Mutations upstream of ppp2ca affect body weight in Asian seabass

Growth is an economically important traits in aquaculture. Previous studies identified ppp2ca as a candidate gene located within a major quantitative trait locus (QTL) for growth in Asian seabass. However, the molecular mechanisms underlying its role in growth regulation remain unclear. In this study, a single nucleotide polymorphism (SNP) in ppp2ca was found significantly associated with body weight. The gene was ubiquitously expressed across 11 examined tissues, with highest levels in the brain and eye, but reduced expression in the muscle of fast-growing fish. Functional assays showed that ppp2ca knockdown promoted cell proliferation, whereas its overexpression suppressed cell proliferation in an Asian seabass cell line. Two upstream mutations—a 10-bp indel and a 218-bp indel, were also identified and characterized. Dual-luciferase reporter assays demonstrated that the 10-bp insertion enhanced ppp2ca expression, while the 218-bp deletion reduced it. Permutation-based two-way ANOVA revealed a significant interaction between the 10 bp insertion and 218 bp deletion on body weight. These findings suggest that these upstream mutations in ppp2ca influence growth in Asian seabass, providing useful markers for selective breeding and key targets for future detailed functional studies on growth regulation.