Genomic selection for low salinity tolerance in the eastern oyster Crassostrea virginica in Louisiana and Chesapeake Bay populations

The use of genomic selection (GS) to improve traits of interest in aquaculture species is growing with the availability of genomic resources for those species. The eastern oyster, Crassostrea virginica, is a major aquaculture product and keystone species along the U.S. mid-Atlantic and Gulf coasts. Populations and production of C. virginica are threatened by several environmental stressors, and in certain coastal regions, episodic low salinity conditions have contributed to mass mortality events. Here we examined the potential for genomic selection to improve tolerance to extreme low salinity (≤ 2) in eastern oysters and report the evaluation of GS models for C. virginica from two regions- Louisiana and Chesapeake Bay. Tissue samples from both mortalities and survivors of the lab-based salinity challenges (salinity 2, 28 °C) were genotyped on the 66 K C. virginica SNP array. We performed a genome wide association study (GWAS) for both challenges and then evaluated the effects of several different parameters on GS prediction accuracy, including model type (GBLUP, Bayesian, and weighted), data filtering, Bayesian modelling parameters, and trait encoding (Gaussian, ordinal, and censored). GWAS revealed a significant region on chromosome 1 in the Chesapeake animals while the Louisiana animals showed only a few significantly associated loci. GS model type had no significant impact on prediction accuracy in the Chesapeake animals, but a large impact in the Louisiana animals. Likewise, prediction accuracy remained consistent in the Chesapeake Bay challenge with as few as 5000 markers, while accuracy in the Louisiana challenge began to decline with fewer than 25,000 markers. This likely reflects the lower relatedness among the Louisiana individuals due to unintended wild overset. Overall, with moderate prediction accuracies (∼0.45–0.55) in both regions, GS shows the potential to improve low salinity tolerance in eastern oysters. This will be beneficial to selective breeding programs and restoration efforts in regions where this trait improves oyster survival.