Reducing DNA extraction costs through factorial design for the DNAdvance Kit

Abstract

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.

Keywords: Cost-effective genotyping; DNA extraction optimization; DNAdvance Kit; Factorial design analysis; White-tailed Deer.

Fig. 1

Interaction effect of tissue mass and reagent volume proportion on DNA concentration. Mean DNA concentrations (ng/µL) are shown for each combination of tissue mass (mg) and reagent volume (as a percentage of the manufacturer’s suggested total volume). Error bars show the standard error of the mean