Technical Note: Anomaly detection for breed purity analysis in pigs using a single breed genotype panel.

Abstract

Recent advancements in genotyping technologies have revolutionized our ability to estimate breed composition in pigs. The classical compositional regression used for this purpose requires a multibreed panel to detect crossbreeding and its application is limited to breeds in the panel. Some breed entities may not have access to multibreed panel but may have access to a single breed panel. We present crossbreeding detection methods based on semi-supervised anomaly detection techniques that use a single breed genotype panel from purebred animals of interest. By utilizing these methods, we identified and assessed breed outliers within large pig genotype panels.