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DNA purity over yield: optimizing extraction and PCR in degraded Asian elephant (Elephas maximus) fecal samples
Supansa Rerkdee1, Worapong Singchat1,2, Thitipong Panthum1,2
1Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
Background:
Non-invasive genetic monitoring is essential for conserving the endangered Asian elephant (Elephas maximus). However, fecal DNA is highly susceptible to degradation and polymerase chain reaction (PCR) inhibition.
Objective:
Various DNA extraction techniques and optimized downstream PCR parameters were compared to establish a workflow that balances DNA quantity and quality.
Methods:
A modified phenol-chloroform-isoamyl alcohol (PCI) protocol was compared with a commercial extraction kit using 35 unpreserved, degraded fecal specimens to evaluate the trade-offs between DNA yield and purity.
Results:
The PCI method produced significantly higher concentrations (> 500 ng/µL in some samples) but poor purity ratios (A260/A280 and A260/A230), resulting in complete PCR failure. In contrast, the kit yielded lower DNA amounts but superior purity (A260/A230 = 2.0-2.2), enabling a 57.1% (20/35) amplification success rate for the mitochondrial D-loop when combined with high-processivity KOD polymerase and optimized Mg2⁺ concentrations. Sanger sequencing confirmed E. maximus mitochondrial DNA in 15 specimens, whereas environmental eDNA was detected in two samples.
Conclusion:
These findings demonstrate that DNA purity, rather than yield, is the critical determinant of PCR success in degraded wildlife samples, underscoring the importance of inhibitor-removal technologies for the reliable and effective management of endangered megafauna.
