Population Genomics, Diagnostic Strain Determination, and SIT Characterization for the Mexican Fruit Fly Anastrepha Ludens

Grants and Contracts Details


Title Population genomics, diagnostic strain determination, and SIT characterization for the Mexican fruit fly Anastrepha ludens Abstract The following is a proposal for the Plant Protection Act FY22. The primary purpose of this agreement is to develop population genomic resources and diagnostic tools for SIT strain determination and colony characterization for the Mexican fruit fly Anastrepha ludens. The Mexican fruit fly is a destructive agricultural pest across its range of Central America and Mexico. It poses a significant threat to U.S. agriculture due to its proximity to citrus production in south Texas and California. Prior work using DNA data sets has demonstrated that populations of the species can be distinguished using genome-wide double-digest Restriction Site Associated sequencing (ddRAD) markers but that increased sample sizes of lab colonies and wild populations are needed to enhance confidence in the technologies (Dupuis et al. 2019 EvolApp 12:1641-1660). In year one of this project, PPA funded work to expand data sets with additional fly collections using ddRAD methods and applied these methods to field collected flies from California and Texas and lab colonies from Black Pupal Strains and Willacy strain in Texas, and this work is underway. In year two of the project, PPA funded work to increase genomic sampling of additional insect colony collections by generating Whole Genome “shotgun” Sequencing (WGS) data for a subset of individuals sequenced during year one. Additionally, year two includes objectives for technology development studies to convert SNP genotyping technology that was developed from ddRAD/WGS data into a multiplex amplicon panel that can be sequenced on in-house Illumina iSeq platforms. This technology can be integrated with other marker systems used to diagnose species to provide a single protocol for Mexican fruit fly diagnosis. In year three of this project (the current suggestion), we will evaluate the efficacy of the sequencing-based diagnostic panel developed in year two. This will be accomplished by sequencing 1) experimentally manipulated fly samples representing a variety of real-world collection conditions (poor DNA preservation, low input tissue quantity, etc.), and 2) series of real-world specimens collected as part of regular monitoring/surveillance efforts in California and Texas over the past ~5 years. This one-year suggestion supports the FY22 Plant Protection Act Implementation Plan by developing and improving identification and diagnostic capacity for high priority pests. The impact of this work includes both real-world validation of the diagnostic panel generated in this project, as well as a workflow for testing the efficacy of such molecular diagnostic tools in real-world settings that can be used for other pest systems. Our research team has extensive expertise in tephritid population genetics and developing molecular diagnostic tools (e.g., Dupuis et al. 2018 Biol Inv 20:1211-1228), which includes the first range-wide population genomic assessment of A. ludens (Dupuis et al. 2019 Evol App 12:1641-1660). With extensive collaborations across the tephritid research community, this project has a high likelihood of success. Specific objectives: The goal of this agreement is to continue developing and improving molecular identification and diagnostic capacity for Anastrepha ludens. We have two specific objectives, all of which expand on our continued development of large population genomic datasets as their foundation. Our objectives are: 1) Create and sequence experimentally manipulated samples that are similar in quality and tissue input quantity to those samples that would be collected as part of real-world surveillance/monitoring efforts (i.e., non-optimal DNA preservation). This objective will allow us to assess robustness, reproducibility, and sensitivity of this diagnostic tool and to understand limitations of this technology. 2) Sequence series of real-world specimens collected as part of regular surveillance efforts in California and Texas over the past ~5 years to provide both information on contemporary pest movements (pathways of invasion) in these regions and a real-world demonstration of this technology. Keywords: population genomics, Diptera, Tephritidae, Anastrepha, recurrently invading pests, molecular diagnostics, pathway analysis
Effective start/end date9/30/229/29/24


  • Animal and Plant Health Inspection Service: $141,119.00


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