Founder analysis and family identification in the current Campolina horse population

Studying the founders' contribution in a population is not a new concept, but still being important because any study involving genetic diversity loss, or inbreeding increase (heterozygosity loss), must begin with a baseline population, in case of a full pedigree, the founder population. In this study, after studying a pedigree comprised of 107,951 horses, along with a dataset including 19 traits measured in 18,695 horses (from the reference population - defined latter), we demonstrated the formation of different lineages and evaluated its impact on the breeding values for each considered animal. The horses born after 1990 (N = 65,634) were treated as the reference population and the pedigree for those animals was extracted considering the referred year as the cutoff to compute the base population (in total, 81,651 horses were included in the final pedigree set). The most influential founders were considered as variables, and their kinship coefficient among all other horses from the reference population was treated as observations in a principal component analysis. Three lineages were found in the current population, formed by 6 stallions and 8 mares; those founders explained about 42.53% of the gene pool in the present population. Almost all founders had negative breeding values for gait scores, which lead to negative genetic averages in the current population. Additionally, after performing analyses within lineages/ groups, the lineages affected genetic correlations among adjusted phenotypes for all studied traits. Our results suggest that the founders' genetic constitution remained important in the population, even after many generations.