Genetic Differentiation of the Two Types of Polish Cold-blooded Horses Included in the National Conservation Program.

Simple Summary In this study we investigated the degree of genetic differentiation among two types of Polish cold-blooded horses, namely Sokolski and Sztumski. Both these horse types are a subject of conservation breeding as their populations have been dramatically reduced during recent decades. These cold-blooded horses are considered as separate breeds, with separate stud books, but yet still their genetic differentiation has not been precisely determined, especially on the genome-wide level. In this study, we characterized genetic differentiation of these two horse populations as well as their genetic variation, admixture patterns, and level of relatedness within populations with the use of single nucleotide polymorphism (SNP) genotyping arrays. We also attempted to detect genome regions with the largest genetic differences between those horses by the detection of so-called diversifying selection signals. The results of this study provide initial evidence supporting decisions made during conservation breeding program design and answer some of the questions raised by the breeders of Sokolski and Sztumski horses. Abstract The current role of the horse as a companion animal resulted in a decrease of interest in breeding and usage of draft horses. This meant that the population of cold-blooded horses in Poland has been dramatically reduced during the last decades. To avoid impoverishment of the gene pool of the local horse population, a conservation program was established which involves draft horses and other local horse breeds. The draft horses bred in Poland can be subdivided in a few horse types of which the most widespread and consolidated are Sztumski and Sokolski horses. These two subpopulations are phenotypically diversified, however, the overall level of their genetic differentiation seems to be relatively low and not precisely determined, especially with the use of molecular markers. In reference to this, in this study we used Illumina genotyping arrays to describe in detail the genetic differentiation of these two cold-blooded horse populations. We describe the genetic distance between them, as well as within-population variation, admixture patterns, and level of relatedness within populations. We also made an attempt to detect genome regions divergently selected between those horses by the detection of diversifying selection signals. The results of this study provide initial evidence supporting breeding decisions that were made during conservation breeding program design and answer questions raised by the breeders of Sokolski and Sztumski horses concerning the level of their genetic variation and differentiation.