Genetic Diversity and Population Structure of Polish Konik Horse Based on Individuals from All the Male Founder Lines and Microsatellite Markers

SIMPLE SUMMARY: We investigated the genetic diversity of Polish Konik in sire lines. The Polish Konik horse is a Polish native horse breed of a primitive type and is one of the breeds managed via a conservation program. Due to the small number of breed founders (six male lines) and paternal lineages with unknown representation, the genetic diversity and structure of the population should be monitored regularly. This is the first characterization of the genetic diversity of Polish Konik paternal lines based on microsatellite markers (STRs). The fixation index (F(ST)), which measures population differentiation, was low for all the studied markers and its mean value was 0.0305. Our analysis also revealed that there has been no inbreeding in the Polish Konik population for the studied group. This monitoring of genetic diversity could be helpful for the Polish Konik breeding and conservation programs and also for making informed decisions in the management of paternal lineages. ABSTRACT: The Polish Konik horse is a primitive native breed included in the genetic resource conservation program in Poland. After World War II, intensive breeding work began, aimed at rebuilding this breed. Now, the whole Polish Konik population is represented by six male founder lines (Wicek, Myszak, Glejt I, Goraj, Chochlik and Liliput). Individuals representing all six paternal lineages were selected based on their breeding documentation. We performed a fragment analysis with 17 microsatellite markers (STRs) recommended by the International Society for Animal Genetics (ISAG). The genetic diversity and structure within the paternal lineages and the whole of the studied group were investigated. The average allelic richness was 6.497 for the whole studied group. The fixation index (F(ST); measure of population differentiation) was low (about 3%), the mean inbreeding coefficient (F(IT)) was low and close to 0, and the mean inbreeding index value (F(IS)) was negative. The mean expected heterozygosity was established at 0.7046 and was lower than the observed heterozygosity. The power of discrimination and power of exclusion were 99.9999%. The cumulative parentage exclusion probability equaled 99.9269% when one parental genotype was known and 99.9996% with both parents’ genotypic information was available. About 3% of the genetic variation was caused by differences in the breed origin and about 97% was attributed to differences among individuals. Our analysis revealed that there has been no inbreeding in the Polish Konik breed for the studied population. The genetic diversity was high, and its parameters were similar to those calculated for native breeds from other countries reported in the literature. However, due to the small number of breed founders and paternal lineages with unknown representation, the population’s genetic diversity and structure should be monitored regularly.