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Identification of Genes Involved in Resistance to Didymella pinodes in Pea by deepSuperSAGE Transcriptome Profiling

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Abstract

Didymella pinodes, causing ascochyta blight, is the most destructive foliar pathogen of dry peas. Despite the importance of this pathogen, very little is known about the mechanisms or genes that control host plant resistance against the fungus. Here we employed deepSuperSAGE genome-wide transcription profiling to identify pea genes involved in resistance to D. pinodes in the wild, resistant Pisum sativum ssp. syriacum accession P665. Two deepSuperSAGE libraries were constructed from leaf RNA of infected and control plants. A total of 17,561 different UniTags were obtained. Seventy per cent of them could be assigned to known sequences from pea or other plants. 509 UniTags were significantly differentially expressed (P < 0.05; fold change ≥2, ≤2) in inoculated versus control plants. Of these, 78 % could be assigned to known sequences from pea or other plants, and 58 % to proteins with known function. Our results suggest that a battery of genes contribute to resistance against D. pinodes in the wild pea accession P665. For example, genes encoding protease inhibitors are activated, and the corresponding proteins may contribute to a lower penetration success. The production of antifungal compounds and strengthening of host cell walls may interfere with the spread of the pathogen. In addition, detoxification of D. pinodes toxins and repair of cell walls could also reduce the damage produced by this devastating necrotroph. Hormones orchestrate metabolic adaptation to D. pinodes infection, since ethylene, ABA and indole-3-acetic acid pathways were up-, while the gibberellic acid pathway was down-regulated.

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References

  • Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7:986–995

    CAS  PubMed  Google Scholar 

  • Bari R, Jones JDG (2009) Role of plant hormones in plant defense responses. Plant Mol Biol 69:473–488

    Article  CAS  PubMed  Google Scholar 

  • Bonshtien A, Lev A, Gibly A, Debbie P, Avni A, Sessa G (2005) Molecular properties of the Xanthomonas AvrRxv effector and global transcriptional changes determined by its expression in resistant tomato plants. Mol Plant–Microbe Interact 18:300–310

    Article  CAS  PubMed  Google Scholar 

  • Bradley DJ, Kjellbom P, Lamb CJ (1992) Elicitor and wound-induced oxidative cross-linking of a plant cell wall proline-rich protein: a novel, rapid defense response. Cell 70:21–30

    Article  CAS  PubMed  Google Scholar 

  • Carrillo E, Rubiales D, Pérez-de-Luque A, Fondevilla S (2013) Characterization of mechanisms of resistance against Didymella pinodes in Pisum spp. Eur J Plant Pathol 135:761–769

    Article  CAS  Google Scholar 

  • Castillejo MA, Susín R, Madrid E, Fernández-Aparicio M, Jorrín JV, Rubiales D (2010a) Two-dimensional gel electrophoresis-based proteomic analysis of the Medicago truncatula–rust (Uromyces striatus) interaction. Ann Appl Biol 157:243–257

    Article  CAS  Google Scholar 

  • Castillejo MA, Curto M, Fondevilla S, Rubiales D, Jorrín J (2010b) Two-dimensional electrophoresis based proteomic analysis of the pea (Pisum sativum) in response to Mycosphaerella pinodes. J Agric Food Chem 58:12822–12832

    Article  CAS  PubMed  Google Scholar 

  • Choi HW, Lee BG, Kim NH, Park Y, Lim CW et al (2008) A role for a menthone reductase in resistance against microbial pathogens in plants. Plant Physiol 148:383–401

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Clulow SA, Lewis BG, Matthews P (1991) A pathotype classification for Mycosphaerella pinodes. Phytopathology 131:322–332

    Google Scholar 

  • Daniels CH, Fristensky B, Wagoner W, Hadwiger LA (1987) Pea genes associated with non-host disease resistance to Fusarium are also active in race-specific disease resistance to Pseudomonas. Plant Mol Biol 8:309–316

    Article  CAS  PubMed  Google Scholar 

  • Die JV, Román B, Nadal S, González-Verdejo CI (2010) Evaluation of candidate reference genes for expression studies in Pisum sativum under different experimental conditions. Planta 232:145–153

    Article  CAS  PubMed  Google Scholar 

  • Diener AC, Ausubel FM (2005) Resistance to Fusarium oxysporum 1, a dominant Arabidopsis disease-resistance gene, is not race specific. Genetics 171:305–321

    Article  CAS  PubMed  Google Scholar 

  • Dixon DP, Hawkins T, Hussey PJ, Edwards R (2009) Enzyme activities and subcellular localization of members of the Arabidopsis glutathione transferase superfamily. J Exp Bot 60(4):1207–1218

    Article  CAS  PubMed  Google Scholar 

  • Fondevilla S, Ávila CM, Cubero JI, Rubiales D (2005) Response to Mycosphaerella pinodes in a germplasm collection of Pisum spp. Plant Breeding 124:313–315

    Article  Google Scholar 

  • Fondevilla S, Satovic Z, Rubiales D, Moreno MT, Torres AM (2008) Mapping of quantitative trait loci for resistance to Mycosphaerella pinodes in Pisum sativum subsp. syriacum. Mol Breeding 21:439–454

    Article  CAS  Google Scholar 

  • Fondevilla S, Küster H, Krajinski F, Cubero JI, Rubiales D (2011) Identification of genes differentially expressed in a resistant reaction to Mycosphaerella pinodes in pea using microarray technology. BMC Genomics 12:28

    CAS  PubMed Central  PubMed  Google Scholar 

  • Franssen SU, Shrestha RP, Bräutigam A, Bornberg-Bauer E, Weber APM (2011) Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMC Genomics 12:227

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Fristensky B, Riggleman RC, Wagoner W, Hadwiger LA (1985) Gene expression in susceptible and disease resistant interactions of peas induced with Fusarium solani pathogens and chitosan. Physiol Plant Pathol 27:15–28

    Article  CAS  Google Scholar 

  • Glazebrook J (2005) Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annu Rev Phytopathol 43:205–227

    Article  CAS  PubMed  Google Scholar 

  • Gosti F, Beaudoin N, Serizet C, Webb AAR, Vartanian N, Giraudat J (1999) ABI1 protein phosphatase 2C is a negative regulator of abscisic acid signaling. Plant Cell 11:1897–1909

    CAS  PubMed Central  PubMed  Google Scholar 

  • He ZH, He D, Kohorn BD (1998) Requirement for the induced expression of a cell wall- associated receptor kinase for survival during the pathogen response. Plant J 14:55–63

    Article  CAS  PubMed  Google Scholar 

  • Hiraga S, Sasaki K, Ito H, Ohashi Y, Matsui H (2001) A large family of class III plant peroxidases. Plant Cell Physiol 42:462–468

    Article  CAS  PubMed  Google Scholar 

  • Jakoby M, Weisshaar B, Dröge-Laser W, Carbajosa JV, Tiedemann J, Kroj T, Parcy F (2002) bZIP transcription factors in Arabidopsis. Trends Plant Sci 7(3):106–111

    Article  CAS  PubMed  Google Scholar 

  • Kaur S, Pembleton LW, Cogan NO, Savin KW, Leonforte T et al (2012) Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers. BMC Genomics 13:104

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kohorn BD, Kohorn SL (2012) The cell wall associated kinases, WAKs as pectin receptors. Front Plant Sci 3:88

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Krishnaswamy SS, Srivastava S, Mohammadi M, Rahman MH, Deyholos MK, Kav NNV (2008) Transcriptional profiling of pea ABR17 mediated changes in gene expression in Arabidopsis thaliana. BMC Plant Biology 8:91

    Article  PubMed Central  PubMed  Google Scholar 

  • Johnson R, Narvaez J, An G, Ryan CA (1989) Expression of proteinase inhibitors I and II in transgenic tobacco plants: effects on natural defense against Manduca sexta. Proc Natl Acad Sci USA 86:9871–9875

    Article  CAS  PubMed  Google Scholar 

  • Iqbal MJ, Yaegashi S, Ahsan R, Shopinski KL, Lightfoot DA (2005) Root response to Fusarium solani f. sp. glycines: Temporal accumulation of transcripts in partially resistant and susceptible soybean. Theor Appl Genet 110:1429–1438

    Article  CAS  PubMed  Google Scholar 

  • Li H, Zhou S, Zhao W, Su S, Peng Y (2009) A novel wall-associated receptor-like protein kinase gene, OsWAK1, plays important roles in rice blast disease resistance. Plant Mol Biol 69:337–346

    Article  CAS  PubMed  Google Scholar 

  • Lu H, Higgins VJ (1999) The effect of hydrogen peroxide on the viability of tomato cells and of the fungal pathogen Cladosporium fulvum. Physiol Mol Plant Pathol 54:131–143

    Article  CAS  Google Scholar 

  • Luo M, Dang P, Bausher MG, Holbrook CC, Lee RD et al (2005) Identification of transcripts involved in resistance responses to leaf spot disease caused by Cercosporidium personatum in peanut (Arachis hypogaea). Phytopathology 95:381–387

    Article  CAS  PubMed  Google Scholar 

  • Mader M, Fussl R (1982) Role of peroxidase in lignification of tobacco cells. Plant Physiol 70:1132–1134

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Marrs KA (1996) The functions and regulation of glutathione S-transferases in plants. Annu Rev Plant Physiol Plant Mol Biol 47:127–158

    Article  CAS  PubMed  Google Scholar 

  • Martin C, Paz-Ares J (1997) MYB transcription factors in plants. Trends Genet 13(2):67–73

    Article  CAS  PubMed  Google Scholar 

  • Matsui H, Nakamura G, Ishiga Y, Toshima H, Inagaki Y et al (2004) Structure and expression of 12-oxophytodienoate reductase (subgroup I) genes in pea, and characterization of the oxidoreductase activities of their recombinant products. Mol Gen Genomics 271:1–10

    Article  CAS  Google Scholar 

  • Matsumura H, Yoshida K, Luo S, Kimura E, Fujibe T et al (2010) High-throughput SuperSAGE for digital gene expression analysis of multiple samples using Next Generation Sequencing. PLoS ONE 5(8):e12010

    Article  PubMed Central  PubMed  Google Scholar 

  • Mayrose M, Ekengren SK, Melech-Bonfil S, Martin GB, Sessa G (2006) A novel link between tomato GRAS genes, plant disease resistance and mechanical stress response. Mol Plant Pathol 7:593–604

    Article  CAS  PubMed  Google Scholar 

  • Molina C, Rotter B, Horres R, Udupa SU, Besser B et al (2008) SuperSAGE: The drought stress-responsive transcriptome of chickpea roots. BMC Genomics 9:553–581

    Article  PubMed Central  PubMed  Google Scholar 

  • Molina C, Zaman-Allah M, Khan F, Fatnassi N, Horres R et al (2011) The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE. BMC Plant Biol 11:31

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Moy P, Qutob D, Chapman BP, Atkinson I, Gijzen M (2004) Patterns of gene expression upon infection of soybean plants by Phytophthora sojae. Mol Plant–Microbe Interact 17:1051–1062

    Article  CAS  PubMed  Google Scholar 

  • Mustafa BM, Coram TE, Pang ECK, Taylor PWJ, Ford R (2009) A cDNA microarray approach to decipher lentil (Lens culinaris) responses to Ascochyta lentis. Aust Plant Pathol 38:617–631

    Article  CAS  Google Scholar 

  • Park C, Peng Y, Chen X, Dardick C, Ruan D et al (2008) Rice XB15, a protein phosphatase 2C, negatively regulates cell death and XA21-mediated innate immunity. PLoS Biology 6(9):e231

    Article  PubMed Central  PubMed  Google Scholar 

  • Prioul S, Frankewitz A, Deniot G, Morin G, Baranger (2004) A Mapping of quantitative trait loci for partial resistance to Mycosphaerella pinodes in pea (Pisum sativum L.) at the seedling and adult plant stages. Theor Appl Genet 108:1322–1334

    Article  CAS  PubMed  Google Scholar 

  • Quilis J, Meynard D, Vila L, Avilés FX, Guiderdoni E, San Segundo B (2007) A potato carboxypeptidase inhibitor gene provides pathogen resistance in transgenic rice. Plant Biotechnol J 5:537–553

    Article  CAS  PubMed  Google Scholar 

  • Riggleman RC, Fristensky B, Hadwiger LA (1985) The disease resistance response in pea is associated with increased levels of specific mRNAs. Plant Mol Biol 4(81):86

    Google Scholar 

  • Ringlia C, Keller B, Ryserb U (2001) Glycine-rich proteins as structural components of plant cell walls. Cell Mol Life Sci 58:1430–1441

    Article  Google Scholar 

  • Rubiales D, Fondevilla S (2012) Future prospects for ascochyta blight resistance breeding in cool season food legumes. Front Plant Sci 3:27

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Salam MU, Galloway J, Diggle J, MacLeod WJ, Maling T (2011) Predicting regional-scale spread of ascospores of Didymella pinodes causing ascochyta blight disease on field pea. Aust Plant Pathol 40(6):640–647

    Article  Google Scholar 

  • Samac DA, Peñuela S, Schnurr JA, Hunt EN, Foster-Hartnett D et al (2011) Expression of coordinately regulated defence response genes and analysis of their role in disease resistance in Medicago truncatula. Mol Plant Pathol 12(8):786–798

    Article  CAS  PubMed  Google Scholar 

  • Schenk PM, Kazan K, Wilson I, Anderson JP, Richmond T et al (2000) Coordinated plant defense responses in Arabidopsis revealed by microarray analysis. Proc Natl Acad Sci USA 97(21):11655–11660

    Article  CAS  PubMed  Google Scholar 

  • Schwechheimer C (2008) Understanding gibberellic acid signaling—are we there yet? Curr Opin Plant Biol 11:9–15

    Article  CAS  PubMed  Google Scholar 

  • Tar’an B, Warkentin T, Somers DJ, Miranda D, Vandenberg A et al (2003) Quantitative trait loci for lodging resistance, plant height and partial resistance to mycosphaerella blight in field pea (Pisum sativum L.). Theor Appl Genet 107:1482–1491

    Article  PubMed  Google Scholar 

  • Tellström V, Usadel B, Thimm O, Still M, Küster H, Niehaus K (2007) The lipopolysaccharide of Sinorhizobium meliloti suppresses defense-associated gene expression in cell cultures of the host plant Medicago truncatula. Plant Physiol 143:825–837

    Article  PubMed Central  PubMed  Google Scholar 

  • Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M (2004) MAPMAN: a user driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37:914–939

    Article  CAS  PubMed  Google Scholar 

  • Timmerman-Vaughan GM, Frew TJ, Russell AC, Khan T, Butler R et al (2002) QTL mapping of partial resistance to field epidemics of ascochyta blight of pea. Crop Sci 42:2100–2111

    Article  CAS  Google Scholar 

  • Timmerman-Vaughan GM, Frew TJ, Butler R, Murray S, Gilpin M et al (2004) Validation of quantitative trait loci for Ascochyta blight resistance in pea (Pisum sativum L.), using populations from two crosses. Theor Appl Genet 109:1620–1631

    Article  CAS  PubMed  Google Scholar 

  • Tivoli B, Banniza S (2007) Comparison of the epidemiology of ascochyta blights on grain legumes. Eur J Plant Pathol 119:59–76

    Article  Google Scholar 

  • Torres MA, Jones JDG, Dangl JL (2005) Pathogen-induced, NADPH oxidasederived reactive oxygen intermediates suppress spread of cell death in Arabidopsis thaliana. Nat Genet 37:1130–1134

    Article  CAS  PubMed  Google Scholar 

  • Thurau T, Kifle S, Jung C, Cai D (2003) The promoter of the nematode resistance gene Hs1pro-1 activates a nematode-responsive and feeding site-specific gene expression in sugar beet (Beta vulgaris L.) and Arabidopsis thaliana. Plant Mol Biol 52:643–660

    Article  CAS  PubMed  Google Scholar 

  • Usadel B, Nagel A, Thimm O, Redestig H, Blaesing OE et al (2005) Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiol 138:1195–1204

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Vandenabeele S, Van Der Kelen K, Dat J, Gadjev I, Boonefaes T et al (2003) A comprehensive analysis of hydrogen peroxide-induced gene expression in tobacco. Proc Natl Acad Sci USA 100:16113–16118

    Article  CAS  PubMed  Google Scholar 

  • Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270:484–487

    Article  CAS  PubMed  Google Scholar 

  • van Loon L, van Strien EA (1999) The families of pathogenesis related proteins, their activities and comparative analysis of PR-1 type proteins. Physiol Mol Plant Pathol 55:85–97

    Article  Google Scholar 

  • Wang X, Vindhya BM, Basnayake S, Zhang H, Li G et al (2009) The Arabidopsis ATAF1, a NAC transcription factor, is a negative regulator of defense responses against necrotrophic fungal and bacterial pathogens. Mol Plant Microbe Interact 22(10):1227–1238

    Article  CAS  PubMed  Google Scholar 

  • Wroth JM (1998) Possible role for wild genotypes of Pisum spp. to enhance ascochyta blight resistance in pea. Aust J Exp Agric 38:469–479

    Article  Google Scholar 

  • Zabala G, Zou J, Tuteja J, Gonzalez DO, Clough SJ, Vodkin LO (2006) Transcriptome changes in the phenylpropanoid pathway of Glycine max in response to Pseudomonas syringae infection. BMC Plant Biol 6:26

    Article  PubMed Central  PubMed  Google Scholar 

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Acknowledgments

The authors thank Professor Günter Kahl for critical revision of the manuscript. Financial support by AGL2011-22524 and GEN2006-27798-C6-6-E/VEG projects is acknowledged. S.F. was funded by FP7-PEOPLE-2011-IEF-300235 and a JAEDoc contract.

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Authors and Affiliations

  1. Institute for Molecular Bioscience, University of Frankfurt, Max-von Laue Str. 9, 60438, Frankfurt am Main, Germany

    Sara Fondevilla

  2. GenXPro, Altenhöferallee 3, 60438, Frankfurt am Main, Germany

    Björn Rotter, Nicolas Krezdorn, Ruth Jüngling & Peter Winter

  3. Institute for Sustainable Agriculture, CSIC, Apdo. 4084, 14080, Córdoba, Spain

    Sara Fondevilla & Diego Rubiales

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  1. Sara Fondevilla
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Correspondence to Sara Fondevilla.

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Fondevilla, S., Rotter, B., Krezdorn, N. et al. Identification of Genes Involved in Resistance to Didymella pinodes in Pea by deepSuperSAGE Transcriptome Profiling. Plant Mol Biol Rep 32, 258–269 (2014). https://doi.org/10.1007/s11105-013-0644-6

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