Revisiting traditional SSR based methodologies

Asian elephant (Elephas maximus) plays a significant role in natural ecosystems and it is considered as an endangered animal. Molecular genetics studies on elephants’ dates back to 1990s. Microsatellite markers have been the preferred choice and have played a major role in ecological, evolutionary and conservation research on elephants over the past 20 years. However, technical constraints especially related to the specificity of traditionally developed microsatellite markers have brought to question their application, specifically when degraded samples are utilized for analysis. Therefore, we analyzed the specificity of 24 sets of microsatellite markers frequently used for elephant molecular work.

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FIG: Relationship among Asian elephants in the National Zoological Garden, Sri Lanka. The phylogenetic tree developed based on the binary data matrix obtained by reading distinctive peaks of fragment analysis data, using UPGMA method. Bootstrap probability values for 1000 bootstrap resamples are indicated at each node.

Comparative wet lab analysis was done with blood and dung DNA in parallel with in silico work. Our data suggest cross-amplification of unspecific products when field-collected dung samples are utilized in assays. The necessity of Asian elephant specific set of microsatellites and or better molecular techniques are highlighted.

Marasinghe, M.S.L.R.P., Nilanthi, R.M.R., Hathurusinghe, H.A.B.M. et al.Revisiting traditional SSR based methodologies available for elephant genetic studies. Sci Rep 11, 8718 (2021). https://doi.org/10.1038/s41598-021-88034-9

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