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ARS Home » Pacific West Area » Hilo, Hawaii » Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center » Tropical Crop and Commodity Protection Research » Research » Research Project #433682

Research Project: Genomic Approaches to Fruit Fly Exclusion and Pathway Analysis (Year 3)

Location: Tropical Crop and Commodity Protection Research

Project Number: 2040-22430-026-27-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2017
End Date: Sep 30, 2020

Objective:
In this current agreement, we plan to expand this project, representing the first year of a new multi-year project. In this first year, we plan to develop genomic resources (whole genome assemblies and annotations) for Bactrocera cucurbitae, B. zonata, B. correcta, and Anastrepha ludens. In addition, utilizing existing specimen repositories for mexfly and medfly, we plant to generate genome-wide SNP panels to be used as diagnostic population panels. To reach these goals we will perform the following. 1. Generate genomic assemblies as a foundational resource for developing genome-wide SNP-based diagnostic resources. 2. Genome-wide SNP survey using genotype-by-sequencing approach. 3. SNP-based population reconstruction and development of diagnostic SNP panel. 4. Refinement, testing, and finalization of SNP genotyping protocols (Target completion 12 months).

Approach:
In this current agreement, representing the third year of a multi-year project we will utilize existing specimen repositories for mexfly and medfly, generate genome-wide SNP panels are being developed as diagnostic population panels. In addition, we will be developing genomic resources for Bactrocera correcta and B. zonata including whole genome assemblies, population SNP panels and diagnostic resources. In addition we plan to develop diagnostic markers for B. cucurbitae as well as finalize genome assemblies for B. cucurbitae, B. zonata, B. correcta, and Anastrepha ludens. We plan to also test SNP diagnostic assays developed from this project across all of these species on intercepted material and additional samples from diverse geographic sources, to demonstrate the effectiveness of each assay and optimize.