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ARS Home » Pacific West Area » Wenatchee, Washington » Physiology and Pathology of Tree Fruits Research » Research » Research Project #426043

Research Project: Integration of Host-Genotype and Manipulation of Soil Biology for Soil-borne Disease Control in Agro-Ecosystems

Location: Physiology and Pathology of Tree Fruits Research

Project Number: 2094-21220-001-00-D
Project Type: In-House Appropriated

Start Date: Nov 25, 2013
End Date: Mar 16, 2017

The long-term objective of this program is to develop and optimize non-fumigant measures for the management of orchard replant disease, with emphasis on pome fruit production systems. This program will identify and manage microbiological resources resident to soil ecosystems that possess a capacity to suppress populations and/or activity of the pathogen/parasite complex that incites apple replant disease. Studies will also aim to optimize such a system through identification of rootstock genotypes that possess a superior capacity to exploit this microbial resource and/or demonstrate resistance to components of the causal pathogen complex. Over the next 3 years this program will focus on the following objectives: Objective 1: Define the functional mechanism(s) that operate soil amendment-based strategies that suppress the pathogen/parasite complex which incites orchard replant disease. Objective 2: Develop and evaluate in the field novel integrated systems to attain the necessary spectrum of pathogen/parasite suppression for control of orchard replant disease. • Sub-objective 2.A Determine whether microbe-mediated rootstock tolerance is expressed across soil systems. • Sub-objective 2.B. Evaluate anaerobic soil disinfestation alone or in concert with Brassicaceae seed meals for the capacity to control orchard replant disease. • Sub-objective 2.C. Assess the influence of fertility management program on re-establishment of the pathogen/parasite complex which incites apple replant disease. Objective 3: Develop molecular markers in rootstock of apple, pear, and/or cherry to identify rootstock resistance or enhance biocontrol. • Sub-objective 3.A. Transcriptome profiling of apple rootstocks in response to the infection by soil-borne necrotrophic pathogens. • Sub-objective 3.B. Comparative analysis of transcriptome profiling between resistant and susceptible apple rootstocks in response to infection by soil-borne necrotrophic pathogens. • Sub-objective 3.C. Characterize the regulation of identified candidate molecular pathways among expanded resistant and susceptible rootstock genotypes.

1: Hypothesis: Optimal long-term efficacy of Brassicaceae seed meal (BSM) amendment and anaerobic soil disinfestation requires a functional soil microbiological community. Employment of anaerobic soil disinfestation (ASD) and BSM will be tested in concert to assess their capacity to provide enhanced control of tree fruit soil-borne pathogens as well as sustained suppression of soil re-infestation by replant causal pathogens. 2: Sub-obj. 2.A Hypothesis: Rootstock genotypes select for unique microbial populations that minimize or accentuate replant disease development. Roots and associated rhizosphere soil will be collected from rootstocks highly susceptible and tolerant to replant disease. Root infestation by replant pathogens will be determined using previously described culture-based and real-time qPCR protocols. The rhizosphere microbiome will be characterized through pyrosequencing-based analyses. 2.B. Hypothesis: Integration of ASD with BSM amendment will provide superior control of apple replant disease. This study will determine the effect of application sequence and BSM application rates on disease control efficacy. Studies will employ 6 main treatments, i.e., ASD alone, BSM alone, ASD followed by BSM, BSM followed by ASD, no treatment control and positive control (pasteurization). Applicable reduced BSM rates in concert with ASD, and application sequence to be utilized in future field trials will be based upon findings from these greenhouse trials. 2C. Hypothesis: Certain currently available and commonly utilized fertilizer inputs will impact re-colonization of orchard soils by replant pathogens. Fertilizer inputs will be applied to orchards recently established on replanted sites. Fertility treatments applied to fumigated soil, include, urea, plant-based compost, and Brassica juncea seed meal. The trial will use a randomized complete block design with 6 replicates. Fungal, oomycete and nematode soil populations and apple root colonization/infestation by the resident pathogen complex, including Cylindrocarpon, Pythium, Phytophthora , Rhizoctonia and Pratylenchus penetrans, will be determined. 3: Sub-obj. 3.A. Studies will analyze sequential transcriptome changes in root tissues after inoculation with specific replant pathogens. Genes exhibiting differential expression after exposure to the pathogen will be identified and examined further. 3.B. Transcriptome profilings between resistant and susceptible rootstock genotypes in response to Pythium ultimum infection will be examined. Gene clusters exhibiting differential expression between rootstocks possessing different resistance phenotypes will be subject to further pathway analysis. 3.C. Hypothesis: Coordinated action of specific genes in the ethylene and jasmonic acid response pathways, as well as others with regulatory and signaling functions, contribute to the relative tolerance of perennial tree rootstocks to soil-borne fungal pathogens. Candidate genes in the apple ET/JA biosynthesis pathways and members of the transcription factor families will be profiled between resistant and susceptible rootstocks and in response to Pythium ultimum infection.