Molecular mechanism of inbreeding effects based on RNA-Seq analysis of the adductor muscle of bay scallop (Argopecten irradians)

Understanding the effects of inbreeding is critical for the long-term viability of shellfish breeding and for understanding inbreeding depression (ID) of the offspring of selfed individuals and full-sib crosses. The bay scallop (Argopecten irradians) is a simultaneous hermaphroditic marine bivalve with distinct male and female gonads and is a species with external fertilization. It is a canonical model invertebrate for analysis of the genetics of ID and evolution of outcrossing mating system. ID in bivalves is well documented with regard to the phenotype and molecular markers aspects, but little is known on how inbreeding affects genome-wide gene expression. Here, we compare the gene expression profiles of adductor muscle of A. irradians lines inbred to F=0.5 with those of its counterpart outbred lines which are originated from the same paternal individual. Inbred and outbred individuals have some differences in growth traits. The shell length and the total weight of inbred scallops are lower than the counterpart of outbred lines. We found that 1 175 genes were up-regulated while 1 390 were down-regulated in inbred lines. Regarding components, differentially expressed genes (DEGs) were concentrated on sarcomeres, contractile filaments, and cell membranes. Among others, whereas regarding their function, the Gene Ontology (GO) was concentrated on transferase, phosphotransferase, peptidase, and others. The DEGs-enriched metabolic pathways mainly belonged to the oxidative phosphorylation pathway and apoptosis pathway. We used another two families to verify our bioinformatic results. The selfed and the outbred family originated from different ancestors, but the selfed family showed obvious ID. By using real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), we verified that DEGs with inbreeding are involved in the oxidative phosphorylation and cell apoptosis pathways, suggesting that inbreeding may affect energy metabolism and homeostasis.