Identification of Growth-Related Single-Nucleotide Polymorphisms in the cAMP-Dependent Protein Kinase Type I Regulatory Subunit-like Gene of the Oriental River Prawn, Macrobrachium nipponense

Macrobrachium nipponense is an economically important freshwater crustacean in China, and growth-related traits are major determinants of its commercial value. Identifying single nucleotide polymorphisms (SNPs) associated with growth-related traits may provide useful molecular markers for the genetic improvement of growth performance. Previous studies have suggested that the cAMP-dependent protein kinase type I regulatory subunit-like gene (Mn-PKA-R1) is involved in the regulation of growth and molting in M. nipponense. In the present study, a cultured full-sib family comprising 120 females and 120 males was used to screen SNPs within the coding region of Mn-PKA-R1, and evaluate their associations with body weight, body length, full length, and abdominal width. Seven SNPs were identified in exon 12, including five nonsynonymous missense variants and two synonymous variants, whereas no SNPs were detected in the other exons examined. The mean effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), Nei’s gene diversity (Nei), and polymorphic information content (PIC) were 1.3561, 0.3048, 0.2350, 0.2340, and 0.1962, respectively, in females, compared with 1.3118, 0.2714, 0.1868, 0.1861, and 0.1512, respectively, in males. Four SNPs were significantly associated with growth-related traits in females: C+82748G and A+82750G were associated with body weight and abdominal width, T+82810G was associated with abdominal width, and A+83324G was associated with body weight, full length, and abdominal width (p < 0.05). No significant genotype–trait associations were detected among the SNP loci that could be statistically evaluated in males. Pairwise r2 values ranged from 0.001 to 0.693 in females and from 0.000 to 0.351 in males, with generally higher values observed in females within the investigated full-sib family. Females also showed slightly higher mean genetic polymorphism parameters than males, while significant SNP–trait associations were detected only in females within this family. These findings provide candidate SNPs for further validation of their potential utility in marker-assisted selection in M. nipponense.