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Research Project: Population Genomic Evaluation of Wild and Cultured Eastern Oyster Populations from the Northeast Region

Location: National Cold Water Marine Aquaculture Center

Project Number: 8030-31000-005-033-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2021
End Date: Aug 31, 2024

This agreement will evaluate genetic diversity within and genetic differentiation between wild and cultured Eastern oyster populations in the Northeast U.S., Maine to New York. It will also inform the development of a well-adapted, resilient, and genetically diverse founder breeding population.

Oyster populations throughout the Northeast region will be identified via communication with the aquaculture and fisheries industry, extension specialists, state regulatory agencies, other stakeholders, as well as literature review. Live adult oysters will be collected from each population, labeled, measured, and maintained in a quarantined, flow-through seawater system equipped with ozone decontamination for effluent at the University of Rhode Island Narragansett Bay campus. Mantle tissue from individual oysters (N= 30-50) will be non-destructively subsampled using an anesthesia protocol developed by USDA ARS. DNA will be extracted according to laboratory standard operating procedures that have been optimized for obtaining high-quality genotype data. Individual oysters will be genotyped at tens of thousands of loci evenly distributed across the oyster genome and multiple genotyping methods will be tested (e.g. GBS, Exome-capture, High-Density SNP panel and whole genome sequencing) to identify the most informative, efficient, cost-effective methods for future research. Genomic data will be analyzed at multiple architectural levels, including SNPs, copy number variants, and both small and large insertions, deletions, and inversions; genomic analyses will be combined with environmental data in landscape (seascape) framework to determine genotype frequencies of both neutral and adaptive loci correlated to environmental conditions and characterize the relative roles of selection, migration, and drift in distributing oyster genomic diversity. In parallel, USDA ARS will maintain and condition quarantined oysters for within and between population genetic crosses. Standard shellfish industry hatchery protocols will be followed when performing crosses, rearing larvae, and during the nursery phase. Resultant seed from each cross will be deployed at field sites representing the range of grow-out conditions at aquaculture farms throughout the Northeast. Primarily, seed will be phenotyped for growth, survival, and disease resistance traits, although other traits can be included per stakeholder recommendation. This cooperative project will cover multiple iterations of the process described above to accommodate logistic limitations (e.g. capacity to hold and spawn oysters in our modest wet lab space) as well as address genetic and phenotypic considerations for building a founder breeding population.