Wild relatives of domestic animals are crucial reservoirs of genetic diversity, yet pervasive hybridization with domestic animals poses significant conservation challenges. Here, we developed a deep learning-based pipeline, consisting of a multi-layer perceptron for SNP panel selection and a Deep Gallus gallus) and 1796 domestic chicken samples, we applied this pipeline to yield the RJF identification model based on a 285-SNP panel. We employed this model to characterize domestic chickens, RJF, and hybrids in the independent genomic datasets from contemporary samples and historical specimens, respectively. The accuracy was 97.8% for historical samples with missing genotypes. The benchmarking multiple hybrid detection tools indicated that the RJF identification model was effective and practical. The further application to the genomic data from wild boar (Sus scrofa), domestic pigs, and their hybrids validated the pipeline. Our method has potential in not only monitoring genetic diversity in wild relatives of domestic animals but also supporting animal genetic resource conservation and management.
Cai et al. (Wed,) studied this question.