Reducing DNA extraction costs through factorial design for the DNAdvance Kit.

Objective: Extracting DNA is essential in wildlife genetic studies, and numerous methods are available. However, the process is costly and time-consuming for non-model organisms, including most wildlife species. Therefore, we optimized a cost-efficient protocol to extract DNA from the muscle tissue of White-tailed Deer using the DNAdvance kit (Beckman Coulter), a magnetic-bead-based approach. We devised a 3 × 3 factorial design using combinations of tissue mass (10 mg, 50 mg, or 100 mg) and reaction volume (25%, 33%, and 50% of the manufacturer's recommended volumes). DNA was extracted for N = 81 tissue sub-samples (9 replicates/treatment).
Results: Our target yield was 500 ng of genomic DNA per sample, sufficient for population genetic assessments. A combination of 50 mg tissue and 25% reaction volume yielded enough DNA at the lowest cost. The factorial design revealed that varying tissue mass and reagent volume significantly affected extracted DNA yield. Our study demonstrates that sufficient DNA can be extracted at 75% lower costs than the manufacturer's standard protocol. Other researchers can directly use our modified DNAdvance protocol to perform cost-effective DNA extractions.
Competing Interests: Declarations. Ethics approval: The animal tissue used in this study was collected through a voluntary statewide CWD testing program facilitated by the Arkansas Game and Fish Commission following the U.S. Fish and Wildlife Service tissue and hair sample protocol. Human ethics and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.
(© 2024. The Author(s).)