Design and Application of a Genome-Wide SNP Array to Improve Conservation Outcomes in the Critically Endangered Southern Corroboree Frog
Davidson, Mikaeylah J., Zenger, Kyall R., Keogh, J. Scott, Berger, Lee, Skerratt, Lee F., and Kosch, Tiffany A. (2026) Design and Application of a Genome-Wide SNP Array to Improve Conservation Outcomes in the Critically Endangered Southern Corroboree Frog. Molecular Ecology Resources, 26 (3). e70080.
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Abstract
Species-specific genomic information has the potential to transform modern conservation management strategies through improved genomic assessment and management outcomes. Gaining genomic insights into genetic diversity, adaptability and potential resilience against infectious diseases is essential to enhance conservation efforts for threatened species. Here, we describe the development of the first custom SNP array for an amphibian, designed for the critically endangered Pseudophryne corroboree, which has experienced a near-total population collapse due to the amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd). The array comprises 48,386 SNPs, with an average density of 5.45 SNPs per Mb and was effective in genotyping multiple tissue types, including non-lethal buccal swabs. Of the SNPs, 82.1% were polymorphic across 910 captive-bred P. corroboree individuals derived from ~54 families. Population genetic analysis revealed evidence of ancestral inbreeding and two historic bottlenecks, one coinciding with the arrival of Bd in Australia. Notably, we demonstrate successful cross-species amplification of 21,077 (43.6%) polymorphic loci in three closely related anurans, highlighting the array's broader utility beyond P. corroboree. This tool represents a valuable resource for investigating the genetic basis of disease resistance and developing management strategies for improving reintroduction outcomes in P. corroboree, while also providing a foundation for advancing conservation genomics in other amphibian species.
| Item ID: | 91554 |
|---|---|
| Item Type: | Article (Research - C1) |
| ISSN: | 1755-0998 |
| Keywords: | amphibian, captive breeding, chytridiomycosis, genomic diversity, Pseudophryne corroboree, SNP chip |
| Copyright Information: | This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. © 2026 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd |
| Funders: | Australian Research Council (ARC) |
| Projects and Grants: | ARC FT190100462, ARC LP200301370 |
| Date Deposited: | 30 Jun 2026 22:35 |
| FoR Codes: | 41 ENVIRONMENTAL SCIENCES > 4104 Environmental management > 410401 Conservation and biodiversity @ 50% 31 BIOLOGICAL SCIENCES > 3102 Bioinformatics and computational biology > 310207 Statistical and quantitative genetics @ 50% |
| SEO Codes: | 18 ENVIRONMENTAL MANAGEMENT > 1806 Terrestrial systems and management > 180604 Rehabilitation or conservation of terrestrial environments @ 50% 10 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 1099 Other animal production and animal primary products > 109999 Other animal production and animal primary products not elsewhere classified @ 50% |
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