A simple, economical protocol for DNA extraction and amplification where there is no lab

Abstract

Genetic analyses are well suited to address many research questions in the study of wild populations, yet species of interest often have distributions that are geographically distant from molecular laboratories, necessitating potentially lengthy transport of biological specimens. Performing basic genetic analyses on site would avoid the project delays and risks of sample quality decline associated with transport, as well as allow original specimens to remain in the country of origin. Further, diagnostic genetic assays performed in the field could provide real-time information allowing for more nimble adjustments to research plans and use of resources. To this end, we developed protocols for reliably performing front-end genetics bench work in the field, without the requirements of electricity or permanent shelter. We validated these protocols on buccal swabs collected during routine capturing of sifaka lemurs (Propithecus verreauxi) at Bezà Mahafaly Special Reserve in Southwest Madagascar and faecal samples collected from captive sifakas (P. coquereli) at the Duke Lemur Center. Our basic protocol pipeline involves a chelating resin based DNA extraction followed by whole genome amplification or polymerase chain reaction using reagents stored at ambient temperature and portable, compact equipment powered by a lightweight solar panel. We achieved a high success rate (>80%) in downstream procedures, demonstrating the promise of such protocols for performing basic genetic analyses in a broad range of field situations.

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Acknowledgements

We thank Sibien Mahereza, Enafa, Elahavelo Efitroarane, Efitiria, Eduoard, Lydia Greene, Roshna Wunderlich, Chloe Chen-Kraus, and Erin Ehmke for helping with sample collection; Rachel Jacobs, Gary Aronsen, and Katie Grogan for lab assistance; Sebastian Kraves of miniPCR for technical support; Yale University, The George Washington University, and James Madison University for funding. We would also like to thank two anonymous reviewers for their helpful comments. All research conformed to institutional and national guidelines. The research conducted at Bezà Mahafaly Special Reserve falls under James Madison University IACUC number A03-14. Research at the Duke Lemur Center was conducted under Duke research number 0-2-16-3 and with Duke IACUC number A168-14-07. This is Duke Lemur Center Publication Number 1345.

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Correspondence to Elaine E. Guevara.

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Supplementary material 1—protocol sheet (DOCX 7100 KB)

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Guevara, E.E., Frankel, D.C., Ranaivonasy, J. et al. A simple, economical protocol for DNA extraction and amplification where there is no lab. Conservation Genet Resour 10, 119–125 (2018). https://doi.org/10.1007/s12686-017-0758-5

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Keywords

  • Population genetics
  • Genotyping
  • Sex-typing
  • Field methods
  • Capacity building
  • Madagascar