Single nucleotide polymorphisms in the actin and crustacean hyperglycemic hormone genes and their correlation with individual growth performance in giant freshwater prawn Macrobrachium rosenbergii

We assessed correlations between single nucleotide polymorphisms (SNPs) in the actin and crustacean hyperglycemic hormone (CHH) genes with individual growth performance in giant freshwater prawn Macrobrachium rosenbergii. Thirty SNPs were detected in the actin and CHH genes in broodstock of three M. rosenbergii strains (Dong Nai, Mekong, and Hawaiian) and their offspring. A preliminary study that evaluated all SNPs suggested an association between SNPs in intron 3 of the CHH gene and individual growth performance. A larger number of offspring (n = 243) then were genotyped and tested for the associations between SNPs in intron 3 and individual growth performance. Four intronic SNPs were associated significantly with three growth traits (body weight, carapace length, and standard length). Of these, CH3-2402 and CH3-2561 were highly correlated with all three traits, while CH3-2407 and CH3-2409 were correlated significantly only with body weight. A further haplotype-trait association analysis confirmed that these four SNP markers were in linkage disequilibrium, and the specific haplotype TGAA had significant associations with high growth (P < 0.01). The implications of these findings with relevance to developing improved culture lines of giant freshwater prawn for the industry in Vietnam are discussed.