Marker-assisted selection (MAS) technology has been successfully applied in selective breeding of aquatic animals. Myostatin (MSTN) is a vital regulator of muscle growth, development, and differentiation. Five single-nucleotide polymorphisms (SNPs) of MSTN (S1: C712T; S2: C714T; S3: C716T; S4: A729G; S5: G753T) have potential application in MAS of Eriocheir sinensis (E. sinensis). Comparisons of the MSTN polymorphisms of wild, breeding and cultured populations of E. sinensis found that the S1 locus strongly deviated from the Hardy–Weinberg equilibrium in the breeding and cultured populations, likely due to continued selective breeding over the past 20 years. Associations of the five SNPs with the survival coefficient and body weight were assessed in cultured juvenile and adult crabs. The results found that the survival coefficient was significantly greater with the CC genotype at the S1 locus in male and female crabs (p < 0.05). Conversely, individuals with the TT genotype at the S1 locus had excellent growth characteristics, with significant differences only in male crabs (p < 0.05). These results suggested that the S1 locus of EsMSTN could be used for MAS of E. sinensis.
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