Mitochondrial DNA and Y chromosome reveal the genetic structure of the native Polish Konik horse population.

Polish Konik remains one of the most important horse breeds in Poland. The primitive, native horses with a stocky body and mouse-like coat color are protected by a conservation program, while their Polish population consists of about 3,480 individuals, representing 16 dam and six sire lines. To define the population's genetic structure, mitochondrial DNA and Y chromosome sequence variables were identified. The mtDNA whole hypervariable region analysis was carried out using the Sanger sequencing method on 233 Polish Koniks belonging to all dam lines, while the Y chromosome analysis was performed with the competitive allele-specific PCR genotyping method on 36 horses belonging to all sire lines. The analysis of the mtDNA hypervariable region detected 47 SNPs, which assigned all tested horses to 43 haplotypes. Most dam lines presented more than one haplotype; however, five dam lines were represented by only one haplotype. The haplotypes were classified into six (A, B, E, J, G, R) recognized mtDNA haplogroups, with most horses belonging to haplogroup A, common among Asian horse populations. Y chromosome analysis allocated Polish Koniks in the Crown group, condensing all modern horse breeds, and divided them into three haplotypes clustering with coldblood breeds (28 horses), warmblood breeds (two horses), and Duelmener Pony (six horses). The clustering of all Wicek sire line stallions with Duelmener horses may suggest a historical relationship between the breeds. Additionally, both mtDNA and Y chromosome sequence variability results indicate crossbreeding before the studbooks closure or irregularities in the pedigrees occurred before the DNA testing introduction.

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

The Polish draft horse (PDH) breed is a result of crossing local mares with imported cold-blooded stallions, such as Belgians, Ardennes, Fjords, and others. A part of the broodmare stock investigated in this study was also imported from various countries, such as Denmark. In this study, we investigate the genetic composition of the PDH by analyzing the whole mitochondrial d-loop variability and comparing it to previously demonstrated whole d-loop sequences of other cold-blooded breeds: Ardennais, Belgian, Breton, Clydesdale, Noriker, Norwegian Fjord, Percheron, and Suffolk. Our results show high nucleotide diversity within the PDH population (π = 0.011), and the existence of two main haplogroups: one of relatively concise origin, with strong kinship to the Belgian breed, and the second showing close relation to the majority of other analyzed cold-blooded breeds. Some of the PDH maternal strains clustered separately, which can be a result of the influence of other unidentified breeds that served as a foundation stock for the present population. This present study explains the genetic relationship of the PDH to other cold-blooded breeds and indicates the high genetic diversity of the breed.