Genome-wide analysis of acute low salinity tolerance in the eastern oyster Crassostrea virginica reveal major loci and potential of genomic selection for trait improvement

As the global demand for seafood increases, research into the genetic basis of traits that can increase aquaculture production is critical. The eastern oyster (Crassostrea virginica) is an important aquaculture species along the Atlantic and Gulf Coasts of the United States, but increases in heavy rainfall events expose oysters to acute low salinity conditions, which negatively impact production. Low salinity survival is known to be a moderately heritable trait, but the genetic architecture underlying this trait is still unknown. In this study, we used ddRAD sequencing to generate genome-wide single nucleotide polymorphism (SNP) data for four F2 families to investigate the genomic regions associated with survival in extreme low salinity (less than 3). SNP data were also used to assess the feasibility of genomic selection for improving this trait. Quantitative trait locus (QTL) mapping and combined linkage disequilibrium analysis revealed significant QTL on eastern oyster chromosome 1 and 7 underlying both survival and day to death in a 36 day experimental challenge. Significant QTL were located in genes related to DNA replication, ion binding and transport, and general response to stress. Genomic selection was investigated using Bayesian linear regression models and prediction accuracies ranged from 0.48 to 0.57. Genomic prediction accuracies were largest using the BayesB prior and prediction accuracies did not substantially decrease when SNPs located within the QTL region on Chr1 were removed, suggesting that this trait is controlled by many genes of small effect. Our results suggest that genomic selection is a viable option for improvement of survival in extreme low salinity.