Interfamily transfer of a plant pattern-recognition receptor confers broad-spectrum bacterial resistance. Nat Biotechnol. 2010;28 : 365–9. doi: 10.1038/nbt.1613 20231819

11. Mendes BMJ, Cardoso SC, Boscariol-Camargo RL, Cruz RB, Mourão Filho FAA, Bergamin Filho A. Reduction in susceptibility to Xanthomonas axonopodis pv. citri in transgenic Citrus sinensis expressing the rice Xa21 gene. Plant Pathology. 2010;59 : 68–75. doi: 10.1111/j.1365-3059.2009.02148.x

12. Afroz A, Chaudhry Z, Rashid U, Ali GM, Nazir F, Iqbal J, et al. Enhanced resistance against bacterial wilt in transgenic tomato (Lycopersicon esculentum) lines expressing the Xa21 gene. Plant Cell Tiss Organ Cult. 2011;104 : 227–237. doi: 10.1007/s11240-010-9825-2

13. Tripathi JN, Lorenzen J, Bahar O, Ronald P, Tripathi L. Transgenic expression of the rice Xa21 pattern-recognition receptor in banana (Musa sp.) confers resistance to Xanthomonas campestris pv. musacearum. Plant Biotechnology Journal. 2014; n/a–n/a. doi: 10.1111/pbi.12170

14. Fradin E, Adb-El-Haliem A, Masini L, van den Berg G, Joosten M, Thomma B. Interfamily transfer of tomato Ve1 mediates Verticillium resistance in Arabidopsis. Plant Physiol. 2011;156 : 2255–65. doi: 10.1104/pp.111.180067 21617027

15. Monaghan J, Zipfel C. Plant pattern recognition receptor complexes at the plasma membrane. Current Opinion in Plant Biology. 2012;15 : 349–357. doi: 10.1016/j.pbi.2012.05.006 22705024

16. Segonzac C, Zipfel C. Activation of plant pattern-recognition receptors by bacteria. Curr Opin Microbiol. 2011;14 : 54–61. doi: 10.1016/j.mib.2010.12.005 21215683

17. Felix G, Duran JD, Volko S, Boller T. Plants have a sensitive perception system for the most conserved domain of bacterial flagellin. Plant J. 1999;18 : 265–76. 10377992

18. Albert M, Jehle AK, Lipschis M, Mueller K, Zeng Y, Felix G. Regulation of cell behaviour by plant receptor kinases: Pattern recognition receptors as prototypical models. Eur J Cell Biol. 2010;89 : 200–7. doi: 10.1016/j.ejcb.2009.11.015 20034699

19. Chinchilla D, Bauer Z, Regenass M, Boller T, Felix G. The Arabidopsis receptor kinase FLS2 binds flg22 and determines the specificity of flagellin perception. Plant Cell. 2006;18 : 465–76. 16377758

20. Takai R, Isogai A, Takayama S, Che FS. Analysis of flagellin perception mediated by flg22 receptor OsFLS2 in rice. Mol Plant Microbe Interact. 2008;21 : 1635–42. doi: 10.1094/MPMI-21-12-1635 18986259

21. Hirai H, Takai R, Iwano M, Nakai M, Kondo M, Takayama S, et al. Glycosylation Regulates Specific Induction of Rice Immune Responses by Acidovorax avenae Flagellin. J Biol Chem. 2011;286 : 25519–30. doi: 10.1074/jbc.M111.254029 21628471

22. Cai R, Lewis J, Yan S, Liu H, Clarke CR, Campanile F, et al. The Plant Pathogen Pseudomonas syringae pv. tomato Is Genetically Monomorphic and under Strong Selection to Evade Tomato Immunity. PLoS Pathog. 2011;7: e1002130. doi: 10.1371/journal.ppat.1002130 21901088

23. Clarke CR, Chinchilla D, Hind SR, Taguchi F, Miki R, Ichinose Y, et al. Allelic variation in two distinct Pseudomonas syringae flagellin epitopes modulates the strength of plant immune responses but not bacterial motility. New Phytologist. 2013; n/a–n/a. doi: 10.1111/nph.12408

24. Trdá L, Fernandez O, Boutrot F, Héloir M-C, Kelloniemi J, Daire X, et al. The grapevine flagellin receptor VvFLS2 differentially recognizes flagellin-derived epitopes from the endophytic growth-promoting bacterium Burkholderia phytofirmans and plant pathogenic bacteria. New Phytol. 2014;201 : 1371–1384. doi: 10.1111/nph.12592 24491115

25. Lopez-Gomez M, Sandal N, Stougaard J, Boller T. Interplay of flg22-induced defence responses and nodulation in Lotus japonicus. J Exp Bot. 2012;63 : 393–401. doi: 10.1093/jxb/err291 21934117

26. Zipfel C, Kunze G, Chinchilla D, Caniard A, Jones JD, Boller T, et al. Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts Agrobacterium-mediated transformation. Cell. 2006;125 : 749–60. 16713565

27. Kunze G, Zipfel C, Robatzek S, Niehaus K, Boller T, Felix G. The N terminus of bacterial elongation factor Tu elicits innate immunity in Arabidopsis plants. Plant Cell. 2004;16 : 3496–507. 15548740

28. Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, et al. A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science. 1995;270 : 1804–6. 8525370

29. Ronald PC, Albano B, Tabien R, Abenes L, Wu KS, McCouch S, et al. Genetic and physical analysis of the rice bacterial blight disease resistance locus, Xa21. Mol Gen Genet. 1992;236 : 113–20. 1362973

30. Song WY, Pi LY, Wang GL, Gardner J, Holsten T, Ronald PC. Evolution of the rice Xa21 disease resistance gene family. Plant Cell. 1997;9 : 1279–87. doi: 10.1105/tpc.9.8.1279 9286106

31. De Jonge R, Peter van Esse H, Maruthachalam K, Bolton MD, Santhanam P, Saber MK, et al. Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing. Proceedings of the National Academy of Sciences. 2012; doi: 10.1073/pnas.1119623109

32. Saijo Y, Tintor N, Lu X, Rauf P, Pajerowska-Mukhtar K, Haweker H, et al. Receptor quality control in the endoplasmic reticulum for plant innate immunity. Embo J. 2009;28 : 3439–49. doi: 10.1038/emboj.2009.263 19763087

33. Saijo Y. ER quality control of immune receptors and regulators in plants. Cell Microbiol. 2010;12 : 716–24. doi: 10.1111/j.1462-5822.2010.01472.x 20408850

34. Haweker H, Rips S, Koiwa H, Salomon S, Saijo Y, Chinchilla D, et al. Pattern recognition receptors require N-glycosylation to mediate plant immunity. J Biol Chem. 2010;285 : 4629–36. doi: 10.1074/jbc.M109.063073 20007973

35. Nekrasov V, Li J, Batoux M, Roux M, Chu ZH, Lacombe S, et al. Control of the pattern-recognition receptor EFR by an ER protein complex in plant immunity. Embo J. 2009;28 : 3428–38. doi: 10.1038/emboj.2009.262 19763086

36. Li J, Zhao-Hui C, Batoux M, Nekrasov V, Roux M, Chinchilla D, et al. Specific ER quality control components required for biogenesis of the plant innate immune receptor EFR. Proc Natl Acad Sci U S A. 2009;106 : 15973–8. doi: 10.1073/pnas.0905532106 19717464

37. Heese A, Hann DR, Gimenez-Ibanez S, Jones AM, He K, Li J, et al. The receptor-like kinase SERK3/BAK1 is a central regulator of innate immunity in plants. Proceedings of the National Academy of Sciences of the United States of America. 2007;104 : 12217–22. 17626179

38. Schulze B, Mentzel T, Jehle AK, Mueller K, Beeler S, Boller T, et al. Rapid heteromerization and phosphorylation of ligand-activated plant transmembrane receptors and their associated kinase BAK1. J Biol Chem. 2010;285 : 9444–51. doi: 10.1074/jbc.M109.096842 20103591

39. Chinchilla D, Shan L, He P, de Vries S, Kemmerling B. One for all: the receptor-associated kinase BAK1. Trends in Plant Science. 2009;14 : 535–41. doi: 10.1016/j.tplants.2009.08.002 19748302

40. Chinchilla D, Zipfel C, Robatzek S, Kemmerling B, Nurnberger T, Jones JD, et al. A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence. Nature. 2007;448 : 497–500. 17625569

41. Schwessinger B, Roux M, Kadota Y, Ntoukakis V, Sklenar J, Jones A, et al. Phosphorylation-Dependent Differential Regulation of Plant Growth, Cell Death, and Innate Immunity by the Regulatory Receptor-Like Kinase BAK1. PLoS Genet. 2011;7: e1002046. doi: 10.1371/journal.pgen.1002046 21593986

42. Roux M, Schwessinger B, Albrecht C, Chinchilla D, Jones A, Holton N, et al. The Arabidopsis Leucine-Rich Repeat Receptor-Like Kinases BAK1/SERK3 and BKK1/SERK4 Are Required for Innate Immunity to Hemibiotrophic and Biotrophic Pathogens. Plant Cell. 2011;23 : 2440–55. doi: 10.1105/tpc.111.084301 21693696

43. Macho AP, Schwessinger B, Ntoukakis V, Brutus A, Segonzac C, Roy S, et al. A Bacterial Tyrosine Phosphatase Inhibits Plant Pattern Recognition Receptor Activation. Science. 2014;343 : 1509–1512. doi: 10.1126/science.1248849 24625928

44. Lu D, Wu S, Gao X, Zhang Y, Shan L, He P. A receptor-like cytoplasmic kinase, BIK1, associates with a flagellin receptor complex to initiate plant innate immunity. Proc Natl Acad Sci U S A. 2010;107 : 496–501. doi: 10.1073/pnas.0909705107 20018686

45. Zhang J, Li W, Xiang T, Liu Z, Laluk K, Ding X, et al. Receptor-like cytoplasmic kinases integrate signaling from multiple plant immune receptors and are targeted by a Pseudomonas syringae effector. Cell Host & Microbe. 2010;7 : 290–301. doi: 10.1016/j.chom.2010.03.007

46. Boudsocq M, Willmann MR, McCormack M, Lee H, Shan L, He P, et al. Differential innate immune signalling via Ca(2+) sensor protein kinases. Nature. 2010;464 : 418–22. doi: 10.1038/nature08794 20164835

47. Boudsocq M, Sheen J. CDPKs in immune and stress signaling. Trends in plant science. 2013;18 : 30–40. doi: 10.1016/j.tplants.2012.08.008 22974587

48. Daudi A, Cheng Z, O’Brien JA, Mammarella N, Khan S, Ausubel FM, et al. The Apoplastic Oxidative Burst Peroxidase in Arabidopsis Is a Major Component of Pattern-Triggered Immunity. The Plant Cell Online. 2012;24 : 275–287. doi: 10.1105/tpc.111.093039 22247251

49. Kadota Y, Sklenar J, Derbyshire P, Stransfeld L, Asai S, Ntoukakis V, et al. Direct Regulation of the NADPH Oxidase RBOHD by the PRR-Associated Kinase BIK1 during Plant Immunity. Mol Cell. 2014;54 : 43–55. doi: 10.1016/j.molcel.2014.02.021 24630626

50. Lozano-Durán R, Macho AP, Boutrot F, Segonzac C, Somssich IE, Zipfel C. The transcriptional regulator BZR1 mediates trade-off between plant innate immunity and growth. eLife. 2013;2. doi: 10.7554/eLife.00983

51. Park C-J, Sharma R, Lefebvre B, Canlas PE, Ronald PC. The endoplasmic reticulum-quality control component SDF2 is essential for XA21-mediated immunity in rice. Plant Science. 2013;210 : 53–60. doi: 10.1016/j.plantsci.2013.05.003 23849113

52. Park CJ, Bart R, Chern M, Canlas PE, Bai W, Ronald PC. Overexpression of the endoplasmic reticulum chaperone BiP3 regulates XA21-mediated innate immunity in rice. PLoS One. 2010;5: e9262. doi: 10.1371/journal.pone.0009262 20174657

53. Chen X, Chern M, Canlas PE, Ruan D, Jiang C, Ronald PC. An ATPase promotes autophosphorylation of the pattern recognition receptor XA21 and inhibits XA21-mediated immunity. Proc Natl Acad Sci U S A. 2010;107 : 8029–34. doi: 10.1073/pnas.0912311107 20385831

54. Chen X, Zuo S, Schwessinger B, Chern M, Canlas PE, Ruan D, et al. An XA21-Associated Kinase (OsSERK2) regulates immunity mediated by the XA21 and XA3 immune receptors. Mol Plant. 2014; ssu003. doi: 10.1093/mp/ssu003 24482436

55. Seo YS, Chern M, Bartley LE, Han M, Jung KH, Lee I, et al. Towards establishment of a rice stress response interactome. PLoS Genet. 2011;7: e1002020. doi: 10.1371/journal.pgen.1002020 21533176

56. Wang YS, Pi LY, Chen X, Chakrabarty PK, Jiang J, De Leon AL, et al. Rice XA21 binding protein 3 is a ubiquitin ligase required for full Xa21-mediated disease resistance. Plant Cell. 2006;18 : 3635–46. doi: 10.1105/tpc.106.046730 17172358

57. Jiang Y, Chen X, Ding X, Wang Y, Chen Q, Song W-Y. The XA21 binding protein XB25 is required for maintaining XA21-mediated disease resistance. Plant J. 2013;73 : 814–823. doi: 10.1111/tpj.12076 23206229

58. Peng Y, Bartley LE, Chen X, Dardick C, Chern M, Ruan R, et al. OsWRKY62 is a negative regulator of basal and Xa21-mediated defense against Xanthomonas oryzae pv. oryzae in rice. Mol Plant. 2008;1 : 446–58. doi: 10.1093/mp/ssn024 19825552

59. Park CJ, Peng Y, Chen X, Dardick C, Ruan D, Bart R, et al. Rice XB15, a protein phosphatase 2C, negatively regulates cell death and XA21-mediated innate immunity. PLoS Biol. 2008;6: e231. doi: 10.1371/journal.pbio.0060231 18817453

60. Tan S, Wang D, Ding J, Tian D, Zhang X, Yang S. Adaptive evolution of Xa21 homologs in Gramineae. Genetica. 2011;139 : 1465–75. doi: 10.1007/s10709-012-9645-x 22451352

61. Lu F, Wang H, Wang S, Jiang W, Shan C, Li B, et al. Enhancement of innate immune system in monocot rice by transferring the dicotyledonous elongation factor Tu receptor EFR. J Integr Plant Biol. 2015; n/a–n/a. doi: 10.1111/jipb.12306

62. Wang S, Sun Z, Wang H, Liu L, Lu F, Yang J, et al. Rice OsFLS2-mediated perception of bacterial flagellins is evaded by Xanthomonas oryzae pvs. oryzae and oryzicola. Molecular Plant. doi: 10.1016/j.molp.2015.01.012

63. Katsuragi Y, Takai R, Furukawa T, Hirai H, Morimoto T, Katayama T, et al. CD2–1, the C-terminal region of flagellin, modulates the induction of immune responses in rice. MPMI. 2015; doi: 10.1094/MPMI-11-14-0372-R

64. Ao Y, Li Z, Feng D, Xiong F, Liu J, Li J-F, et al. OsCERK1 and OsRLCK176 play important roles in peptidoglycan and chitin signaling in rice innate immunity. Plant J. 2014;80 : 1072–1084. doi: 10.1111/tpj.12710 25335639

65. Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, et al. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics. 2008;9 : 204. doi: 10.1186/1471-2164-9-204 18452608

66. Lee BM, Park YJ, Park DS, Kang HW, Kim JG, Song ES, et al. The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice. Nucleic Acids Res. 2005;33 : 577–86. doi: 10.1093/nar/gki206 15673718

67. Ochiai H, Inoue Y, Takeya M, Sasaki A, Kaku H. Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity. Japan Agricultural Research Quarterly. 2005;39 : 275.

68. González JF, Degrassi G, Devescovi G, De Vleesschauwer D, Höfte M, Myers MP, et al. A proteomic study of Xanthomonas oryzae pv. oryzae in rice xylem sap. Journal of Proteomics. 2012;75 : 5911–5919. doi: 10.1016/j.jprot.2012.07.019 22835776

69. Qian G, Zhou Y, Zhao Y, Song Z, Wang S, Fan J, et al. Proteomic Analysis Reveals Novel Extracellular Virulence-Associated Proteins and Functions Regulated by the Diffusible Signal Factor (DSF) in Xanthomonas oryzae pv. oryzicola. Journal of proteome research. 2013;12 : 3327–41. doi: 10.1021/pr4001543 23688240

70. Sharma R, De Vleesschauwer D, Sharma MK, Ronald PC. Recent advances in dissecting stress-regulatory crosstalk in rice. Mol Plant. 2013;6 : 250–260. doi: 10.1093/mp/sss147 23292878

71. Liu W, Liu J, Triplett L, Leach JE, Wang G-L. Novel Insights into Rice Innate Immunity against Bacterial and Fungal Pathogens. Annual Review of Phytopathology. 2014;52: null. doi: 10.1146/annurev-phyto-102313-045926

72. Zhang H, Wang S. Rice versus Xanthomonas oryzae pv. oryzae: a unique pathosystem. Curr Opin Plant Biol. 2013;16 : 188–195. doi: 10.1016/j.pbi.2013.02.008 23466254

73. Kawano Y, Shimamoto K. Early signaling network in rice PRR-mediated and R-mediated immunity. Curr Opin Plant Biol. 2013;16 : 496–504. doi: 10.1016/j.pbi.2013.07.004 23927868

74. Xiang Y, Cao Y, Xu C, Li X, Wang S. Xa3, conferring resistance for rice bacterial blight and encoding a receptor kinase-like protein, is the same as Xa26. Theor Appl Genet. 2006;113 : 1347–55. doi: 10.1007/s00122-006-0388-x 16932879

75. Chen X, Shang J, Chen D, Lei C, Zou Y, Zhai W, et al. A B-lectin receptor kinase gene conferring rice blast resistance. The Plant Journal. 2006;46 : 794–804. doi: 10.1111/j.1365-313X.2006.02739.x 16709195

76. Lee SW, Han SW, Sririyanum M, Park CJ, Seo YS, Ronald PC. Retraction. A type I-secreted, sulfated peptide triggers XA21-mediated innate immunity. Science. 2013;342 : 191. doi: 10.1126/science.342.6155.191-a 24115422

77. Bahar O, Pruitt R, Luu DD, Schwessinger B, Daudi A, Liu F, et al. The Xanthomonas Ax21 protein is processed by the general secretory system and is secreted in association with outer membrane vesicles. PeerJ. 2014;2: e242. doi: 10.7717/peerj.242 24482761

78. Li J. Multi-tasking of somatic embryogenesis receptor-like protein kinases. Curr Opin Plant Biol. 2010; doi: 10.1016/j.pbi.2010.09.004

79. Zuo S, Zhou X, Chen M, Zhang S, Schwessinger B, Ruan D, et al. OsSERK1 regulates rice development but not immunity to Xanthomonas oryzae pv. oryzae or Magnaporthe oryzae. J Integr Plant Biol. 2014; doi: 10.1111/jipb.12290

80. Holton N, Nekrasov V, Ronald PC, Zipfel C. The Phylogenetically-Related Pattern Recognition Receptors EFR and XA21 Recruit Similar Immune Signaling Components in Monocots and Dicots. PLoS Pathog. 2015;11: e1004602. doi: 10.1371/journal.ppat.1004602 25607985

81. Xiang T, Zong N, Zou Y, Wu Y, Zhang J, Xing W, et al. Pseudomonas syringae effector AvrPto blocks innate immunity by targeting receptor kinases. Curr Biol. 2008;18 : 74–80. doi: 10.1016/j.cub.2007.12.020 18158241

82. Park CJ, Han SW, Chen X, Ronald PC. Elucidation of XA21-mediated innate immunity. Cell Microbiol. 2010;12 : 1017–25. doi: 10.1111/j.1462-5822.2010.01489.x 20590657

83. Chen X, Ronald PC. Innate immunity in rice. Trends Plant Sci. 2011;16 : 451–9. doi: 10.1016/j.tplants.2011.04.003 21602092

84. Kishimoto K, Kouzai Y, Kaku H, Shibuya N, Minami E, Nishizawa Y. Perception of the chitin oligosaccharides contributes to disease resistance to blast fungus Magnaporthe oryzae in rice. The Plant Journal. 2010;64 : 343–54. doi: 10.1111/j.1365-313X.2010.04328.x 21070413

85. Furukawa T, Inagaki H, Takai R, Hirai H, Che F-S. Two distinct EF-Tu epitopes induce immune responses in rice and Arabidopsis. Molecular Plant-Microbe Interactions. 2013; doi: 10.1094/MPMI-10-13-0304-R

86. Schoonbeek H, Wang H-H, Stefanato FL, Craze M, Bowden S, Wallington E, et al. Arabidopsis EF-Tu receptor enhances bacterial disease resistance in transgenic wheat. New Phytol. 2015; n/a–n/a. doi: 10.1111/nph.13356

87. Hiei Y, Ohta S, Komari T, Kumashiro T. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J. 1994;6 : 271–282. 7920717

88. Chern MS, Fitzgerald HA, Canlas PE, Navarre DA, Ronald PC. Overexpression of a rice NPR1 homolog leads to constitutive activation of defense response and hypersensitivity to light. Mol Plant Microbe Interact. 2005;18 : 511–20. 15986920

89. Park C-J, Lee S-W, Chern M, Sharma R, Canlas PE, Song M-Y, et al. Ectopic expression of rice Xa21 overcomes developmentally controlled resistance to Xanthomonas oryzae pv. oryzae. Plant Science. 2010;179 : 466–471. doi: 10.1016/j.plantsci.2010.07.008 21076626

90. Nakagawa T, Kurose T, Hino T, Tanaka K, Kawamukai M, Niwa Y, et al. Development of series of gateway binary vectors, pGWBs, for realizing efficient construction of fusion genes for plant transformation. J Biosci Bioeng. 2007;104 : 34–41. doi: 10.1263/jbb.104.34 17697981

91. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14: R36. doi: 10.1186/gb-2013-14-4-r36 23618408

92. Kawahara Y, de la Bastide M, Hamilton J, Kanamori H, McCombie Wr, Ouyang S, et al. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice. 2013;6 : 1–10. doi: 10.1186/1939-8433-6-4 24280096

93. Team RC. R: A language and environment for statistical computing. R Foundation for Statistical Computing. 2012. ISBN 3-900051-07-0,[Available from: www.R-project.org/]; 2013.

94. Wickham H. ggplot2: elegant graphics for data analysis. Springer; 2009.

95. McCarthy DJ, Chen Y, Smyth GK. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic acids research. 2012;40 : 4288–4297. doi: 10.1093/nar/gks042 22287627

96. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26 : 139–140. doi: 10.1093/bioinformatics/btp616 19910308

97. Keller A, Eng J, Zhang N, Li X, Aebersold R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Molecular systems biology. 2005;1.