The Karayaka is the most populous sheep breed in the
Black Sea region of Turkey. In the present study, we investigated the intra-
and inter-population genetic relationships among indigenous Karayaka
sheep subpopulations. Nine microsatellites were genotyped for 64 individuals from Samsun, Ordu, Giresun and Tokat provinces. The average number of alleles (
Karayaka sheep, one of the native Turkish sheep breeds, has been bred under harsh environmental conditions in the Black Sea region of Turkey. Although the history of the Karayaka breed is unknown, the name of “Karayaka” comes from Karayaka village of Tokat province in the Black Sea region (Yalcin, 1986). This breed is distributed along the eastern half of the Black Sea coast, especially in the provinces of Ordu, Giresun, Samsun and Tokat. Karayaka is an important breed for meat production for consumers (Karaman et al., 2013). The sheep population of Turkey was 37 276 050 in 2019 (TUIK, 2019). Karayaka sheep are estimated to constitute 4.5 % of total sheep population in Turkey. Due to its meat quality, Karayaka is highly appreciated and intensively raised in the region.
The conservation of Turkish livestock species has been organized by Turkish Ministry of Agriculture and Forestry with FAO's partnership. Until now, genetic characterization studies on native Turkish sheep breeds and other livestock species have been performed by using microsatellite and other techniques in several studies (Ozmen et al., 2020; Ameur et al., 2020; Kirikci et al., 2018; Ağaoğlu, 2010; Cemal et al., 2013; Das et al., 2015; Elmaci et al., 2007; Kurar et al., 2012; Oner et al., 2013; Ozdemir et al., 2016; Özşensoy, 2011; Yilmaz et al., 2014). These studies provided a reasonable picture of the genetic variation and relationships among native Turkish sheep breeds, but most of those studies were on many breeds.
One of the effective breeding strategies for livestock is to collect extensive knowledge about genetic structure at the population level of a breed (Groeneveld et al., 2010). There has been no study on the genetic relationships among Karayaka sheep subpopulations. Therefore, we aimed to evaluate the genetic relationships within and among Karayaka sheep subpopulations, which has been bred as purebred over the years and reflect the breed's original characteristics.
All experimental procedures and animal management were performed under veterinary supervision according to the Animal Care and Use Guidelines of Ondokuz Mayıs University of Local Ethical Committee.
A total of 64 blood samples were collected from Karayaka sheep
populations (16 samples from each population) raised in the provinces of
Samsun, Ordu, Giresun and Tokat from the Black Sea region of Turkey.
Sampling locations are shown on the map prepared using ArcGIS software
(Fig. 1). It was considered that sampled animals were unrelated. In order
to make sure, we controlled the pedigree records, stored by the Sheep and
Goat Breeders' Association of Turkey. Blood samples were stored at
Sampling locations of Karayaka sheep subpopulations.
Microsatellites used in the study were selected from the microsatellite list recommended by ISAG/FAOs MoDAD (Measurement of Domestic Animal Diversity)
program (FAO, 2004). Microsatellites, their primer sequences and
chromosome numbers are given in Table 1. Annealing temperatures (ranged from
55.9 to 63.4
Microsatellite marker names, primer sequences, chromosome and GenBank accession numbers.
The number of alleles, allelic richness, the values of observed
heterozygosity (
Genetic parameters such as allele number and allelic richness are a good indicator of genetic diversity within populations for studied markers (Hassen et al., 2012). Genetic diversity parameters belong to locus are given in Table 2. In the present study, a total of 148 alleles were observed, with an average number of alleles of 16.44. The highest and lowest number of alleles for all loci was observed 22 at the BM1314 and 8 at the CSSM47 loci. The highest and lowest allele number for populations was observed 87 in Ordu and 65 in Giresun. The average allelic richness was calculated as 9.887. The allelic richness values of the highest and lowest for all loci were detected 12.875 at BM1314 locus and 5.824 at CSSM47 locus (Table 2), while the populations the highest and lowest allelic richness values were 8.644 in Ordu and 6.791 in Giresun (Table 3).
The genetic diversity parameters for all studied loci.
Abbreviations:
The first step of revealing the genetic diversity is to prefer using polymorphic microsatellite markers (Álvarez et al., 2004). The polymorphism information content (PIC) values were calculated for studied markers. The PIC values for all loci ranged between 0.923 at BM1314 loci and 0.723 at CSSM47 loci, with an average of 0.866 in Table 2. The PIC mean values were estimated for Samsun, Ordu, Giresun and Tokat subpopulations as 0.689, 0.827, 0.737 and 0.730, respectively (Table 3). It has been suggested that all loci studied are highly informative because the PIC values to be calculated at the locus are higher than 0.50 (Botstein et al., 1980).
The observed and expected heterozygosity are the most often used parameters
in the studies of population genetics (Nei, 1973). The mean
The genetic diversity of Karayaka sheep subpopulations based on the nine microsatellite markers.
Abbreviations: MNA, mean allele number; NPA, private allele number;
The private allele number was calculated comparing populations (Table 3). The numbers of private alleles for both locus and population are given in Table S1 in the Supplement. We observed a total of 53 private alleles, 28 of which had a frequency over 5 %. The highest private allele number (11) was observed in HUJ616 and the lowest (1) in CSSM47. The highest private allele number (16) was observed in Samsun and Ordu, whereas the lowest (10) was observed in Tokat.
Wright's
Wright's
Genetic similarities for Karayaka sheep subpopulations were revealed with FCA. All the subpopulations were separated from each other, whereas Samsun subpopulation was clustered in the different place than other subpopulations (Fig. 2).
FCA results showing the relationship between the subpopulations.
To evaluate the genetic structure and level of admixture among the studied
subpopulations, the most likely
The results of the
Genetic differentiation between the populations were compared on the basis
of pairwise
Pairwise
There are several studies that are interested in the genetic diversity of different sheep breeds in Turkey (Gutierrrez-Gil et al., 2006; Koban, 2004; Yildiran and Cakir, 2012; Yilmaz et al., 2014). In the previous studies of Karayaka breed in literature the numbers of samples were too low. Moreover, there was not another study investigating the Karayaka breed subpopulations. Therefore, we aimed to investigate the genetic diversity and relationships in Karayaka sheep subpopulations by collecting more samples from geographically distinct populations.
The used markers in this study were highly polymorphic because of the PIC values were higher than 0.50 (Botstein et al., 1980). The PIC mean value for the studied loci was 0.866, ranged from 0.723 (CSSM47) to 0.923 (BM1314). This means that all studied markers are highly polymorphic. The average value of PIC was higher than values obtained from the other sheep breeds (Dossybayev et al., 2019; Guang-Xin et al., 2019). The mean number of alleles was 16.44 with a total of 148. The values obtained were higher than those of some previous studies with Asia and Europe sheep breeds (Ceccobelli et al., 2009; Khaleel et al., 2018). Although the mean number of alleles obtained was higher than those by Yilmaz et al. (2014), it was lower than those obtained by Yildiran and Cakir (2012). This difference could be explained by the number of the used loci and different breeds. In the present study, the microsatellites with the highest and lowest allele number were BM1314 (22) and CSSM47 (8), respectively. Similar results were reported by other studies (ranged from 8 to 12 in BM1314 and from 3 to 4 in CSSM47) (Arora and Bhatia, 2004; Singh et al., 2015; Girish et al., 2007).
In the present study, the mean value of expected heterozygosity (
Results of both FCA and Structure for the Ordu and Giresun subpopulations were more similar than the rest of the other subpopulations. This result could be attributed to the fact that the animals shared the same areas in the grazing season. The existence of genetic variability and distinction among populations could have important consequences for maintaining genetic diversity, planning of breeding programs and conservation studies in the future (Wu et al., 2015). The high genetic diversity within a population and differentiation among populations could be due to either geographic distance or allelic richness and other factors.
Conservation studies in livestock should be done at the population levels of a specific breed. Because this provides comprehensive knowledge of the genetic diversity and genetic structure among and within populations and possibilities for determination of conservation strategies. We studied isolated populations consisting of a low number and pure breeding. This kind of population could be more vulnerable to genetic drifts. This work provides the first evidence for genetic relationships among Karayaka sheep subpopulations. Consequently, Karayaka sheep subpopulations were genetically different from each other in terms of nine microsatellite loci, meaning that this breed has discrete subpopulations; this should be taken into consideration when preparing conservation programs and future breeding strategies.
The data sets are available upon request from the corresponding author.
The supplement related to this article is available online at:
KK and MAC participated in the collection of blood samples. KK performed the laboratory analysis. KK and LM performed statistical analysis of data. All authors wrote the article. KK, MAC and LM edited the article. All the revisions were done by KK and LM. All authors read and approved the final paper.
The authors declare that they have no conflict of interest.
The authors would like to thank the Sheep and Goat Breeders' Association of Turkey for collaboration in collecting samples.
This research has been supported by Ondokuz Mayıs University (project no. PYO.ZRT.1901.14.003).
This paper was edited by Steffen Maak and reviewed by Kairat Dossybayev and one anonymous referee.