Transcriptome analysis of inbreeding depression in the Pacific oyster Crassostrea gigas

Abstract

The Pacific oyster (Crassostrea gigas) is widely cultured worldwide. Because intercrossing inbred strains improves yield (heterosis), development of inbred lines is needed to implement this breeding strategy. However, inbreeding usually reduces the mean phenotypic value shown by characters connected with physiological efficiency or reproductive capacity. The effects of inbreeding on growth and survival of C. gigas have been reported by numerous studies. However, effects of inbreeding on gene expression still remains to be explored in oysters. In this study, the relationship between gene expression and inbreeding depression was investigated in an inbred line of the Pacific oyster. Two inbred groups, an F1 group containing 15 inbreeding families and an F2 group containing 15 families with a presumed relative higher inbreeding level performing worse in growth and survival rate compared to the F1 group, were constituted by using this inbred line. The shell height and survival rate of two inbred groups were compared with those of the wild group including 15 families (CF). A total of 9 RNA-seq libraries were constructed using oyster gills. Based on differential gene analysis, 2430 differentially expressed genes (DEGs) in the F1 group and 3741 in the F2 group were identified respectively compared to the CF group. A total of 1746 common DEGs were counted shared in two inbred groups, of which 911 were up-regulated and 835 were down-regulated. GO and KEGG analysis showed that common DEGs were significantly enriched in the immune response and actin nucleation pathways. Additionally, 695 DEGs were identified between two inbred groups, and GO analysis revealed that these DEGs were significantly in the pathways related to immune and stress response. Our results show the preliminary exploration of the effect of inbreeding on gene expression of C. gigas, which is helpful for us to better understand and manage inbreeding depression of bivalves, and may potentially benefit the breeding of oyster in aquaculture.