Validation of SNPs in heat shock protein gene of Macrobrachium rosenbergii (De Man, 1879) using Sanger sequencing

Abstract

Macrobrachium rosenbergii also know as giant freshwater prawn, is a commercially important species of crustacean cultured extensively throughout Southeast Asia. Giant freshwater prawn has always been concerned as a suitable species for aquaculture because it can be grown in both fresh and low salinity waters. However, now the wild stocks of M. rosenbergii is declining due to the over-harvesting, habitat loss and increased pollution and these cause the loss of genetic diversity due to the small population size. So it is essential now to discover the genetic diversity present among the different stock of Macrobrachium rosenbergii for proper maintenance of the stock and to decrease the inbreeding depression in the stocks by cross breeding of genetically different stocks. With these aim in a previous study, we develop a total of eight single nucleotide polymorphism in heat shock gene among the four different stock from Gujarat, Maharashtra, Kolkata and Kerala using next-generation sequencing approach (Ion Torrent). In our current study we resequenced the heat shock protein gene using Sanger sequencing method to validate the SNPs generated from the previous study. We collected 23 individuals from Kerala and after sequencing the 23 gDNA, we found that five SNPs are common to the previous study. These SNPs are considered as the validated SNPs and only one novel SNPs was discovered from the current study. We also reported three and two haplotypes from the HSP21 and HSP70 gene respectively, which shows the genetic diversity within the Kerala shock. The validate SNPs could be used as a molecular marker in marker-assisted selection in the development of the QLTs for this species.