A SNP in Cathepsin L is associated with carapace length trait in giant freshwater prawn Macrobrachium rosenbergii

Giant freshwater prawn, Macrobrachium rosenbergii, is one of the major cultivated crustacean species in China. In recent years, a slow growth syndrome (SGS) has severely influenced the production, and the exact cause has not been clearly determined. In the present study, normal and SGS prawns were collected in 2016, 2017, and 2020. One-way ANOVA analysis showed significant difference in all growth traits examined between normal and SGS groups (P < 0.05). Cathepsin L (CatL) DNA fragment was cloned and re-sequenced, leading to identification of 41 SNPs. Among these SNPs and another four SNPs located in crustacean hyperglycemic hormone (CHH) that showed association with M. rosenbergii growth in Vietnam populations, 24 SNPs including two from the CHH gene were selected for association analysis. Eight out of the 24 SNPs were polymorphic in our population, in which SNP CatL-322 showed significant association with SGS (FDR adjusted P < 0.05). Fisher’s exact test was further conducted, and two intronic SNPs, CatL-322 and CHH-2409, showed significant association with carapace length of M. rosenbergii, explaining about 15 % of phenotypic variation in total. The two SNPs were further screened in a second population, and solid evidence was obtained. We compared the growth of different genotypes at each locus and confirmed that T allele at CatL-322 locus and G allele at CHH-2409 locus were beneficial to growth performance (P < 0.05). These two SNPs potentially can be applied in marker assisted selection in future M. rosenbergii breeding programs.