Genome-wide association study reveals E2F3 as the candidate gene for scallop growth

Abstract

Yesso scallop (Patinopecten yessoensis) is one of the most economically important shellfish in aquaculture industry of China, and improving growth rate has become a central task of the Yesso scallop farming industry. By far, genetic studies on Yesso scallop growth are very limited and there is no systematic screening of the growth-related genes or loci for this species. In the present study, we conducted a genome-wide association study (GWAS) for six growth traits of Yesso scallop utilizing over nine thousand single nucleotide polymorphism (SNP) markers. Two significantly growth-associated SNPs were identified and the SNP showed the lowest P value was located in E2F transcription factor 3 (E2F3), the gene being reported as important regulator of cell proliferation and cell cycle. Further analysis in another population identified a new growth-associated SNP in this gene. Moreover, two tandemly repeated E2F3s (PyE2F3-1 and PyE2F3-2) were found at this locus, and PyE2F3-1 expression was significantly correlated with the values of shell length, shell height, body weight, and adductor muscle weight in Yesso scallop. Our data suggest that PyE2F3-1 might be a positive regulator of shell and soft tissues growth, and it could be a candidate gene for Yesso scallop breeding aiming at growth improvement.