Genotypic and phenotypic analysis of eastern oyster populations for use in aquaculture

Authors: CARASQUILLO, ANGEL - University Of Rhode Island; Proestou, Dina; HUDSON, ROBERT - University Of Rhode Island; PREZIOSI, BRIAN - University Of Maine; GOMEZ-CHIARRI, MARTA - University Of Rhode Island

Submitted to: Journal of Shellfish Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/21/2024
Publication Date: 12/15/2024
Citation: Carasquillo, A., Proestou, D.A., Hudson, R., Preziosi, B., Gomez-Chiarri, M. 2024. Genotypic and phenotypic analysis of eastern oyster populations for use in aquaculture. Journal of Shellfish Research. 43(3):421-42. https://doi.org/10.2983/035.043.0313.
DOI: https://doi.org/10.2983/035.043.0313

Interpretive Summary: To start a regional eastern oyster selective breeding program, founder individuals must be chosen from existing populations. Two approaches for choosing founders are to: 1) use phenotype data to identify high performing populations and 2) characterize genetic diversity in existing populations and design crosses that maximize it in the new breeding population. In this study, we measured performance (growth and survival) and quantified genetic diversity for four wild, native New England eastern oyster populations at a Rhode Island oyster farm. We also compared their performance and genetics to two commercial/selected lines of mid-Atlantic origin that are currently used by eastern oyster aquaculture practitioners in the Northeast. Growth and survival varied among the populations tested. The two commercial lines performed best with respect to growth; however, wild Connecticut and Rhode Island populations survived as well if not better than the commercial lines. The native populations were also more genetically diverse and significantly less inbred than the commercial lines. Although this was a relatively limited test, the results demonstrate the need for genetically improved germplasm specific to the Northeast USA and will inform the selection of founders for a regional eastern oyster breeding program.

Technical Abstract: Increased production of eastern oysters (Crassostrea virginica) will be needed to meet consumer demand for seafood. To meet this demand for seafood in the face of disease and climate change, selective breeding has been proposed as a solution. This study evaluated the phenotypic traits of survival, growth, yield and disease acquisition of four wild eastern oyster (Crassostrea virginica) populations and two commercial lines from the Northeastern US at a Rhode Island growing site. This study also investigated the genetic parameters of genetic difference between subpopulations (FST), inbreeding (FROH), runs of homozygosity, proportion of polymorphic loci, and heterozygosity in these populations. Shell height varied between populations (48mm to 79mm) as did survival (18% to 68%) and yield (3,744mm to 27,085mm). Prevalence of the protozoan diseases Dermo and MSX was high between populations, and intensity for both diseases varied between populations. All populations had a similarly high proportion of polymorphic loci (0.88 to 0.99) and moderate heterozygosity (0.29 to 0.31). The commercial lines, however, did have a significantly longer percentage of the genome in a run of homozygosity (ROH), a greater number of ROHs and higher FROH. Pairwise FST values varied (0.01 to 0.08), with the wild populations being more genetically similar to one another than to the commercial lines which were also genetically distinct from each other. This analysis provides an example of how phenotype and genotype information could be analyzed to inform the selection of founders for a breeding program.