Effectiveness of Salmon Carcass Tissue for Use in DNA Extraction and Amplification in Conservation Genetic Studies

Abstract

AbstractA key concern in conservation genetic studies is obtaining viable DNA for analysis. In Pacific salmon Oncorhynchus spp., carcasses represent a feasible alternative for obtaining this tissue. However, the relative speed with which a salmon carcass decomposes can affect the quality of the extracted DNA. We extracted DNA from three different tissues (anal fin, operculum, and scales) obtained from carcasses of Chinook salmon O. tshawytscha at three different levels of decomposition (slight, moderate, and extensive). Freshly euthanized fish were included as a control. Extraction of DNA was accomplished using two common methods: the Chelex method and the Qiagen DNeasy spin column method. For each extracted sample, polymerase chain reaction (PCR) was used to amplify one small microsatellite locus (170–375 base pairs [bp]), one large nuclear locus (971 bp), and one large mitochondrial locus (1,300 bp). Results suggest that DNA suitable for PCR amplification at all three loci can be readily obtained from carcasses with slight decay. Qiagen spin columns appeared to provide the best extraction method, and fin clips were the optimal tissue type. Qiagen spin columns were the only extraction method that yielded DNA suitable for PCR from carcasses with moderate to extreme decay, although positive results were less reliable. Chelex extractions proved effective for amplifying small microsatellite loci from fin and scale samples but only those from carcasses with slight decay. With further optimization of techniques, we believe salmon carcasses can be used as a suitable source of tissue for DNA extraction and subsequent study in a conservation genetics framework.