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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 #431469

Research Project: Genomic Approaches to Fruit Fly Exclusion and Pathway Analysis - Year 2

Location: Tropical Crop and Commodity Protection Research

Project Number: 2040-22430-026-22-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Jul 1, 2016
End Date: Sep 30, 2019

Objective:
Develop diagnostic resources to support identification and eradication of pest fruit flies. In this current agreement, we plan to expand on the prior year’s Farm Bill project, representing the second year of a multi-year project. In this first year, we developed and are currently developing genomic resources (whole genome assemblies and annotations) for the melon fly (Bactrocera cucurbitae) and the mexfly (Anastrepha ludens). In addition, utilizing existing specimen repositories for mexfly and medfly, generate genome-wide SNP panels are being developed as diagnostic population panels. The second year of this project expands this to new pest fruit fly species. This includes developing genomic resources for Bactrocera correcta and B. zonata including whole genome assemblies, population SNP panels and diagnostic resources through collaboration with our University of Hawaii and USDA APHIS colleagues to assist in sample collections and curation of wild collected material.

Approach:
Develop draft genome references for pest fruit fly species and develop diagnostic assays for source determination of pest flies and species discrimination. Specifically, we are generating genome assemblies for B. correcta and B. zonata through generation lab lines suitable for genomic DNA sequencing followed by assembly and deposit into public database. Functional annotation and protein prediction will be performed in addition to attempt chromosome scale scaffolding with long range information if needed. Utilizing this assembly along with a world-wide collection of wild specimens, a genome-wide SNP survey for B. correcta and B. zonata will be performed using reduced-representation sequencing. This will define the population structure of these species, which will be the basis for developing diagnostic assays. Genotyping panel for B. correcta and B. zonata will be developed using a subset of these SNPs and tested on samples representing worldwide distribution in addition to intercepted material if available.