Enhancing genetic management in captive Asian elephants: Evaluation of mitochondrial single-nucleotide polymorphism markers for improved breeding and conservation in the Elephant Kingdom, Thailand

Background and Aim: Maintaining genetic diversity and preventing inbreeding depression in captive Asian elephants (Elephas maximus) are crucial challenges that require effective breeding management and conservation strategies. This study aimed to assess genetic diversity and evaluate the effectiveness of currently available molecular markers as breeding management tools in captive Asian elephant populations at the Elephant Kingdom (EK) in Thailand. Materials and Methods: Data were collected from identification certificates of elephants at the EK, including age, sex, parentage, and genotypes of 16 mitochondrial single-nucleotide polymorphisms (mtSNPs). An observation-based pedigree was constructed to estimate pedigree-based kinship coefficients, which were compared to molecular-based kinship coefficients. Population and genetic diversity indices were analyzed. Pedigree-based and molecular-based kinship coefficients were compared to evaluate marker efficiency. Results: The population had a balanced sex ratio of 0.97:1 (male: female). Based on the 16 mtSNPs, the mean observed heterozygosity and expected heterozygosity were 0.4451 and 0.5278, respectively, indicating a heterozygous deficit. The pedigree-based and molecular-based kinship coefficients differed significantly and negatively correlated (r = −0.28, p < 0.05). The molecular-based method estimated higher kinship coefficients than the pedigree-based method. Conclusion: Evaluation of mtSNP markers highlights their utility in assessing genetic diversity and kinship in captive Asian elephant populations in EK, Thailand. However, the observed discrepancies between pedigree-based and molecular-based kinship estimates underscore the limitations of the current mtSNP panel. The findings emphasize the need for integrating nuclear SNPs to enhance the precision of genetic management strategies, enabling better-informed decisions to preserve genetic diversity and mitigate inbreeding risks in conservation breeding programs, not only for the EK but also as a framework that can be adapted for broader conservation efforts. Keywords: Asian elephants, conservation breeding, genetic diversity, kinship coefficients, molecular markers, pedigree analysis.