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. 2021 Apr 9;11(4):1067.
doi: 10.3390/ani11041067.

Evaluation of Genetic Diversity and Structure of Turkish Water Buffalo Population by Using 20 Microsatellite Markers

Emel Özkan Ünal  1 , Raziye Işık  2 , Ayşe Şen  1 , Elif Geyik Kuş  3 , Mehmet İhsan Soysal  1
Affiliations

Evaluation of Genetic Diversity and Structure of Turkish Water Buffalo Population by Using 20 Microsatellite Markers

Emel Özkan Ünal et al. Animals (Basel). .

Abstract

The present study was aimed to investigate the genetic diversity among 17 Turkish water buffalo populations. A total of 837 individuals from 17 provincial populations were genotyped, using 20 microsatellites markers. The microsatellite markers analyzed were highly polymorphic with a mean number of alleles of (7.28) ranging from 6 (ILSTS005) to 17 (ETH003). The mean observed and expected heterozygosity values across all polymorphic loci in all studied buffalo populations were 0.61 and 0.70, respectively. Observed heterozygosity varied from 0.55 (Bursa (BUR)) to 0.70 (Muş (MUS)). It was lower than expected heterozygosity in most of the populations indicating a deviation from Hardy-Weinberg equilibrium. The overall value for the polymorphic information content of noted microsatellite loci was 0.655, indicating their suitability for genetic diversity analysis in buffalo. The mean FIS value was 0.091 and all loci were observed significantly deviated from Hardy-Weinberg Equilibrium (HWE), most likely based on non-random breeding. The 17 buffalo populations were genetically less diverse as indicated by a small mean FST value (0.032 ± 0.018). The analysis of molecular variance (AMOVA) analysis indicated that about 2% of the total genetic diversity was clarified by population distinctions and 88 percent corresponded to differences among individuals. The information produced by this study can be used to establish a base of national conservation and breeding strategy of water buffalo population in Turkey.

Keywords: Turkish water buffalo; genetic diversity; genetic structure; heterozygosity; microsatellite loci.

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Conflict of interest statement

The parts of the project, members of the university and the company, don’t have any “Conflict of Interest” in that project or paper and this paper will not provide any economical benefits to company.

Figures

Figure 1
Figure 1
The pairwise FST distances between the studied 17 Turkish water buffalo populations. Color-codes are identified on the scale at the right side of the figure (ns = not significant, blank significant p < 0.001, pairwise populations FST values and significant were shown in Supplementary Table S3c). İstanbul/Çatalca-IST; Tekirdağ/Saray-TEK; Balıkesir-BAL; Bursa-BUR; Düzce-DUZ; Giresun-GIR; Amasya-AMS; Tokat-TOK; Çorum-COR; Sinop-SIN; Samsun-SAM; Afyon-AFY; Kayseri (KAY), Sivas-SVS; Muş-MUS, Bitlis-BIT; Diyarbakır-DYB.
Figure 2
Figure 2
Neighbor-net dendrogram constructed from Reynold’s genetic distances among 17 Turkish water buffalo populations. I Cluster I; II Cluster II; Marmara Region (MRM): İstanbul/Çatalca-IST; Tekirdağ/Saray-TEK; Balıkesir-BAL; Bursa-BUR; Black Sea Region (BSR): Düzce-DUZ; Giresun-GIR; Amasya-AMS; Tokat-TOK; Çorum-COR; Sinop-SIN; Samsun-SAM; Aegean Region (AER): Afyon-AFY; Central Anatolian Region (CAR): Kayseri (KAY), Sivas-SVS; Eastern Anatolia Region (EAR): Muş-MUS, Bitlis-BIT; Southeast Anatolian Region (SAR): Diyarbakır-DYB.
Figure 3
Figure 3
Tree-dimensional principal component analysis (PCA) plot of Turkish water buffalo populations based on 20 microsatellite data. I Cluster I; II Cluster II; Marmara Region (MRM): İstanbul/Çatalca-IST; Tekirdağ/Saray-TEK; Balıkesir-BAL; Bursa-BUR; Black Sea Region (BSR): Düzce-DUZ; Giresun-GIR; Amasya-AMS; Tokat-TOK; Çorum-COR; Sinop-SIN; Samsun-SAM; Aegean Region (AER): Afyon-AFY; Central Anatolian Region (CAR): Kayseri (KAY), Sivas-SVS; Eastern Anatolia Region (EAR): Muş-MUS, Bitlis-BIT; South East Anatolian Region (SAR): Diyarbakır-DYB.
Figure 4
Figure 4
(A) Plot of (∆K) values for each K from 1 to 20. (B) Clustering analysis by structure for the full-loci dataset assuming K = 2. Blue: Cluster I; Red: Cluster II; Population name abbreviations are labeled below the structure result (Marmara Region (MRM): İstanbul/Çatalca—IST; Tekirdağ/Saray—TEK; Balıkesir—BAL; Bursa—BUR; Black Sea Region (BSR): Düzce—DUZ; Giresun—GIR; Amasya—AMS; Tokat—TOK; Çorum—COR; Sinop—SIN; Samsun—SAM; Aegean Region (AER): Afyon—AFY; Central Anatolian Region (CAR): Kayseri (KAY), Sivas—SVS; Eastern Anatolia Region (EAR): Muş—MUS, Bitlis—BIT; South East Anatolian Region (SAR): Diyarbakır—DYB).
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