Application of forensic science technique to the management of an endangered horse population

Implementing conservation strategies needs the knowledge of relationships inside the concerned population. The aim of the study was to find tools to help breeders to manage their horse population. The Skyros pony is an indigenous Greek breed. The breed risk status is defined as critical-maintained according to the criteria from the Food and Agriculture Organization. Partial pedigree information is available, but its quality is poor as the average number of generation-equivalents is under 0.8 for the first known generation and under 1.4 for the second to the fifth. Further, 99 living individuals were genotyped at 16 microsatellite loci in order to check the registered parentage. For ungenotyped animals, conditional expectation of gene contents was calculated given molecular and pedigree data. As said in other studies, the animal genetics literature often seems unaware of relevant developments in human genetics (and conversely). In this study, an approach called Familial Searching was tested. This is used in forensic science, in addition to matching DNA evidence directly to criminal profiles, to search for people (present in a database) who are related to an individual that left DNA evidence at a scene of crime. This method is based on the calculation of likelihood ratios (LR) between genotype of an individual and genotypes of each other individuals of the database. The pedigree was used as ‘local’ prior information, i.e. relating to specific pairs of individuals. General knowledge about the studied population (generation interval, sexual maturity, …) was considered as ‘global’ prior information. Including prior information reduced the number of comparisons from over 50%. First results showed that the parents were always classified into the 5 highest LR. These results simplified parentage verifications, it allowed the detection of 90% of false parentage (LR=0). New links were created in the pedigree through detection of unregistered parents, what involved a reduction of the percentage of animals with one or both unknown parents and consequently an increase of the number of generation-equivalents. The pedigree of the breed was thus improved.