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

Abstract

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 poorly understood. 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 (<3). SNP data were also used to assess the feasibility of genomic selection (GS) for improving this trait. Quantitative trait locus (QTL) mapping and combined linkage disequilibrium analysis revealed significant QTL on eastern oyster chromosomes 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/RNA function and repair, ion binding and membrane transport, and general response to stress. GS 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 GS will likely be a viable option for improvement of survival in extreme low salinity.

Keywords: Crassostrea virginica; BGLR; QTL mapping; genomic selection; oyster aquaculture; salinity tolerance.

Figure 1.

Number dead for each of the four F₂ families over the 36-day acute low salinity (2.2) challenge. N = 132, 111, 114, and 106 for families 11, 22, 43, and 65, respectively.

Figure 2.

LOD plots for QTL identified from the 2-part model, day to death conditional on survival, for family 11 (top left), 43 (bottom left), and 22 (top right). LOD plot in the bottom right shows the QTL identified from the single-QTL scan for day to death for family 65. For the 2-part models, red lines indicate the QTL associated with mean day to death conditional on the probability of survival (LOD_pµ), black lines represent QTL associated with the probability of survival (LOD_p), and gray lines indicate QTL associated with mean day to death (LOD_µ). Horizontal, dotted lines indicate the 5% significance threshold at the genome-wide level after 1000 permutations for each respective test (by color).

Figure 3.

Scree plot showing the percent variance explained by (A) all 372 PCA components and (B) the first 40 components. PCA plots showing (C) population structure when plotting the first two components against each other (k = 4), and (D) the lack of structure when components 6 and 7 are plotted.

Figure 4.

Combined LD analysis of survival (A,B) and day to death (1–36 days, C,D) for the four recombinant families exposed to acute low salinity (2.2) for 36 days. QQ plots (right) and Manhattan plots (left) depicting −log₁₀(p) values from the combined LD analysis for genome-wide SNPs and survival (A) and day to death (B). Blue horizontal lines in Manhattan plots represent significance threshold after correcting for multiple tests.

Figure 5.

Realized genomic prediction accuracies for survival and day to death in the extreme low salinity challenge. Regression models were run for both traits including all SNPs and after removing SNPs in the significant region on chromosome 1 (red outline). Each bar represents the average value of the 50 and 25 separate 20%/80% cross-validation sets for RKHS and marker models (BayesB, BRR), respectively, divided by the square root of the respective estimated heritability value, 0.406 for day to death and 0.539 for survival. Error bars represent standard error of the mean.