Detecting SNP markers discriminating horse breeds by deep learning

The assignment of an individual to the true population of origin using a low-panel of discriminant SNP markers is one of the most important applications of genomic data for practical use. The aim of this study was to evaluate the potential of different Artificial Neural Networks (ANNs) approaches consisting Deep Neural Networks (DNN), Garson and Olden methods for feature selection of informative SNP markers from high-throughput genotyping data, that would be able to trace the true breed of unknown samples. The total of 795 animals from 37 breeds, genotyped by using the Illumina SNP 50k Bead chip were used in the current study and principal component analysis (PCA), log-likelihood ratios (LLR) and Neighbor-Joining (NJ) were applied to assess the performance of different assignment methods. The results revealed that the DNN, Garson, and Olden methods are able to assign individuals to true populations with 4270, 4937, and 7999 SNP markers, respectively. The PCA was used to determine how the animals allocated to the groups using all genotyped markers available on 50k Bead chip and the subset of SNP markers identified with different methods. The results indicated that all SNP panels are able to assign individuals into their true breeds. The success percentage of genetic assignment for different methods assessed by different levels of LLR showed that the success rate of 70% in the analysis was obtained by three methods with the number of markers of 110, 208, and 178 tags for DNN, Garson, and Olden methods, respectively. Also the results showed that DNN performed better than other two approaches by achieving 93% accuracy at the most stringent threshold. Finally, the identified SNPs were successfully used in independent out-group breeds consisting 120 individuals from eight breeds and the results indicated that these markers are able to correctly allocate all unknown samples to true population of origin. Furthermore, the NJ tree of allele-sharing distances on the validation dataset showed that the DNN has a high potential for feature selection. In general, the results of this study indicated that the DNN technique represents an efficient strategy for selecting a reduced pool of highly discriminant markers for assigning individuals to the true population of origin.