Selection of SNP Panels for Parentage Testing

Abstract

Correct parentage assignment is a fundamental requirement for a successful breeding program so that production performances can be linked back to the correct families to improve estimates of breeding values. In this study, we evaluated the influence of SNP panel sizes for parentage testing in two species (cattle and sheep) with very different genetic structures. Results suggest that small parentage panels will not port well across breeds and should be designed specifically for a particular breed. If cross breed panels are needed around 450 SNP should be used. Finally, we developed an evolutionary algorithm based on differential evolution to optimize selection of SNP marker panels for parentage assignment. Results show that the algorithm is more efficient at selecting markers for the panel than rule based marker selection.