Polymorphisms of the growth hormone gene in domesticated red sea bream populations (Pagrus major) based on minisatellite genotypes and nucleotide sequences

The genetic diversity of the growth hormone gene in domesticated red sea bream (pmaGH) was evaluated using a minisatellite DNA marker located in intron 3 (pmaGH22) and nucleotide sequences. The number of alleles of pmaGH22 was largely decreased in domesticated strains of red sea bream, and the possibility of selection pressures was also detected based on the analysis of the Hardy–Weinberg equilibrium in some strains. However, each strain inherited a small number of alleles of pmaGH22, and the entire domesticated population (combining all strains) showed a large number of alleles (n = 17), similar to the allelic richness of the wild population (n = 18.5). Based on nucleotide sequencing analysis, three synonym mutations were found in the coding regions, and also several SNPs and indels were found in the noncoding regions. In addition, four genealogies of growth hormone haplotypes were identified based on principal coordinate analysis, and these genealogies of pmaGH partly reflected allele size ranges of pmaGH22. Several haplotypes shared alleles of pmaGH22, and also fragment size homoplasy in pmaGH22 was suspected. These alleles of pmaGH22 and the haplotypes will be a useful indicator for divergence of pmaGH and for broodstock individual selection with minimum inbreeding effect.