Optimisation of a microfluidic SNP assay for accurate hybrid class detection in the European wildcat (Felis silvestris)

Abstract Anthropogenic hybridisation between wild and domestic taxa poses a significant threat to species integrity, including the endangered European wildcat. To enable reliable molecular assessment of admixture with domestic cats and to increase the accuracy of hybrid class assignment we optimised an existing reduced microfluidic 96 Single Nucleotide Polymorphism (SNP) panel. We selected SNPs from a genome-wide dataset for maximum F ST between both taxa and replaced 60 SNPs from the previous 96 SNP panel. Comparison of both panels based on simulated hybrid genotypes and real-world genotypes proof the higher discriminatory power of the optimised panel, which allows for reliable assignment of F1 and F2 hybrids, as well as 1st and 2nd generation backcrosses. Additionally, we successfully tested the panel for both tissue and non-invasively collected hair samples, demonstrating the suitability of the new panel for implementation in wildcat monitoring programmes.