Design and Application of a Genome-Wide SNP Array to Improve Conservation Outcomes in the Critically Endangered...

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.