Genetic characterization of the horse breeds from the Netherlands using single nucleotide polymorphisms

Interest on preservation and improvement of performance, fitness and aesthetic traits have created diverse populations in modern horses. This study aims to comprehend genetic diversity status within and across breeds or types of horses sampled in the Netherlands. The genetic diversity is important to maintain survival and adaptive potential of populations and avoid inbreeding in the long term. This study will also identify potential regions of selection. To our knowledge it is the first study to use single nucleotide polymorphism (SNP) information in a diversity study for the horses in the Netherlands. Principal component analysis (PCA) was performed using 203 randomly selected horses (about 20 per breed) and 43,721 autosomal SNPs that remained after pruning for call rate per SNP, per horse and minor allele frequency. The relationships among breeds were visualized by plotting the first two principal components. The Friesian breed seemed genetically distant from the other breeds in the dataset. The relationships among breeds will also be quantified based on FST values. Runs of homozygosity (ROH) using the software PliNK will be determined to identify the regions of selection. Also, diversity indices as heterozygosity (observed and expected) and fixation index (FIS) values will be investigated to understand within breed diversity.