Genetic diversity and population structure of Mongolian regional horses with 14 microsatellite markers

Abstract

Objective: This study aimed to identify the genetic diversity and population structure of Mongolian horse populations according to the province of residence (Khentii, KTP; Uvs, USP; Omnogovi and Dundgovi, GOP; Khovsgol, KGP) using 14 microsatellite (MS) markers.

Methods: A total of 269 whole blood samples were obtained from the four populations (KTP, USP, GOP, KGP) geographically distinct provinces. Multiplex polymerase chain reaction (PCR) was conducted using 14 MS markers (AHT4, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, and VHL20), as recommended by the International Society for Animal Genetics. Capillary electrophoresis was conducted using the amplified PCR products, alleles were determined. Alleles were used for statistical analysis of genetic variability, Nei's DA genetic distance, principal coordinate analysis (PCoA), factorial corresponding analysis (FCA), and population structure.

Results: On average, the number of alleles, expected heterozygosity (HExp), observed heterozygosity (HObs), and polymorphic information content among all populations were 11.43, 0.772, 0.757, and 0.737, respectively. In the PCoA and FCA, GOP, and KGP were genetically distinct from other populations, and the KTP and USP showed a close relationship. The two clusters identified using Nei's DA genetic distance analysis and population structure highlighted the presence of structurally clear genetic separation.

Conclusion: Overall, the results of this study suggest that genetic diversity between KTP and USP was low, and that between GOP and KGP was high. It is thought that these results will help in the effective preservation and improvement of Mongolian horses through genetic diversity analysis and phylogenetic relationships.

Keywords: Genetic Diversity; Horse; Microsatellites; Mongolia; Relationships; Structure.

Figure 1

Four Mongolian horse populations from the five provinces of Mongolia. 1. Khentii province (KTP); 2. Uvs province (USP); 3. Omnogovi and Dundgovi province (GOP); and 4. Khovsgol province (KGP).

Figure 2

Neighbor-Joined tree showing the genetic distances among the four populations using Nei’s DA genetic distance on the basis of allele frequencies from the 14 MS loci. The number in the branch indicates the percentage of occurrence after 1,000 bootstrap replicates. MS, microsatellite; KTP, Khentii province; USP, Uvs province; GOP, Omnogovi and Dundgovi province; KGP, Khovsgol province.

Figure 3

Principal Coordinate Analysis of allele frequencies from the 14 MS loci genotypes in four populations using GenAIEx. MS, microsatellite; KTP, Khentii province; USP, Uvs province; GOP, Omnogovi and Dundgovi province; KGP, Khovsgol province.

Figure 4

Factorial correspondence analysis of allele frequencies from the 14 MS loci genotypes in four populations using Genetix. MS, microsatellite; KTP, Khentii province; USP, Uvs province; GOP, Omnogovi and Dundgovi province; KGP, Khovsgol province.

Figure 5

Structure analysis of the four horse populations. Cluster results from a structure analysis of 269 horses from four populations and based on 14 microsatellite (MS) markers. Each genotyped horse is represented by a single vertical line divided into K colors, where K is the number of clusters assumed in each structure analysis. Each vertical bar represents an individual horse. The colors on each vertical bar represent the probability of the individual belonging to each cluster.