International Journal of Plant Genomics
Volume 2017, Article ID 8950746, 14 pages
https://doi.org/10.1155/2017/8950746
Research Article
Comparative Transcriptome Analysis Reveals a Preformed Defense System in Apple Root of a Resistant Genotype of G.935 in the Absence of Pathogen
1USDA-ARS, Tree Fruit Research Laboratory, Wenatchee, WA 98801, USA
2USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA
3Tree Fruit Research Institute, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning 10081, China
Correspondence should be addressed to Yanmin Zhu; vog.adsu.sra@uhz.nimnay
Received 14 October 2016; Revised 9 February 2017; Accepted 1 March 2017; Published 30 March 2017
Academic Editor: Anca Macovei
Copyright © 2017 Yanmin Zhu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Linked References
- J. D. G. Jones and J. L. Dangl, “The plant immune system,” Nature, vol. 444, no. 7117, pp. 323–329, 2006. View at Publisher · View at Google Scholar · View at Scopus
- P. N. Dodds and J. P. Rathjen, “Plant immunity: towards an integrated view of plant-pathogen interactions,” Nature Reviews Genetics, vol. 11, no. 8, pp. 539–548, 2010. View at Publisher · View at Google Scholar · View at Scopus
- J. L. Dangl, D. M. Horvath, and B. J. Staskawicz, “Pivoting the plant immune system from dissection to deployment,” Science, vol. 341, no. 6147, pp. 746–751, 2013. View at Publisher · View at Google Scholar · View at Scopus
- Y. Jamir, M. Guo, H.-S. Oh et al., “Identification of Pseudomonas syringae type III effectors that can suppress programmed cell death in plants and yeast,” Plant Journal, vol. 37, no. 4, pp. 554–565, 2004. View at Publisher · View at Google Scholar · View at Scopus
- P. He, L. Shan, N.-C. Lin et al., “Specific bacterial suppressors of MAMP signaling upstream of MAPKKK in arabidopsis innate immunity,” Cell, vol. 125, no. 3, pp. 563–575, 2006. View at Publisher · View at Google Scholar · View at Scopus
- K. Nomura, S. DebRoy, Y. H. Lee, N. Pumplin, J. Jones, and S. Y. He, “A bacterial virulence protein suppresses host innate immunity to cause plant disease,” Science, vol. 313, no. 5784, pp. 220–223, 2006. View at Publisher · View at Google Scholar · View at Scopus
- T. Boller and S. Y. He, “Innate immunity in plants: an arms race between pattern recognition receptors in plants and effectors in microbial pathogens,” Science, vol. 324, no. 5928, pp. 742–743, 2009. View at Publisher · View at Google Scholar · View at Scopus
- F. N. Martin and J. E. Loper, “Soilborne plant diseases caused by Pythium spp. ecology, epidemiology, and prospects for biological control,” Critical Reviews in Plant Sciences, vol. 18, no. 2, pp. 111–181, 1999. View at Publisher · View at Google Scholar · View at Scopus
- S. Kamoun, O. Furzer, J. D. G. Jones et al., “The Top 10 oomycete pathogens in molecular plant pathology,” Molecular Plant Pathology, vol. 16, no. 4, pp. 413–434, 2015. View at Publisher · View at Google Scholar · View at Scopus
- M. Mazzola, “Elucidation of the microbial complex having a causal role in the development of apple replant disease in Washington,” Phytopathology, vol. 88, no. 9, pp. 930–938, 1998. View at Publisher · View at Google Scholar · View at Scopus
- Y. Zhu, S. Shin, and M. Mazzola, “Genotype responses of two apple rootstocks to infection by Pythium ultimum causing apple replant disease,” Canadian Journal of Plant Pathology, vol. 38, no. 4, pp. 483–491, 2016. View at Publisher · View at Google Scholar
- E. Vergne, X. Grand, E. Ballini et al., “Preformed expression of defense is a hallmark of partial resistance to rice blast fungal pathogen Magnaporthe oryzae,” BMC Plant Biology, vol. 10, article 206, 2010. View at Publisher · View at Google Scholar · View at Scopus
- A. Lanubile, V. Maschietto, S. De Leonardis, P. Battilani, C. Paciolla, and A. Marocco, “Defense responses to mycotoxin-producing fungi Fusarium proliferatum, F. subglutinans, and Aspergillus flavus in kernels of susceptible and resistant maize genotypes,” Molecular Plant-Microbe Interactions, vol. 28, no. 5, pp. 546–557, 2015. View at Publisher · View at Google Scholar · View at Scopus
- B. Langmead and S. L. Salzberg, “Fast gapped-read alignment with Bowtie 2,” Nature Methods, vol. 9, no. 4, pp. 357–359, 2012. View at Publisher · View at Google Scholar · View at Scopus
- S. F. Altschul, W. Gish, W. Miller, E. W. Meyers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990. View at Publisher · View at Google Scholar · View at Scopus
- K. J. Livak and T. D. Schmittgen, “Analysis of relative gene expression data using real-time quantitative PCR and the method,” Methods, vol. 25, pp. 402–408, 2001. View at Google Scholar
- J. Browse, “Jasmonate passes muster: a receptor and targets for the defense hormone,” Annual Review of Plant Biology, vol. 60, pp. 183–205, 2009. View at Publisher · View at Google Scholar · View at Scopus
- A. Robert-Seilaniantz, M. Grant, and J. D. G. Jones, “Hormone crosstalk in plant disease and defense: more than just Jasmonate-salicylate antagonism,” Annual Review of Phytopathology, vol. 49, pp. 317–343, 2011. View at Publisher · View at Google Scholar · View at Scopus
- A. Miya, P. Albert, T. Shinya et al., “CERK1, a LysM receptor kinase, is essential for chitin elicitor signaling in Arabidopsis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 49, pp. 19613–19618, 2007. View at Publisher · View at Google Scholar · View at Scopus
- X.-C. Zhang, X. Wu, S. Findley et al., “Molecular evolution of lysin motif-type receptor-like kinases in plants,” Plant Physiology, vol. 144, no. 2, pp. 623–636, 2007. View at Publisher · View at Google Scholar · View at Scopus
- P. Singh and L. Zimmerli, “Lectin receptor kinases in plant innate immunity,” Frontiers in Plant Science, vol. 4, article 124, 2013. View at Publisher · View at Google Scholar · View at Scopus
- K. Bouwmeester and F. Govers, “Arabidopsis L-type lectin receptor kinases: phylogeny, classification, and expression profiles,” Journal of Experimental Botany, vol. 60, no. 15, pp. 4383–4396, 2009. View at Publisher · View at Google Scholar · View at Scopus
- B. G. Forde and M. R. Roberts, “Glutamate receptor-like channels in plants: a role as amino acid sensors in plant defence?” F1000Prime Reports, vol. 6, article 37, 2014. View at Publisher · View at Google Scholar · View at Scopus
- M. B. Price, J. Jelesko, and S. Okumoto, “Glutamate receptor homologs in plants: functions and evolutionary origins,” Frontiers in Plant Science, vol. 3, article 235, 2012. View at Publisher · View at Google Scholar · View at Scopus
- F. Van Breusegem and J. F. Dat, “Reactive oxygen species in plant cell death,” Plant Physiology, vol. 141, no. 2, pp. 384–390, 2006. View at Publisher · View at Google Scholar · View at Scopus
- S. R. Ramirez and C. Basu, “Comparative analyses of plant transcription factor databases,” Current Genomics, vol. 10, no. 1, pp. 10–17, 2009. View at Publisher · View at Google Scholar · View at Scopus
- J. L. Riechmann, J. Heard, G. Martin et al., “Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes,” Science, vol. 290, no. 5499, pp. 2105–2110, 2000. View at Publisher · View at Google Scholar · View at Scopus
- P. Bednarek, “Chemical warfare or modulators of defence responses-the function of secondary metabolites in plant immunity,” Current Opinion in Plant Biology, vol. 15, no. 4, pp. 407–414, 2012. View at Publisher · View at Google Scholar · View at Scopus
- E. E. Rogers, J. Glazebrook, and F. M. Ausubel, “Mode of action of the Arabidopsis thaliana phytoalexin camalexin and its role in Arabidopsis-pathogen interactions,” Molecular Plant-Microbe Interactions, vol. 9, no. 8, pp. 748–757, 1996. View at Publisher · View at Google Scholar · View at Scopus
- A. Sellam, B. Iacomi-Vasilescu, P. Hudhomme, and P. Simoneau, “In vitro antifungal activity of brassinin, camalexin and two isothiocyanates against the crucifer pathogens Alternaria brassicicola and Alternaria brassicae,” Plant Pathology, vol. 56, no. 2, pp. 296–301, 2007. View at Publisher · View at Google Scholar · View at Scopus
- R. J. Grayer and T. Kokubun, “Plant-fungal interactions: the search for phytoalexins and other antifungal compounds from higher plants,” Phytochemistry, vol. 56, no. 3, pp. 253–263, 2001. View at Publisher · View at Google Scholar · View at Scopus
- C. Delker and M. Quint, “Expression level polymorphisms: heritable traits shaping natural variation,” Trends in Plant Science, vol. 16, no. 9, pp. 481–488, 2011. View at Publisher · View at Google Scholar · View at Scopus
- A. Druka, E. Potokina, Z. Luo et al., “Expression quantitative trait loci analysis in plants,” Plant Biotechnology Journal, vol. 8, no. 1, pp. 10–27, 2010. View at Publisher · View at Google Scholar · View at Scopus
- D. Kliebenstein, “Quantitative genomics: analyzing intraspecific variation using global gene expression polymorphisms or eQTLs,” Annual Review of Plant Biology, vol. 60, pp. 93–114, 2009. View at Publisher · View at Google Scholar · View at Scopus
- C. Peterhänsel and T. Lahaye, “Be fruitful and multiply: gene amplification inducing pathogen resistance,” Trends in Plant Science, vol. 10, no. 6, pp. 257–260, 2005. View at Publisher · View at Google Scholar · View at Scopus
- M. Wolter, K. Hollricher, F. Salamini, and P. Schulze-Lefert, “The mlo resistance alleles to powdery mildew infection in barley trigger a developmentally controlled defence mimic phenotype,” Molecular and General Genetics, vol. 239, no. 1-2, pp. 122–128, 1993. View at Publisher · View at Google Scholar · View at Scopus
- S. Lòpez-Fernàndez, S. Compant, U. Vrhovsek et al., “Grapevine colonization by endophytic bacteria shifts secondary metabolism and suggests activation of defense pathways,” Plant and Soil, vol. 405, no. 1-2, pp. 155–175, 2016. View at Publisher · View at Google Scholar · View at Scopus
- M. van Hulten, M. Pelser, L. C. van Loon, C. M. J. Pieterse, and J. Ton, “Costs and benefits of priming for defense in Arabidopsis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 14, pp. 5602–5607, 2006. View at Publisher · View at Google Scholar · View at Scopus
- R. Bari and J. D. G. Jones, “Role of plant hormones in plant defence responses,” Plant Molecular Biology, vol. 69, no. 4, pp. 473–488, 2009. View at Publisher · View at Google Scholar · View at Scopus
- K. M. Pajerowska-Mukhtar, M. S. Mukhtar, N. Guex et al., “Natural variation of potato allene oxide synthase 2 causes differential levels of jasmonates and pathogen resistance in Arabidopsis,” Planta, vol. 228, no. 2, pp. 293–306, 2008. View at Publisher · View at Google Scholar · View at Scopus
- M. Berrocal-Lobo and A. Molina, “Ethylene response factor 1 mediates Arabidopsis resistance to the soilborne fungus Fusarium oxysporum,” Molecular Plant-Microbe Interactions, vol. 17, no. 7, pp. 763–770, 2004. View at Publisher · View at Google Scholar · View at Scopus
- P. J. Rushton, I. E. Somssich, P. Ringler, and Q. J. Shen, “WRKY transcription factors,” Trends in Plant Science, vol. 15, no. 5, pp. 247–258, 2010. View at Publisher · View at Google Scholar · View at Scopus
- N. De Geyter, A. Gholami, S. Goormachtig, and A. Goossens, “Transcriptional machineries in jasmonate-elicited plant secondary metabolism,” Trends in Plant Science, vol. 17, no. 6, pp. 349–359, 2012. View at Publisher · View at Google Scholar · View at Scopus
- S. Shin, J. Lv, G. Fazio, M. Mazzola, and Y. Zhu, “Transcriptional regulation of ethylene and jasmonate mediated defense response in apple (Malus domestica) root during Pythium ultimum infection,” Horticulture Research, vol. 1, article 53, 2014. View at Publisher · View at Google Scholar
- S. Shin, P. Zheng, G. Fazio, M. Mazzola, D. Main, and Y. Zhu, “Transcriptome changes specifically associated with apple (Malus x domestica) root defense response during Pythium ultimum infection,” Physiological and Molecular Plant Pathology, vol. 94, pp. 16–26, 2016. View at Publisher · View at Google Scholar · View at Scopus
- B. C. Meyers, A. W. Dickerman, R. W. Michelmore, S. Sivaramakrishnan, B. W. Sobral, and N. D. Young, “Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily,” Plant Journal, vol. 20, no. 3, pp. 317–332, 1999. View at Publisher · View at Google Scholar · View at Scopus
- J. L. Dangl and J. D. G. Jones, “Plant pathogens and integrated defence responses to infection,” Nature, vol. 411, no. 6839, pp. 826–833, 2001. View at Publisher · View at Google Scholar · View at Scopus
- F. Jupe, L. Pritchard, G. J. Etherington et al., “Identification and localisation of the NB-LRR gene family within the potato genome,” BMC Genomics, vol. 13, no. 1, article 75, 2012. View at Publisher · View at Google Scholar · View at Scopus
- R. Marathe, R. Anandalakshmi, Y. Liu, and S. P. Dinesh-Kumar, “The tobacco mosaic virus resistance gene, N,” Molecular Plant Pathology, vol. 3, no. 3, pp. 167–172, 2002. View at Publisher · View at Google Scholar · View at Scopus
- X. Zhang, S. Shiu, A. Cal, and J. O. Borevitz, “Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays,” PLoS Genetics, vol. 4, no. 3, Article ID e1000032, 2008. View at Publisher · View at Google Scholar · View at Scopus
- C. M. Herrera and P. Bazaga, “Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory,” Molecular Ecology, vol. 20, no. 8, pp. 1675–1688, 2011. View at Publisher · View at Google Scholar · View at Scopus
- S. Feng and S. E. Jacobsen, “Epigenetic modifications in plants: an evolutionary perspective,” Current Opinion in Plant Biology, vol. 14, no. 2, pp. 179–186, 2011. View at Publisher · View at Google Scholar · View at Scopus
- R. Velasco, A. Zharkikh, J. Affourtit et al., “The genome of the domesticated apple (Malus × domestica Borkh.),” Nature Genetics, vol. 42, no. 10, pp. 833–839, 2010. View at Publisher · View at Google Scholar · View at Scopus