Grants and Contracts Details
Description
Accelerating climate change and globalization are driving unexpected changes in the distribution of
invasive pest species. Accurate and rapid species identification and pathway analysis are critical to
effective management but oftentimes pests belong to closely related species groups that are
morphologically indistinct yet have different ecological impacts. For these, genomic diagnostic
marker panels are an important tool for identification. However, genotype calling and analysis
relies on bioinformatic pipelines that require a high level of expertise to execute and interpret: a
significant barrier to the wide-scale adoption of a powerful phytosanitary resource. To overcome
this barrier, this postdoctoral project intends to develop a user-friendly, end-to-end software
program for sequence-based diagnostic tool analysis. Starting with next-generation sequencing
data, it will flexibly analyze sequence data or call genotypes for probabilistic species identification,
down to strain or population depending on the panel, and if applicable, perform geographic
source/pathway analysis. Accessibility will be addressed with secure online hosting and the
creation of a user-friendly interface. By emphasizing standardization, the software will be
intentionally designed as a universal framework for sequencing-based diagnostics, providing
flexibility for diverse, taxonomically difficult pest groups. Thus, the proposed work contributes to
the AFRI Farm Bill Priority Area: Plant Health and Production and Animal Products and Program
Area: 1c. Pests and Beneficial Species in Agricultural Production Systems (Program Area Priority
Code: A1112) as a rapid, flexible resource for pest management and fits the AFRI EWD goal of
“Advancing Science” by providing training that is highly relevant to the future of the USDA.
Status | Finished |
---|---|
Effective start/end date | 9/1/23 → 6/30/24 |
Funding
- National Institute of Food and Agriculture: $146,000.00
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