Ascertaining optimal protocols for DNA extraction of different qualities of pike (Esox lucius) tissue samples – a comparison of commonly used solid phase extraction methods

High quality DNA extractions are a prerequisite for genetic studies of a variety of organisms including fish. The current study focusedon the applicability of different commercially available solid phase extraction (SPE) methods as the easiest and fastest methods for DNA extraction and their efficiency with different tissue qualities. These were represented by different kinds of pike tissues (fins, muscle, scales) preserved with different methods and stored at different temperatures over different periods of time (0.5 to 10.0 years). All DNA extractions were analysed according to their yield, purity, integrity and functionality in PCR based downstream analysis. Additionally mechanical pre-treatment of poor quality tissues (e.g. old or aged tissues) and efficient ethanol preservation of frozen bulk fin tissue were investigated. All SPE methods yielded functional DNA from very different qualities of pike tissues as shown by PCR analysis of small nuclear (microsatellite) and large mitochondrial (complete D-loop) DNA fragments. DNA from poor quality tissue can be extracted using single column SPE and in some cases mechanical pre-treatment even improved the yield. Good quality tissue as obtained e.g. from commercial fishermen as frozen bulk material is more efficiently preserved by thawing in ethanol at room temperature than at 2-8°C. DNA from these and air dried tissues was very efficiently prepared by applying reverse SPE in 96-well format, allowing for fast processing of a multitude of samples for high through put analysis.