Genomic Selection for Dermo Resistance in the Eastern Oyster Crassostrea virginica: Production and Laboratory Testing of F1 Generation

Genomic selection was conducted in the eastern oyster using a 66K single-nucleotide polymorphism (SNP) array to improve resistance to dermo disease caused by Perkinsus marinus. Oysters from a Florida wild population were divided into a training and a breeding population; oysters from the training population were challenged with P. marinus in the laboratory, separated into dead (“susceptible”) and alive (“resistant”) phenotypes, and genotyped with the array. A genome-wide association study identified no major loci for dermo resistance confirming the polygenic nature of the trait. Dermo resistance as measured by binary survival had an estimated heritability of 0.255 ± 0.115. Markers and associated genes were identified including some related to phagocytosis providing insights into dermo resistance. Markers were ranked according to their association with dermo resistance, and marker-sets were evaluated with five statistical models for prediction accuracy by cross-validation. The genomic best linear unbiased prediction model with the top 10K markers that produced the highest prediction accuracy was used to calculate genomic estimated breeding values (GEBVs) for genotyped oysters from the breeding population. The top 36 individuals with the highest GEBVs were bred to produce a genomic up-selected group (FLGS), and the bottom 39 individuals with the lowest GEBVs were bred to produce a down-selected control group (FLC). A phenotypically selected group (FLP) was produced using 46 survivors from the dermo challenge. When progenies from the three groups were challenged with dermo, FLGS showed a 20.4% increase in survival over down-selected FLC, whereas the survival increase in FLP was not significant. These results suggest that dermo resistance can be more effectively improved by genomic selection than phenotypic selection.