Ancestry dynamics and trait selection in a designer cat breed

The Bengal cat breed was developed from intercrosses between the Asian leopard cat, Prionailurus bengalensis, and the domestic cat, Felis silvestris catus, with a last common ancestor 6 million years ago. Predicted to contain ~95% of their genome from domestic cats, regions of the leopard cat genome are thought to account for unique pelage traits and ornate color patterns of the Bengal breed, which are similar to those of ocelots and jaguars. We explore ancestry distribution and selection signatures in the Bengal breed using reduced representation and whole genome sequencing from 905 cats. Overall, leopard cat introgressions are reduced twofold from expectation and include examples of genetic incompatibility—reduced expression of a leopard cat gene in a domestic cat background—underlying the color traits Charcoal and contributing to coat color variation. Leopard cat introgressions do not show strong signatures of selection; instead, selective sweeps in Bengal cats are associated with domestic, rather than leopard cat haplotypes, and harbor candidate genes for pelage and color pattern. We identify the molecular and phenotypic basis of one selective sweep as reduced expression of the Fgfr2 gene, which underlies Glitter, a desirable trait that affects hair texture and light reflectivity.