Genetic Characterization of Native Donkey (Equus asinus) Populations of Turkey Using Microsatellite Markers

Abstract

This study presents the first insights to the genetic diversity and structure of the Turkish donkey populations. The primary objectives were to detect the main structural features of Turkish donkeys by microsatellite markers. A panel of 17 microsatellite markers was applied for genotyping 314 donkeys from 16 locations of Turkey. One hundred and forty-two alleles were identified and the number of alleles per locus ranged from 4 to 12. The highest number of alleles was observed in AHT05 (12) and the lowest in ASB02 and HTG06 (4), while ASB17 was monomorphic. The mean H_O in the Turkish donkey was estimated to be 0.677, while mean H_E was 0.675. The polymorphic information content (PIC) was calculated for each locus and ranged from 0.36 (locus ASB02) to 0.98 (locus AHT05), which has the highest number of alleles per locus in the present study. The average PIC in our populations was 0.696. The average coefficient of gene differentiation (G_ST) over the 17 loci was 0.020 ± 0.037 (p < 0.01). The G_ST values for single loci ranged from -0.004 for LEX54 to 0.162 for COR082. Nei's gene diversity index (H_t) for loci ranged from 0.445 (ASB02) to 0.890 (AHT05), with an average of 0.696. A Bayesian clustering method, the Structure software, was used for clustering algorithms of multi-locus genotypes to identify the population structure and the pattern of admixture within the populations. When the number of ancestral populations varied from K = 1 to 20, the largest change in the log of the likelihood function (K) was when K = 2. The results for K = 2 indicate a clear separation between Clade I (KIR, CAT, KAR, MAR, SAN) and Clade II (MAL, MER, TOK, KAS, KUT, KON, ISP, ANT, MUG, AYD and KAH) populations.

Keywords: Equus asinus; Turkey; donkey; genetic diversity; microsatellites; molecular markers.

Figure 1

Geographic distribution of the 16 donkey populations included in the study. The details of the regions are given in Table 1.

Figure 2

Graphical representation of pairwise F_ST distances between the 16 Turkish donkey populations studied. Color-codes are defined on the scale at the right side of the figure. (ns: not significant, blank significant p < 0.05; p < 0.01; p < 0.001). Kırklareli-KIR, İstanbul/Çatalca—CAT, Malkara—MAL, Amasya/Merzifon—MER, Tokat—TOK, Kastamonu—KAS, Kütahya—KUT, Muğla—MUG, Aydın—AYD, Isparta—ISP, Kahramanmaraş—KAH, Antalya—ANT, Konya—KON, Kars—KAR, Mardin—MAR, Şanlıurfa—SAN.

Figure 3

Neighbour-net dendrogram constructed from Reynold’s genetic distances among 16 Turkish donkey population (Kırklareli—KIR, İstanbul/Çatalca—CAT, Malkara—MAL, Amasya/Merzifon—MER, Tokat—TOK, Kastamonu—KAS, Kütahya—KUT, Muğla—MUG, Aydın—AYD, Isparta—ISP, Kahramanmaraş—KAH, Antalya—ANT, Konya—KON, Kars—KAR, Mardin—MAR, Şanlıurfa—SAN).

Figure 4

Clustering analysis by structure for the full-loci dataset assuming K = 2. Population name abbreviations are labeled below the structure result (Kırklareli—KIR, İstanbul/Çatalca—CAT, Malkara—MAL, Amasya/Merzifon—MER, Tokat—TOK, Kastamonu—KAS, Kütahya—KUT, Muğla—MUG, Aydın—AYD, Isparta—ISP, Kahramanmaraş—KAH, Antalya—ANT, Konya—KON, Kars—KAR, Mardin—MAR, Şanlıurfa—SAN). The geographical regions are labeled above the structure results (MRM: Marmara, BSR: Black sea region; AER: The Aegean region, CAR: The Central Anatolia region, MDR: The Mediterranean region, EAR: Eastern Anatolia region SAR: South East Anatolian region).