Polymorphisms of the GH gene 3′ partial sequence and their associations with growth traits and muscle composition in juvenile grass carp (Ctenopharyngodon idella)

In order to comprehend whether the polymorphism of grass carp GH gene was associated with growth traits and muscle compositions, 156 individuals from Yangtze River were used in this study. Nine polymorphic loci were found in the GH gene 3′ partial sequence: G2825A、G2914T、T2966G、A3002T、T3022C、A3301G、C3463T、C3547T、C3620T, which were named SNP1-SNP9 respectively. Nine loci were not significantly deviated from Hardy-Weinberg equilibrium based on Chi-square test (P>0.05), and performed moderate polymorphism (0.25<PIC<0.5). The results of linkage disequilibrium showed that SNP3, SNP4, SNP5 were a set of completed linkage disequilibrium (r²=1) and SNP2, SNP7, SNP9 were a set of completed linkage disequilibrium (r²=1). Haplotype analysis for five loci in GH 3′partial sequence revealed 6 haplotypes, which Hap1(30.4%) had the greatest proportion, Hap6(4.8%) had the lowest proportion. A general linear model and multiple comparisons were used to analyze the correlation between those single nucleotide polymorphisms (SNPs) and grass carp traits. The results showed that the body weight, body length and fat content of individuals with the homozygous mutant genotype at SNP2 and SNP3 were significantly higher than wide-type and heterozygous mutant genotype. Similar results were found in diplotype combinations analysis. The body weight, body length and fat content of combination with heterozygous mutant genotype at SNP2 and SNP3 were significantly higher than other combinations. The results showed that the polymorphism of SNP2 and SNP3 in grass carp GH gene had a significant correlation with growth traits and muscle composition (P<0.05), and it might have utility as markers for practical breeding programs for growth traits and muscle composition in grass carp. Meanwhile, we have laid a foundation for further research on the functional verification of the relevant mutation sites.