Development of methods for detection of SNPs in Activin type IIB receptor and a preliminary study on association between its polymorphism and growth parameters of the Asian seabass Lates calcarifer

Molecular markers that allow selection of juveniles and broodstock with a high growth performance are useful for the aquaculture industry. In this study, association between single nucleotide polymorphisms (SNPs) of the Activin type IIB receptor (LcActRIIB) and growth-related parameters of Asian seabass Lates calcarifer juveniles were examined by PCR-direct sequencing. Three SNPs (G > A(c.965+g.7), C > A > T (c.965+g.33) and G > A (c.965+g.189)) generating seven composite SNP genotypes (diplotypes) were found in the LcActRIIB gene segment (398 bp). Among three identified SNPs, only a G > A(c.965+g.7) SNP showed significant association with growth traits (average body weight, total length, hepatic weight and hepatosomatic index) of examined fish (P < 0.01). Significant association between diplotypes and growth-related parameters were found. Juveniles exhibiting diplotypes I-V showed greater growth-related parameters than those exhibiting diplotypes VI (P < 0.001; N = 57). Simple methods for rapid genotyping of a G > A(c.965+g.7) SNP were successfully developed based on gel-based bi-allelic PCR amplification of specific alleles (Bi-PASA) and real-time PCR-based PASA analyses (N = 99). Identical genotypes were consistently obtained from different detection methods.