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

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 Sokólski 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 Sokólski and Sztumski horses concerning the level of their genetic variation and differentiation.

Suitability of Pedigree Information and Genomic Methods for Analyzing Inbreeding of Polish Cold-Blooded Horses Covered by Conservation Programs

“…The study of genomic inbreeding was based on 175 cold-blooded horses, belonging to two types, namely Sokólski ( n = 106) and Sztumski ( n = 69), which were previously analyzed for genetic differentiation [ 15 ] and selection signatures [ 16 ].…”

“…Genomic inbreeding was evaluated based on Neogen Equine Community array (Illumina, San Diego, CA, USA) data, including genotypes for 65,157 SNPs with an average inter-marker distance in EquCab2.0 genome of 36.3 kb. SNP data were filtered as previously described [ 16 ]. In brief, the filters included a MAF (minor allele frequency) threshold of 5% and <20% of missing genotypes in the whole studied population.…”

“…This removed another 109 SNPs that did not map to the newer assembly. Based on these filtered data, four inbreeding measures were calculated, similarly as in our previous study [ 16 , 17 ]: (i) the usual variance-standardized relationship minus 1 (F GRM ), (ii) method-of-moments F coefficient estimate (similar to F IS ), (iii) F coefficient based on the correlation between uniting gametes (F UNI ) [ 18 ], and (iv) runs of homozygosity (ROH)-based coefficient (F ROH , including ROH segments with lengths above 1 Mb) [ 19 ] using Plink v1.90b4 software [ 20 ]. The first three coefficients were calculated using Plink --ibc command, while the ROH-based coefficient was calculated by identification of ROH, covering a minimum of 30 SNPs, as in our previous study in cattle [ 21 ] and evaluation of a genome portion covered by ROH as proposed by McQuillan et al [ 19 ].…”

Mitochondrial Whole D-Loop Variability in Polish Draft Horses of Sztumski Subtype

“…Presently, only two types of Polish draft horse, namely Sokólski and Sztumski, remain actively breeding, and they are both under the National Program for Protection of Genetic Resources [ 30 ]. Since 1964, when the first volume of the PDH studbook was published, two separate sections of the studbook have been maintained in Poland due to a clear heritable difference in type and phenotypical traits and genetic differentiation [ 2 ]. In this study, the analysis of whole d-loop variation of mtDNA was applied to investigate the origin and variability of the PDH maternal lines that have been formed over multiple generations.…”

“…Łużycki in Poland). Plenty of international efforts have been made to maintain several populations under the FAO (Food and Agriculture Organization of the United Nations) to preserve the gene pool and to protect the horses’ biodiversity and cultural heritage; however, these actions were conservative and had no relative impact on the self-reconstruction of populations [ 2 ].…”