12-plex highly polymorphic microsatellite marker set for parentage analysis in Banija spotted pigs

Microsatellites (MS) have been, for the last two decades, widely used for parentage analysis in all types of livestock, including pigs. Conservation efforts on Banija spotted pigs included genetic characterization of the breed with MS markers. Since recent comparison of pedigree and MS data revealed some inconsistencies, the aim of this study was to develop a set of highly polymorphic and heterozygous MS markers, which could be used for parentage analysis and to prevent pedigree errors. 12 MS markers with the polymorphic information content (PIC) above 0.62 were chosen and combined into a single multiplex polymerase chain reaction (PCR). The combined non-exclusion probability for one candidate parent (NE-1P) was 0.00246149, the combined NE-1P given the genotype of a known parent of the opposite sex (NE-2P) was 0.00003739 and combined non-exclusion probability for a candidate parent pair (NE-PP) was 0.00000003. Due to a high information content of selected MS markers it was possible to obtain high accuracy in parentage assignment, which was confirmed by analyzing actual data with known genetic relationships.