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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Food Quality Laboratory » Research » Research Project #437166

Research Project: Understand and Mitigate Fungicide Resistance in Penicillium spp

Location: Food Quality Laboratory

Project Number: 8042-42430-002-007-T
Project Type: Trust Fund Cooperative Agreement

Start Date: Apr 6, 2020
End Date: Feb 24, 2024

1. Evaluate pathogenic fitness of resistant populations with different fungicide resistance phenotypes. To assess potential fitness penalties, usually associated with fungicide resistance, in isolates with different resistance phenotypes and their ability to survive, sporulate, and cause blue mold under various conditions. Such information is critical to estimate the real-world risks of control failures, especially when storage is extended and to help predict where resistance may develop and persist. 2. Determine the genomic makeup of Penicillium species with various fungicide resistance phenotypes to postharvest fungicides. To: 1) accurately identify these new Penicillium species recently found in WA and assess their sensitivities to currently labeled materials to ensure that all current fungicides control these emerging Penicillium species; and to 2) elucidate genome sequences of Penicillium isolates with different resistance phenotypes. This knowledge is crucial to understand the role of management practices in population changes over time and to develop early detection tools in the future. 3. Assess the efficacy of various approaches to mitigate resistance in Penicillium spp. Evaluate the efficacy of annual and biannual rotation scenarios, with and without sanitation using discriminatory dose screening. We will also evaluate the efficacy of some chemo-sensitizers to reverse or reduce resistance in resistant populations to regain decay control using existing postharvest fungicides labeled for pome fruits.

To determine if fungicide resistant isolates are associated with defects in their ability to grow, sporulate, and proliferate, their fitness will be evaluated using a variety of in vitro tests which will be conducted by ARS and the cooperator (WSU): colony radial growth, spore production, and conidial germination. WSU will assess the practical impact of fungicide resistance in Penicillium spp. in causing decay failures on fungicide-treated fruit after harvest, Penicillium spp. isolates will be analyzed in vivo for their ability to cause decay on Academy® (difenoconazole + fludioxonil), Merect® (thiabendazole), Penbotec™ (pyrimethanil), and Scholar® (fludioxonil)-treated apple fruit. Fruit will be assessed monthly for decay, and each treatment will have three replicate trays each containing 20 fruit. WSU will identify isolates to species using a combination of classical mycological and genetic methods. Individual sequences, along with concatenated loci will be used to generate phylogenetic trees to assess new species relationships with known blue mold species that cause apple postharvest decay. ARS will utilize Next generation sequencing technology (Illumina platform) to obtain the whole genome sequences of 15 Penicillium spp. isolates based on differences in their fungicide resistance profiles. Raw sequence reads will be generated by the Illumina MiSeq platform. All reads will be used to generate de novo assemblies with Velvet Optimiser 2.2.0 and HGAP3. The quality of the final assembly should be reflected by the resulting number of scaffolds, which is indicative of a high quality assembly along with BUSCO analysis. ARS will assist the cooperator (WSU) by determining the impact of fungicide rotation and chemosensitizers to reduce or reverse fungicide resistance in Penicillium spp. populations obtained from packinghouses that do yearly and within year rotation of different postharvest fungicides. Tests will be performed using both in vitro and in vivo methods with 10 different chemosensitizers.