Comparison of DNA-extraction Methods Suitable for PCR-based Applications to Identify Shrimp Species in Commercial Products

Abstract

Seven different methods of DNA extraction were performed and compared in order to have the better DNA quality and quantity from specific seafood matrix such as various types of shrimp products. Thus, the nucleic acids extraction efficiency was evaluated according to DNA purity for PCR amplification. To evaluate the interaction of the different parameters, a multivariate regression, PLS approach was used to treat the results of PCR amplification of fresh and processed shrimp. The principal component (PCs) characterized the PCR amplification of shrimp (62% of all variance) with 59.0 and 3.0% for PC1 and PC2 respectively. Based on PC1 analysis, a positive correlation was obtained between the extraction procedures using PCI/SDS, DNeasy Tissue Kit (QIAGEN), TRITON and CTAB, and the results of PCR amplification. In addition to the successful optimization of DNA yield, the multivariate analysis revealed the different factors that affected the PCR amplification including the type of sample matrix. The comparison of the seven extractions methods, in this paper, has highlighted the efficacy of the SDS/PCI precipitation method for fresh and processed shrimp.