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Title:   Author  item
                                            Shin, Sungitem
                                            ZHENG, PING - Washington State Universityitem
                                            Fazio, Gennaroitem
                                            Mazzola, Markitem
                                            MAIN, DORRIE - Washington State Universityitem
                                            Zhu, Yanmin
  Submitted to: Physiological and Molecular Plant Pathology
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 3/6/2016
                                    Publication  Date: 3/15/2016
                                    Citation: Shin, S.B., Zheng, P., Fazio, G., Mazzola, M., Main, D., Zhu, Y. 2016. Transcriptome changes specifically associated with apple (Malus domestica) root defense response during Pythium ultimum infection. Physiological and Molecular Plant Pathology. 94:16-26.Interpretive Summary: Although pre-plant fumigation of orchard soils is the primary method for the control of apple replant disease (ARD), the future availability of currently used fumigants could be restricted due to environmental concerns. The understanding of the defense response to apple rootstocks to necrotrophic soilborne pathogens that incite ARD is crucial for better utilization of natural resistance to manage this disease syndrome. In this study, root tissues of apple seedlings inoculated with Pythium ultimum, were sampled at 0, 1, 4, 8, 24, 48, 72 and 96 hours post inoculation (hpi) along with mock inoculated tissue at each time point. A high throughput and large-scale RNA-Seq based transcriptome profiling was performed on these samples to reveal the systematic changes in apple root tissues. The peak defense response occurred at 48 hpi based on the number of the identified genes along the infection process. The analysis of genome-wide gene expression revealed many aspects of re-direction of cellular activities upon pathogen infection, such as the oxido-reduction balance, trans-membrane trafficking, hormone signaling and secondary metabolisms. This dataset constitutes the first experimental evidences of a molecular framework related to the defense responses in apple root system.  The individual genes can serve as the candidates to delineate their relationship with resistant phenotype among rootstock germplasm. The further study along this direction may lead to the development of predicative molecular tools for more efficiently breeding of resistant rootstocks to ARD.
                                Technical Abstract: The defense response of apple rootstocks to necrotrophic soilborne pathogens that incite apple replant disease (ARD) has not been investigated. In this study, root tissues of apple seedlings inoculated with Pythium ultimum, were sampled at 0, 1, 4, 8, 24, 48, 72 and 96 hours post inoculation (hpi) along with mock inoculated tissue at each time point. RNA-Seq based transcriptome profiling was performed on these samples with a minimum of 20 million reads per sample; read mapping, transcript discovery and differentially expressed gene (DEG) identification was carried out using CLC Genomics Workbench software suit, followed by Gene Ontology and pathway analyses. The peak defense response occurred at 48 hpi based on the number of the identified DEGs along the infection process. Transcriptomic changes related to oxido-reduction balance, trans-membrane trafficking and metabolic activities indicated the re-direction of cellular activities to combat P. ultimum infection. DEGs functioning in hormone signaling including ethylene, jasmonate, gibberellin, cytokinin, and auxin, and those encoding NAC, WRKY, MYB, and ERF transcription factors were mostly identified from 24-48 hpi; DEGs encoding enzymes in several biosynthesis pathways of secondary metabolisms and cell wall modification proteins are consistently up-regulated during the later stage of infection. DEGs encoding defense and stress related proteins such as chitin elicitor receptor kinase and  wall-associated receptor kinase (WAK), endochitinase (PR4), thaumatin (PR5)-like protein, laccase, mandelonitrile lyase, and cyanogenic beta-glucosidase were also highly induced. The dataset constitutes the first experimental evidence of a molecular framework for defense responses in apple root system.


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