Genetic Variability and Population Structure of Polish Konik Horse Maternal Lines Based on Microsatellite Markers

Abstract

Summary: The aim of this study is to reveal the genetic variability and population structure of maternal lines of the Polish Konik—a native Polish horse breed of the primitive type included in the Polish conservation programme. The analysis was carried out on the basis of 17 microsatellite markers routinely used for parentage testing. The structural analysis indicated the likelihood of three genetic clusters (using the Structure and Structure Harvester software). F-statistics indicated a low level of inbreeding. All mean population coefficients were close to those obtained for representatives of male founder lines. The population seemed to be stable. However, due to a previous bottleneck event, breeding strategies should focus on avoiding inbreeding depression, preventing the decrease of genetic variability, and sustaining the active female lines. The aim of the conservation programme is to maintain the population size of endangered livestock breeds of less economic importance at a level that ensures the survival of the breed, the preservation of genetic diversity, and the preservation of as many pedigree lines as possible. The Polish Konik, a native Polish primitive-type horse breed and is one of the breeds included in such a programme in Poland. Presently, there are only 16 (of the 35 maternal lines known in 1962), some of which are endangered. We examined the genetic variability and structure of the Polish Konik maternal lines (176 individuals) on the basis of the pedigree data and 17 microsatellite markers (STRs) from parentage testing. The overall mean number of alleles was 7.647 (±0.411), the effective number of alleles was 3.935 (±0.271), the mean number of alleles for which the frequency was equal to or lower than 5% was 4.471 (±0.286), and the mean information index was 1.506 (±0.087). The structure of the population and admixture patterns were calculated with the Structure and Structure Harvester software. The structural analysis indicated three likely genetic clusters; as the most optimal K value was estimated as 3, with ∆K of 15.4188. The F-statistics results indicated a low level of inbreeding (average inbreeding coefficient FIT was 0.0188, coefficient of differentiation FST was 0.0304, and mean inbreeding index value FIS was −0.0119). Variability monitoring should be carried out in order to avoid inbreeding depression, while breeding strategies should be designed to prevent the decrease of genetic variability in the Polish horse breed and to sustain the active female lines.

Unlocking Horse Y Chromosome Diversity

“…Recently, many studies have been focused on the loss of biodiversity [ 23 , 24 , 25 ] or the increase in deleterious genotypes [ 26 ] caused by such inbreeding (as reviewed in [ 7 ]). In the last 200 years, the inbreeding practice led to the phenotypical expression at homozygous sites of deleterious variants [ 27 ], as highlighted when the coefficients are calculated in order to evaluate the genetic diversity among different horse breeds [ 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 ,…”

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

“…Moreover, Cieślak et al (2017) , for the first time, suggested that mtDNA results do not fully correspond to the official pedigree data. Another study focused on assessing the genetic diversity and structure of the Polish Konik breed based on 17 microsatellite markers ( Fornal et al, 2021 ), and this presented no signs of inbreeding and the assignment of the horses using Structure software into (most likely) three clusters. However, the study conducted by Mackowski et al (2015) found 8.6% of inbreeding.…”

Genetic Diversity and Genetic Differentiation of Populations of Golden-Backed Carp (Cyprinus carpio var. Jinbei) in Traditional Rice Fields in Guizhou, China

“…Monitoring the genetic diversity and genetic structure of small biological populations is crucial for protecting their genetic diversity and the uniqueness of the gene pool [ 30 ]. Golden-backed carp cultivation is ongoing, but basic research and reports on their genetic breeding are very scarce; therefore, we studied the current state of genetic diversity.…”