Molecular Identification of African Elephant (Loxodonta africana) via Target Gene (cytb) Quantitative PCR: A Case Study in Wildlife Conservation Genetics

Background: The African elephants (Loxodonta africana) are considered critically endangered due to poaching, habitat destruction and human-wildlife conflict. However, effective monitoring and protection of elephant populations require noninvasive and reliable methods for DNA detection. Purpose: This study aimed at determining the sensitivity, specificity and robustness of a cytochrome b gene-based qPCR assay for detecting African elephant DNA in various sample such as feces, skin and hair. Methods: qPCR assay was developed using the FAM and HEX channels for detecting African elephant DNA and an internal control. The assay was tested on 9 elephant DNA samples and non-target species that is Arabian Oryx. Serial dilutions of elephant DNA. Cq values and DNA concentrations were measured and analyzed to assess performance validation. CFX Maestro Software (BIO RAD) and QuantaSoft Software for the Qx200 Droplet Reader were referred to analyze qPCR assay. Cq was mainly referred as the key statistical indicator for the interpretation of data which represented cycle at which fluorescence exceeds a threshold of 30 Cq values. Results: The results showed high sensitivity with Cq values ranging from 15.31 to 22.32 for African elephant samples whereas no amplification for non-target species Cq values>36 was reported. The assay detected DNA concentrations as low as 7.6 copies/µL in diluted samples. The internal control confirmed no amplification inhibition indicating successful PCR across all samples. Conclusions: YouSeq African Elephant qPCR Test Kit is a reliable, sensitive and effective tool for detecting African elephant DNA from non-invasive samples. It provided a robust method for wildlife conservation and forensic applications especially for anti-poaching efforts and population monitoring.