Skin Swabbing as a Noninvasive Alternative to Fin Clipping for Commercial Automated Genotyping

Fin clipping remains the most common sampling method for genotyping zebrafish, yet it requires anesthesia and tissue removal, raising animal welfare concerns and potentially impacting behavior in the short term. To address this, we have validated a non-invasive skin swabbing technique that eliminates the need for fin clipping adults while maintaining genotyping accuracy during automated genotyping. This method involves gently swabbing the fish's skin to collect mucus and epidermal cells for DNA extraction. This approach avoids anesthesia, reduces handling stress, and is much less invasive than traditional fin clipping with limited tissue injury. We conducted a comparative analysis of swab-derived DNA against traditional fin clip samples sent for automated genotyping. Swab and fin clips samples taken from the same animal matched genotype results, demonstrating substantial promise as a refinement for automated genotyping under the 3Rs framework. Further testing of the swabbing technique, transport, and sample processing was optimized across nine sessions. Key aspects of the collection technique include focusing on consistent swabbing pressure and sample dry time. Proper technique is critical to ensuring robust and reproducible genotyping outcomes. Our findings indicate that skin swabbing offers a welfare-improving alternative to fin clipping for automated genotyping. Broad adoption of this technique has the potential to enhance animal welfare standards while maintaining scientific rigor, aligning with the principles of the 3Rs and advancing non-invasive research practices in zebrafish facilities worldwide. While the current success rate indicates some limitations relative to fin clip genotyping results with automated genotyping, swabbing remains a promising refinement that can substantially improve welfare in zebrafish facilities.