Transcriptome Analysis of Strong Selection Due to Inbreeding at the Early Life Stage of Crassostrea gigas

Inbreeding usually reduces the mean phenotypic value of various traits. In Crassostrea gigas, inbreeding depression at the early life stage might be particularly remarkable because of a high mutational load that is difficult to purge. In this study, the effects of inbreeding on the survival rate and gene expression at the early life stage were investigated. Two inbred groups containing five F1 families and five F2 families with a theoretically higher degree of inbreeding were constructed based on an inbred strain. Meanwhile, 5 families were established as the control group (CF) based on the wild population. The results showed that the survival rate of the CF group was significantly higher than those of the two inbred groups. Differential gene analysis showed 1616 common differentially expressed genes (DEGs) in the two inbred groups, which were significantly enriched in pathways associated with immune response, nutrient restriction, and virus infection. By weighted gene co-expression network analysis (WGCNA), 19 common DEGs were enriched in M21, the functional module most closely related to inbreeding, and 6 of them were related to immunity. Notably, the survival rate of F2 was higher than that of F1. A total of 643 DEGs between F1 and CF were screened out, which did not show differential expression between F2 and CF, and these genes were significantly enriched in pathways associated with protein synthesis. These results contribute to a more comprehensive understanding of the genetic mechanism behind the effect of inbreeding on the early survival rate of oyster larvae.