Effectiveness of nine polymorphic microsatellite markers in parentage testing in Posavina, Croatian Coldblood and Lipizzaner horse breeds in Croatia

The global biodiversity crisis extends to autochthonous local breeds of livestock. There is an increasing danger that these rare breeds become extinct and with them their locally adapted gene pool. Modern molecular tools such as parentage testing using microsatellite genotyping are powerful in guiding management and conservation. We tested nine microsatellite markers in three Croatian horse breeds and obtained high exclusion probabilities (EPs) for the most common test scenario 'one parent and offspring known and the other parent tested' (99.9% in Posavina and Croatian Coldblood and 99.3% in Lipizzaner), despite that Lipizzaner has an overall lower genetic variability at microsatellite loci. To become a useful tool in breed management in countries with developing economies, genetic screening systems must be designed to be statistically powerful yet economically viable. Therefore, a suite of six markers that can be run in two multiplex systems and which still gives high exclusion probabilities (99.5% in Posavina and Croatian Coldblood and 98% in Lipizzaner) was chosen.