Pedigree analysis in the German Paint Horse: Genetic variability and the influence of pedigree quality

Pedigree information of the German Paint Horse was analysed in order to assess genetic variability within this population. A data set consisting of 14,313 horses was provided by the German Paint Horse Breeding Association. Three reference populations of registered Paint horses born in Germany between the years 2000 and 2009 (1), between 2000 and 2009 based on a manually improved pedigree (2) and between 1990 and 1999 (3) were defined. For all three reference populations the quality of pedigree information, average inbreeding coefficients, effective number of founders, effective number of ancestors, effective number of founder genomes and most important ancestors were analysed. One aim of this study was to compare the results before and after the pedigree was improved. The current Paint Horse population in Germany (reference population 2) has an average number of complete generation-equivalent of 4.77. Average inbreeding coefficients are 0.49% for all and 0.41% for five considered generations. The number of founders for the current population is 4341. The effective number of founders is 963, the effective number of ancestors is 186.1 and the effective number of remaining genomes in the reference population is 118.5. Half of the gene pool of the current German population is explained by 120 animals. These rather high values indicate a good genetic diversity within the breed. However, results have to be interpreted carefully as depth of pedigree and the rather low average generation equivalent of the German Paint Horse have to be taken into account.