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Dryad

Skin swabbing protocol to collect DNA samples from small-bodied fish species

Abstract

Fish species are commonly used as experimental models in the laboratory. DNA is routinely collected from these animals to permit identification of their genotype. The current standard procedure to sample DNA is fin clipping, which involves anaesthetising individuals and removing a portion of the caudal fin. While fin clipping reliably generates good quality DNA samples for downstream applications, there is evidence that it can alter health and welfare, leading to infection and impacting on the fish’s behaviour. This in turn can result in greater variation in the data collected. In a recent study we adapted a skin swabbing protocol to collect DNA from small-bodied fish, including sticklebacks and zebrafish, without the use of anaesthetics or sharp instruments. A rayon-tipped swab was used to collect mucus from the flank of the fish which was then used for DNA extraction. We subsequently demonstrated that – compared to fin clipping – skin swabbing triggered fewer changes in stress axis activation and behaviour. We also found that swabbing had a smaller impact on subsequent data collection, potentially allowing smaller sample sizes in experimental groups after using this technique, so reducing animal use. Here we provide a detailed protocol explaining how to collect DNA samples using skin swabs from small laboratory fish. Skin swabbing is a refined technique to collect DNA from fish, with the potential to reduce the number of animals used in experiments as well.