Theoretical and Applied Genetics

, Volume 131, Issue 4, pp 787–800 | Cite as

Transcriptome signatures of tomato leaf induced by Phytophthora infestans and functional identification of transcription factor SpWRKY3

  • Jun Cui
  • Pinsan Xu
  • Jun Meng
  • Jingbin Li
  • Ning Jiang
  • Yushi Luan
Original Article


Key message

SpWRKY3 was identified as a resistance gene to Phytophthora infestans from Solanum pimpinellifolium L3708 and its transgenic tomato showed a significant resistance to P. infestans. This finding reveals the potential application of SpWRKY3 in future molecular breeding.


Transcription factors (TFs) play crucial roles in the plant response to various pathogens. In this present study, we used comparative transcriptome analysis of tomatoes inoculated with and without Phytophthora infestans to identify 1103 differentially expressed genes. Seven enrichment GO terms (level 4) associated with the plant resistance to pathogens were identified. It was found that thirty-five selected TF genes from GO enriched term, sequence-specific DNA binding transcription factor activity (GO: 0003700), were induced by P. infestans. Of these TFs, the accumulation of a homologous gene of WRKY (SpWRKY3) was significantly changed after P. infestans induction, and it was also isolated form P. infestans-resistant tomato, Solanum pimpinellifolium L3708. Overexpression of SpWRKY3 in tomato positively modulated P. infestans defense response as shown by decreased number of necrotic cells, lesion sizes and disease index, while the resistance was impaired after SpWRKY3 silencing. After P. infestans infection, the expression levels of PR genes in transgenic tomato plants overexpressed SpWRKY3 were significantly higher than those in WT, while the number of necrotic cells and the reactive oxygen species (ROS) accumulation were fewer and lower. These results suggest that SpWRKY3 induces PR gene expression and reduces the ROS accumulation to protect against cell membrane injury, leading to enhanced resistance to P. infestans. Our results provide insight into SpWRKY3 as a positive regulator involved in tomato–P. infestans interaction, and its function may enhance tomato resistance to P. infestans.



This work is supported by Grants from the National Natural Science Foundation of China (Nos. 31471880 and 61472061).

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest.

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  1. Adachi H, Nakano T, Miyagawa N, Ishihama N, Yoshioka M, Katou Y, Yaeno T, Shirasu K, Yoshioka H (2015) WRKY transcription factors phosphorylated by MAPK regulate a plant immune NADPH oxidase in Nicotiana benthamiana. Plant Cell 27:2645–2663CrossRefPubMedPubMedCentralGoogle Scholar
  2. Al-Abdallat AM, Ali-Sheikh-Omar MA, Alnemer LM (2015) Overexpression of two ATNAC3-related genes improves drought and salt tolerance in tomato (Solanum lycopersicum L.). Plant Cell Tiss Organ Cult 120:989–1001CrossRefGoogle Scholar
  3. Amorim LL, da Fonseca-Dos-Santos R, Guida-Santos M, Crovella S, Benko-Iseppon AM (2017) Transcription factors involved in plant resistance to pathogens. Curr Protein Pept Sci 18:335–351CrossRefPubMedGoogle Scholar
  4. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bradley DJ, Kjellbom P, Lamb CJ (1992) Elicitor- and wound-induced oxidative cross-linking of a proline-rich plant cell wall protein: a novel, rapid defense response. Cell 70:21–30CrossRefPubMedGoogle Scholar
  6. Buscaill P, Rivas S (2014) Transcriptional control of plant defence responses. Curr Opin Plant Biol 20:35–46CrossRefPubMedGoogle Scholar
  7. Canonne J, Marino D, Jauneau A, Pouzet C, Brière C, Roby D, Rivas S (2011) The Xanthomonas type III effector XopD targets the Arabidopsis transcription factor MYB30 to suppress plant defense. Plant Cell 23:3498–3511CrossRefPubMedPubMedCentralGoogle Scholar
  8. Cao WH, Liu J, He XJ, Mu RL, Zhou HL, Chen SY, Zhang JS (2007) Modulation of ethylene responses affects plant salt-stress responses. Plant Physiol 143:707–719CrossRefPubMedPubMedCentralGoogle Scholar
  9. Chen Y, Halterman DA (2017) Phytophthora infestans effectors IPI-O1 and IPI-O4 each contribute to pathogen virulence. Phytopathology 107:600–606CrossRefPubMedGoogle Scholar
  10. Chen X, Liu J, Lin G, Wang A, Wang Z, Lu G (2013) Overexpression of AtWRKY28 and AtWRKY75 in Arabidopsis enhances resistance to oxalic acid and Sclerotinia sclerotiorum. Plant Cell Rep 32:1589–1599CrossRefPubMedGoogle Scholar
  11. Cheng MN, Huang ZJ, Hua QZ, Shan W, Kuang JF, Lu WJ, Qin YH, Chen JY (2017) The WRKY transcription factor HpWRKY44 regulates CytP450-like1 expression in red pitaya fruit (Hylocereus polyrhizus). Hortic Res 4:17039CrossRefPubMedPubMedCentralGoogle Scholar
  12. Choi C, Hwang SH, Fang IR, Kwon SI, Park SR, Ahn I, Kim JB, Hwang DJ (2015) Molecular characterization of Oryza sativa WRKY6, which binds to W-box-like element 1 of the Oryza sativa pathogenesis-related (PR) 10a promoter and confers reduced susceptibility to pathogens. New Phytol 208:846–859CrossRefPubMedGoogle Scholar
  13. Cui J, Luan Y, Jiang N, Bao H, Meng J (2017) Comparative transcriptome analysis between resistant and susceptible tomato allows the identification of lncRNA16397 conferring resistance to Phytophthora infestans by co-expressing glutaredoxin. Plant J 89:577–589CrossRefPubMedGoogle Scholar
  14. Derksen H, Rampitsch C, Daayf F (2013) Signaling cross-talk in plant disease resistance. Plant Sci 207:79–87CrossRefPubMedGoogle Scholar
  15. Deslandes L, Olivier J, Theulieres F, Hirsch J, Feng DX, Bittner-Eddy P, Beynon J, Marco Y (2002) Resistance to Ralstonia solanacearum in Arabidopsis thaliana is conferred by the recessive RRS1-R gene, a member of a novel family of resistance genes. Proc Natl Acad Sci USA 99:2404–2409CrossRefPubMedPubMedCentralGoogle Scholar
  16. Deslandes L, Olivier J, Peeters N, Feng DX, Khounlotham M, Boucher C, Somssich I, Genin S, Marco Y (2003) Physical interaction between RRS1-R, a protein conferring resistance to bacterial wilt, and PopP2, a type III effector targeted to the plant nucleus. Proc Natl Acad Sci USA 100:8024–8029CrossRefPubMedPubMedCentralGoogle Scholar
  17. Du Y, Mpina MH, Birch PR, Bouwmeester K, Govers F (2015) Phytophthora infestans RXLR effector AVR1 interacts with exocyst component Sec5 to manipulate plant immunity. Plant Physiol 169:1975–1990PubMedPubMedCentralGoogle Scholar
  18. El Hadrami A, Adam LR, Daayf F (2011) Biocontrol treatments confer protection against Verticillium dahliae infection of potato by inducing antimicrobial metabolites. Mol Plant Microbe Interact 24:328–335CrossRefPubMedGoogle Scholar
  19. Garner CM, Kim SH, Spears BJ, Gassmann W (2016) Express yourself: transcriptional regulation of plant innate immunity. Semin Cell Dev Biol 56:150–162CrossRefPubMedGoogle Scholar
  20. Guo C, Guo R, Xu X, Gao M, Li X, Song J, Zheng Y, Wang X (2014) Evolution and expression analysis of the grape (Vitis vinifera L.) WRKY gene family. J Exp Bot 65:1513–1528CrossRefPubMedPubMedCentralGoogle Scholar
  21. Guttman DS, McHardy AC, Schulze-Lefert P (2014) Microbial genome-enabled insights into plant-microorganism interactions. Nat Rev Genet 15:797–813CrossRefPubMedGoogle Scholar
  22. Huang S, Gao Y, Liu J, Peng X, Niu X, Fei Z, Cao S, Liu Y (2012) Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. Mol Genet Genomics 287:495–513CrossRefPubMedGoogle Scholar
  23. Huang YJ, Yin XR, Zhu CQ, Wang WW, Grierson D, Xu CJ, Chen KS (2013) Standard addition quantitative real-time PCR (SAQPCR): a novel approach for determination of transgene copy number avoiding PCR efficiency estimation. PLoS ONE 8:e53489CrossRefPubMedPubMedCentralGoogle Scholar
  24. Ishihama N, Yoshioka H (2012) Post-translational regulation of WRKY transcription factors in plant immunity. Curr Opin Plant Biol 15:431–437CrossRefPubMedGoogle Scholar
  25. Ishihama N, Yamada R, Yoshioka M, Katou S, Yoshioka H (2011) Phosphorylation of the Nicotiana benthamiana WRKY8 transcription factor by MAPK functions in the defense response. Plant Cell 23:1153–1170CrossRefPubMedPubMedCentralGoogle Scholar
  26. Jiang Y, Guo L, Liu R, Jiao B, Zhao X, Ling Z, Luo K (2016) Overexpression of Poplar PtrWRKY89 in transgenic Arabidopsis leads to a reduction of disease resistance by regulating defense-related genes in salicylate- and jasmonate-dependent signaling. PLoS ONE 11:e0149137CrossRefPubMedPubMedCentralGoogle Scholar
  27. Jiao Y, Wang D, Wang L, Jiang C, Wang Y (2017) VqMAPKKK38 is essential for stilbene accumulation in grapevine. Hortic Res 4:17058CrossRefPubMedPubMedCentralGoogle Scholar
  28. King SR, McLellan H, Boevink PC, Armstrong MR, Bukharova T, Sukarta O, Win J, Kamoun S, Birch PR, Banfield MJ (2014) Phytophthora infestans RXLR effector PexRD2 interacts with host MAPKKK ε to suppress plant immune signaling. Plant Cell 26:1345–1359CrossRefPubMedPubMedCentralGoogle Scholar
  29. Kotchoni SO, Gachomo EW (2006) The reactive oxygen species network pathways: an essential prerequisite for perception of pathogen attack and the acquired disease resistance in plants. J Biosci 31:389–404CrossRefPubMedGoogle Scholar
  30. Lai Z, Vinod K, Zheng Z, Fan B, Chen Z (2008) Roles of Arabidopsis WRKY3 and WRKY4 transcription factors in plant responses to pathogens. BMC Plant Biol 8:68CrossRefPubMedPubMedCentralGoogle Scholar
  31. Li J, Brader G, Palva ET (2004) The WRKY70 transcription factor: a node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense. Plant Cell 16:319–331CrossRefPubMedPubMedCentralGoogle Scholar
  32. Li C, Yan JM, Li YZ, Zhang ZC, Wang QL, Liang Y (2013) Silencing the SpMPK1, SpMPK2, and SpMPK3 genes in tomato reduces abscisic acid-mediated drought tolerance. Int J Mol Sci 14:21983–21996CrossRefPubMedPubMedCentralGoogle Scholar
  33. Li JB, Luan YS, Yin YL (2014) SpMYB overexpression in tobacco plants leads to altered abiotic and biotic stress responses. Gene 547:145–151CrossRefPubMedGoogle Scholar
  34. Li J, Luan Y, Liu Z (2015) SpWRKY1 mediates resistance to Phytophthora infestans and tolerance to salt and drought stress by modulating reactive oxygen species homeostasis and expression of defense-related genes in tomato. Plant Cell Tiss Organ Cult 123:67–81CrossRefGoogle Scholar
  35. Luan Y, Cui J, Zhai J, Li J, Han L, Meng J (2015) High-throughput sequencing reveals differential expression of miRNAs in tomato inoculated with Phytophthora infestans. Planta 241:1405–1416CrossRefPubMedGoogle Scholar
  36. Luan Y, Cui J, Wang W, Meng J (2016) MiR1918 enhances tomato sensitivity to Phytophthora infestans infection. Sci Rep 6:35858CrossRefPubMedPubMedCentralGoogle Scholar
  37. Luan Y, Cui J, Li J, Jiang N, Liu P, Meng J (2018) Effective enhancement of resistance to Phytophthora infestans by overexpression of miR172a and b in Solanum lycopersicum. Planta. (Epub ahead of print) PubMedGoogle Scholar
  38. Mittler R, Vanderauwera S, Gollery M, Van Breusegem F (2004) Reactive oxygen gene network of plants. Trends Plant Sci 9:490–498CrossRefPubMedGoogle Scholar
  39. Noutoshi Y, Ito T, Seki M, Nakashita H, Yoshida S, Marco Y, Shirasu K, Shinozaki K (2005) A single amino acid insertion in the WRKY domain of the Arabidopsis TIR-NBS-LRR-WRKY-type disease resistance protein SLH1 (sensitive to low humidity 1) causes activation of defense responses and hypersensitive cell death. Plant J 43:873–888CrossRefPubMedGoogle Scholar
  40. Nowicki M, Fooled MR, Nowakowska M, Kozik EU (2012) Potato and tomato late blight caused by Phytophthora infestans: an overview of pathology and resistance breeding. Plant Dis 96:4–17CrossRefGoogle Scholar
  41. Ohme-Takagi M, Shinshi H (1995) Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7:173–182CrossRefPubMedPubMedCentralGoogle Scholar
  42. Pandey SP, Somssich IE (2009) The role of WRKY transcription factors in plant immunity. Plant Physiol 150:1648–1655CrossRefPubMedPubMedCentralGoogle Scholar
  43. Peng X, Hu Y, Tang X, Zhou P, Deng X, Wang H, Guo Z (2012) Constitutive expression of rice WRKY30 gene increases the endogenous jasmonic acid accumulation, PR gene expression and resistance to fungal pathogens in rice. Planta 236:1485–1498CrossRefPubMedGoogle Scholar
  44. Peng X, Wang H, Jang JC, Xiao T, He H, Jiang D, Tang X (2016) OsWRKY80-OsWRKY4 module as a positive regulatory circuit in rice resistance against Rhizoctonia solani. Rice (NY) 9:63CrossRefGoogle Scholar
  45. Qiu JL, Fiil BK, Petersen K, Nielsen HB, Botanga CJ, Thorgrimsen S, Palma K, Suarez-Rodriguez MC, Sandbech-Clausen S, Lichota J, Brodersen P, Grasser KD, Mattsson O, Glazebrook J, Mundy J, Petersen M (2008) Arabidopsis MAP kinase 4 regulates gene expression through transcription factor release in the nucleus. EMBO J 27:2214–2221CrossRefPubMedPubMedCentralGoogle Scholar
  46. Rodewald J, Trognitz B (2013) Solanum resistance genes against Phytophthora infestans and their corresponding avirulence genes. Mol Plant Pathol 14:740–757CrossRefPubMedGoogle Scholar
  47. Rushton P, Somssich I, Ringler P, Shen Q (2010) WRKY transcription factors. Trends Plant Sci 15:247–258CrossRefPubMedGoogle Scholar
  48. Ryu HS, Han M, Lee SK, Cho JI, Ryoo N, Heu S, Lee YH, Bhoo SH, Wang GL, Hahn TR, Jeon JS (2006) A comprehensive expression analysis of the WRKY gene superfamily in rice plants during defense response. Plant Cell Rep 25:836–847CrossRefPubMedGoogle Scholar
  49. Segarra G, Santpere G, Elena G, Trillas I (2013) Enhanced Botrytis cinerea resistance of Arabidopsis plants grown in compost may be explained by increased expression of defense-related genes, as revealed by microarray analysis. PLoS ONE 8:e56075CrossRefPubMedPubMedCentralGoogle Scholar
  50. Seo PJ, Lee AK, Xiang F, Park CM (2008) Molecular and functional profiling of Arabidopsis pathogenesis-related genes: insights into their roles in salt response of seed germination. Plant Cell Physiol 49:334–344CrossRefPubMedGoogle Scholar
  51. Shen QH, Saijo Y, Mauch S, Biskup C, Bieri S, Keller B, Seki H, Ulker B, Somssich IE, Schulze-Lefert P (2007) Nuclear activity of MLA immune receptors links isolate-specific and basal disease-resistance responses. Science 315:1098–1103CrossRefPubMedGoogle Scholar
  52. Su XH, Zhou P, Wang R, Luo ZP, Xia ZL (2015) Overexpression of the maize psbA gene enhances sulfur dioxide tolerance in transgenic tobacco. Plant Cell Tiss Organ Cult 120:303–311CrossRefGoogle Scholar
  53. Tasset C, Bernoux M, Jauneau A, Pouzet C, Brière C, Kieffer-Jacquinod S, Rivas S, Marco Y, Deslandes L (2010) Autoacetylation of the Ralstonia solanacearum effector PopP2 targets a lysine residue essential for RRS1-R-mediated immunity in Arabidopsis. PLoS Pathog 6:e1001202CrossRefPubMedPubMedCentralGoogle Scholar
  54. Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641CrossRefGoogle Scholar
  55. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111CrossRefPubMedPubMedCentralGoogle Scholar
  56. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protoc 7:562–578CrossRefGoogle Scholar
  57. Turnbull D, Yang L, Naqvi S, Breen S, Welsh L, Stephens J, Morris J, Boevink PC, Hedley PE, Zhan J, Birch PRJ, Gilroy EM (2017) RXLR effector AVR2 up-regulates a brassinosteroid-responsive bHLH transcription factor to suppress immunity. Plant Physiol 174:356–369CrossRefPubMedPubMedCentralGoogle Scholar
  58. Vie AK, Najafi J, Winge P, Cattan E, Wrzaczek M, Kangasjärvi J, Miller G, Brembu T, Bones AM (2017) The IDA-LIKE peptides IDL6 and IDL7 are negative modulators of stress responses in Arabidopsis thaliana. J Exp Bot 68:3557–3571CrossRefPubMedGoogle Scholar
  59. Wang H, Meng J, Peng X, Tang X, Zhou P, Xiang J, Deng X (2015) Rice WRKY4 acts as a transcriptional activator mediating defense responses toward Rhizoctonia solani, the causing agent of rice sheath blight. Plant Mol Biol 89:157–171CrossRefPubMedGoogle Scholar
  60. Wawra S, Trusch F, Matena A, Apostolakis K, Linne U, Zhukov I, Stanek J, Koźmiński W, Davidson I, Secombes CJ, Bayer P, van West P (2017) The RxLR motif of the host targeting effector AVR3a of Phytophthora infestans is cleaved before secretion. Plant Cell 29:1184–1195PubMedPubMedCentralGoogle Scholar
  61. Wi SJ, Ji NR, Park KY (2012) Synergistic biosynthesis of biphasic ethylene and reactive oxygen species in response to hemibiotrophic Phytophthora parasitica in tobacco plants. Plant Physiol 159:251–265CrossRefPubMedPubMedCentralGoogle Scholar
  62. Xia XJ, Wang YJ, Zhou YH, Tao Y, Mao WH, Shi K, Asami T, Chen Z, Yu JQ (2009) Reactive oxygen species are involved in brassinosteroid-induced stress tolerance in cucumber. Plant Physiol 150:801–814CrossRefPubMedPubMedCentralGoogle Scholar
  63. Ye J, Wang X, Hu TX, Zhang FX, Wang B, Li CX, Yang TX, Li HX, Lu YE, Giovannoni JJ, Zhang Y, Ye Z (2017) An InDel in the promoter of Al-ACTIVATED MALSTE TRANSPORTER9 selected during tomato domestication determines fruit malate contents and aluminum tolerance. Plant Cell 29:2249–2268CrossRefPubMedPubMedCentralGoogle Scholar
  64. Yu F, Huaxia Y, Lu W, Wu C, Cao X, Guo X (2012) GhWRKY15, a member of the WRKY transcription factor family identified from cotton (Gossypium hirsutum L.), is involved in disease resistance and plant development. BMC Plant Biol 12:144CrossRefPubMedPubMedCentralGoogle Scholar
  65. Zhang C, Liu L, Zheng Z, Sun Y, Zhou L, Yang Y, Cheng F, Zhang Z, Wang X, Huang S, Xie B, Du Y, Bai Y, Li J (2013) Fine mapping of the Ph-3 gene conferring resistance to late blight (Phytophthora infestans) in tomato. Theor Appl Genet 126:2643–2653CrossRefPubMedGoogle Scholar
  66. Zhang C, Liu L, Wang X, Vossen J, Li G, Li T, Zheng Z, Gao J, Guo Y, Visser RG, Li J, Bai Y, Du Y (2014) The Ph-3 gene from Solanum pimpinellifolium encodes CC-NBS-LRR protein conferring resistance to Phytophthora infestans. Theor Appl Genet 127:1353–1364CrossRefPubMedPubMedCentralGoogle Scholar

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© Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  1. 1.School of Life Science and BiotechnologyDalian University of TechnologyDalianChina
  2. 2.School of Computer Science and TechnologyDalian University of TechnologyDalianChina

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