Turkish Sheep Breeds Research Articles

Genome-wide discovery of selection signatures in four Anatolian sheep breeds revealed by ddRADseq

High-density genomic data analyzed by accurate statistical methods are of potential to enlighten past breeding practices such as selection by unraveling fixed regions. In this study, four native Turkish sheep breeds (80 samples) were genotyped via 296.097 single nucleotide polymorphisms (SNPs) detected by double-digest restriction site-associated DNA (ddRADseq) library preparation combined with the Illumina HiSeq X Ten instrument in order to identify genes under selection pressure. A total of 32, 136, 133, and 119 protein-coding genes were detected under selection pressure by runs of homozygosity (ROH), integrated haplotype score (iHS), the ratio of extended haplotype homozygosity (Rsb), and fixation index (FST) approaches, respectively. Of these, a total of 129 genes were identified by at least two statistical models which overlapped with a total of 52 quantitative trait loci (QTL)-associated SNPs, known to be related to fiber diameter, milk content, body weight, carcass traits, some blood parameters, and entropion. A total of six genes under selection pressure were validated by three statistical approaches five of which are of potential to be integrated into animal breeding since they were associated with wool fiber diameter (ZNF208B), behaviors related to neurocognitive development (CBX1 and NFE2L1), adaptation to high-altitude (SDK1), and anxiety causing internal stress (GSG1L). The sixth gene (COPZ1) turned out to play an important role in coping with different types of cancer in mammals. In particular, ROH analysis uncovered significant findings that the Güney Karaman (GKR) had experienced different selection practices than the Akkaraman (AKR) breed. Moreover, some genes specifically under selection in the GKR breed turned out to be associated with olfaction (OR6K6, OR6N1, OR6N2, and OR4C16), survival during the gestation period (PRR15L), and heat stress (CDK5RAP9). The results of this study imply that GKR may become genetically different from the AKR breed at the genome level due to most probably experiencing different adaptation processes occurring in raised climatic conditions. These differences should be conserved to face future challenges, while other native Turkish sheep breeds could be monitored via genome-wide high-density SNP data to obtain deeper knowledge about the effects of natural selection.

Placental Characteristics Classification of Various Native Turkish Sheep Breeds.

Simple SummaryThe aim of this study was to classify placental characteristics of Akkaraman, Morkaraman, Karayaka, Awassi, Malya, and Bafra native sheep breeds using the hierarchical clustering method. As a result, six breeds were separated into three clusters: the first cluster consisted of Bafra, Karayaka, and Awassi breeds; the second consisted of Akkaraman and Malya breeds; and the third cluster included only the Morkaraman breed.The aim of this study was to classify placental characteristics of Akkaraman, Morkaraman, Karayaka, Awassi, Malya, and Bafra sheep breeds using the hierarchical clustering method. In total, 240 individual data records were used as experimental material. Placental characteristics such as total cotyledon surface area, small and large cotyledon length, small cotyledon depth, etc. were used as explanatory variables to classify the breeds’ characteristics. Hierarchical clustering was used with the nearest neighbour method with Euclidean distance in order to classify the sheep breeds’ variations. As a result, six breeds were separated into three clusters: the first cluster consisted of Bafra, Karayaka, and Awassi breeds; the second consisted of Akkaraman and Malya breeds; and the third cluster included only the Morkaraman breed. Bafra and Karayaka were pointed as the nearest breeds, with a similarity of 98.7% in terms of placental characteristics. The similarity rate of the Akkaraman and Malya breeds was at a level of 97.5%, whereas it was 96.8% for Bafra, Karayaka, and Awassi breeds. The similarity of Akkaraman, Karayaka, Awassi, Malya, and Bafra sheep breeds was estimated as 95.7%. The overall similarity was found to be at a level of 93.2% among sheep breeds. The outcomes of the study might be useful as a selection tool for reproductivity and can be used to select the breed to be reared.

Documentation of extensive genetic diversity in the Ovar-DRB1 gene in native Turkish sheep

Indigenous breeds have a high level of genetic diversity that might contribute to develop animal breeds with desired traits such as disease resistance and high productivity. Major histocompatibility complex (MHC) is a key component of adaptive immune system and consists of highly polymorphic genes that take part in adaptive immune response and disease resistance. Exploring and understanding the effect of polymorphisms in MHC could be beneficial to future animal breeding strategies. In this study, we sequenced the highly polymorphic Exon2 of the ovine DRB1 gene using Sanger sequencing to explore the diversity of this gene in six indigenous Turkish sheep breeds and two crossbreeds. In total, 894 haplotypes from 447 sheep were investigated, and 69 different haplotypes including 27 novel ones were identified. Among the identified haplotypes there were common and breed specific haplotypes. There was a relatively high diversity of the alleles within indigenous breeds. Allelic diversity patterns were mostly associated with geographical differences. The results of this study highlight the genetic variation within indigenous breeds which has important implications for biodiversity and the adaptability of breeds to specific environments. There is value to further studies which include other genomic regions and traits, and these could guide breeding strategies.

The Identification of Genetic Variation in Insulin-Like Growth Factors-I (IGF-I) Gene Region in Some Turkish Sheep Breeds

Insulin-like growth factors (IGFs) is known as peptides with important metabolic effects required for cellular growth and metabolism. IGF-I is synthesized in liver tissue under control of growth hormone (GH) and released to blood. In the process of GH to accelerate growth, IGF-I occupies a large place. IGF-I clearly showed its important effects on the growth of animal studies. In this study, the IGF-I genes of sheep were amplified by polymerase chain reaction (PCR) in sheep breeds (Akkaraman, Kivircik, Awassi, Sakiz, Daglıc, Morkaraman, Malya Karayaka (15 to 20 sheep per breed)) reared in Turkey. Informative restriction fragment length polymorphisms (RFLPs) were obtained with HaeII enzyme. The digestion of IGF-I gene with Hae II produced two alleles and three genotypes. Genotype frequencies were 59%, 19%and 22% for AA, BB and AB genotypes, respectively. Alleles frequencies were 0.70 for A allele and 0.30 for B allele. This study indicates the genetic profiles of the IGF-1 gene in native Turkish sheep breeds.

Detecting fecal egg count (FEC) for gastrointestinal nematodes of adult Turkish sheep with different scrapie related PRNP haplotypes

Scrapie is a transmissible spongiform encephalopathy caused by prions and leads to neurodegeneration in the Central Nervous System (CNS) of sheep and goats. Genetic resistance/susceptibility to scrapie is well studied and it is known that the variations of 136th, 154th and 171st codons at the ovine PRNP gene have a major effect on the development of the disease. Many studies demonstrated that selection for PRNP genotypes has not influenced other performance traits, nevertheless, there is a knowledge gap about the possible link between the PRNP gene and the status of the other important diseases that affect the sheep population worldwide. In the present study, we tested whether there is an association between scrapie-related PRNP genotypes and fecal egg count (FEC) of gastrointestinal nematodes in seven adult Turkish sheep breeds. For this purpose, FEC scores of studied sheep (n = 253) were determined and the same animals were genotyped for the PRNP gene. Finally, an association analysis was performed for scrapie resistant (ARR), susceptible (VRQ), and wild-type (ARQ) haplotypes. Based on our statistical analysis, it is concluded that PRNP genotypes have no positive or negative effect on the FEC scores of adult sheep.

Assessment of genetic diversity and differentiation among four indigenous Turkish sheep breeds using microsatellites.

Conservation and breeding programmes of livestock species depend on determination of genetic diversity. Today in livestock species, microsatellite markers are commonly used to reveal population structure and genetic diversity in both breeds and varieties. In this study, population structure, genetic diversity, and differentiation among four native Turkish sheep breeds including Güney Karaman, Kangal, Norduz, and Karakas were assessed by using 21 microsatellite loci. By genotyping 120 individuals belonging to four sheep breeds, a total of 275 different alleles, 37 of which were private alleles, were observed across all loci. The mean number of alleles per breed ranged from 7.28 (Güney Karaman) to 8.09 (Karakas), while allelic richness ranged from 7.22 (Güney Karaman) to 7.87 (Karakas). Mean observed heterozygosity varied from 0.60 (Kangal) to 0.66 (Norduz and Karakas). The lowest pairwise value (0.084) was between Kangal and Karakas populations, while the highest pairwise value (0.142) was between Norduz and Karakas populations. Polymorphic information content (PIC) values, ranging from 0.71 (ETH10) to 0.91 (OarFCB304), were highly polymorphic (PIC 0.5) and informative in studied populations. In the present study, the results of phylogenetic analysis were of importance, since all studied populations have been accepted as Akkaraman varieties till today. However, factorial correspondence and structure analysis, pairwise values, and an unweighted pair group method with arithmetic mean analysis (UPGMA) dendrogram revealed that Güney Karaman and Norduz populations have became genetically different from the Akkaraman breed due being raised in different parts of Turkey under different climatic conditions together with their breeding practices. Therefore, we recommend that more comprehensive molecular studies should be conducted to clarify genetic differentiation of Akkaraman sheep varieties.

Association of toll-like receptor 4 (TLR 4) gene exon 3 variants with serostatus of the ovine Johne’s disease (paratuberculosis) in Turkish sheep

In the present study, the effect of exon 3 of the toll-like receptor 4 (TLR4) gene on ovine Johne?s disease (OJD) serostatus was tested in Turkish sheep breeds. Initially, a retrospective cohort was performed using indirect ELISA on a commingled flock consisting of 3 native and 4 composite breeds (n = 1750). Case-control matched pairs were constructed according to the breed type and age (n = 188). Subsequently, exon 3 of the TLR4 gene was sequenced and coding variants were investigated. A total of 15 single nucleotide polymorphisms (SNPs) were detected and 12 of those SNPs were nonsynonymous. Next, 3 haplotype blocks consisting of these SNPs were constructed. The McNemar's test was conducted on both the SNPs and haplotypes. As a consequence, within the detection limits (power, 0.95; odds ratio > 3.3), no association was detected between the OJD serostatus and TLR4 exon 3 coding variants in Turkish sheep.

Assessment of genetic diversity of Turkish and Algerian native sheep breeds

In Algeria and Turkey, the sheep production systems are based on the under extensive rural conditions and their genetic management has led to increased homozygosity and hence productivity loss. The identification of inter-breed and intra-breed genetic diversity plays a key role in the shaping of conservation and breeding programs. The present study was conducted to investigate the genetic diversity of native sheep breeds reared in Turkey and Algeria. A total of 240 animals from four Algerian (Hamra, Ouled Djellal, Sidaou, and Tazegzawt) and four Turkish (White Karaman, South Karaman, Karacabey Merino, and Kıvırcık) native sheep breeds were genotyped with fourteen microsatellite markers recommended by FAO. A total of 340 alleles were detected from fourteen markers studied. All the eight breeds exhibited moderate to high levels of genetic diversity, with a slight superiority of the Algerian sheep breeds. Overall FIS value was low, but highly significant (p < 0.001). It may have been due to the high inbreeding within the population. The mean global coefficient of gene differentiation (GST) showed that approximately 94.0 % of the genetic variation was within-population. The highest number of private alleles with a frequency above 5 % was observed in Ouled Djellal sheep. Structure analysis of populations studied revealed the most appropriate K with four genetic clusters. As the result, the dendrogram showed that the Algerian sheep breeds were completely separated from the Turkish sheep breeds furthermore the Bayesian clustering revealed a high level of admixture, especially in Algerian sheep populations.

Assessment of genetic diversity of Turkish and Algerian native sheep breeds

In Algeria and Turkey, the sheep production systems are based on the under extensive rural conditions and their genetic management has led to increased homozygosity and hence productivity loss. The identification of inter-breed and intra-breed genetic diversity plays a key role in the shaping of conservation and breeding programs. The present study was conducted to investigate the genetic diversity of native sheep breeds reared in Turkey and Algeria. A total of 240 animals from four Algerian (Hamra, Ouled Djellal, Sidaou, and Tazegzawt) and four Turkish (White Karaman, South Karaman, Karacabey Merino, and Kıvırcık) native sheep breeds were genotyped with fourteen microsatellite markers recommended by FAO. A total of 340 alleles were detected from fourteen markers studied. All the eight breeds exhibited moderate to high levels of genetic diversity, with a slight superiority of the Algerian sheep breeds. Overall FIS value was low, but highly significant (p < 0.001). It may have been due to the high inbreeding within the population. The mean global coefficient of gene differentiation (GST) showed that approximately 94.0 % of the genetic variation was within-population. The highest number of private alleles with a frequency above 5 % was observed in Ouled Djellal sheep. Structure analysis of populations studied revealed the most appropriate K with four genetic clusters. As the result, the dendrogram showed that the Algerian sheep breeds were completely separated from the Turkish sheep breeds furthermore the Bayesian clustering revealed a high level of admixture, especially in Algerian sheep populations.

Genetic characterization of some Turkish sheep breeds based on the sequencing of the Ovar-DRB1 gene in the major histocompatibility complex (MHC) gene region.

In this research, Ovar-DRB1 gene in the major histocompatibility complex (MHC) gene region was surveyed by DNA sequencing in some of the native sheep breeds that are reared in Turkey. A total of 80 samples were collected from eight different Turkish native sheep breeds, and these samples were used for DNA sequencing.The exon 2 region of Ovar-DRB1 in the MHC gene region was polymerase chain reaction (PCR) amplified and sequenced. A total of 25 new alleles were revealed in the Ovar-DRB1 gene in Turkish native sheep breeds with 24 variable sites; only 13 sites were parsimony informative. The average pairwise genetic distance was 0.029 % for the Ovar-DRB1 gene exon 2 region. The sequence variations at eight different positions (7026, 7036, 7040, 7053, 7059, 7069, 7131 and 7214) are found in all of the studied samples. G C transversion at position 7081 is only seen in Akkaraman sheep breed, whereas T C transition at position 7097 is only seen in one sample from the Akkaraman breed. Overall, two main groups were detected among the 25 alleles from Turkish native sheep breeds. All Daǧliç and Kivircik alleles and one allele from Karayaka, Malya and Sakiz are grouped together while all the other breeds are grouped in the other branch.

The analysis of mitochondrial data indicates the existence of population substructure in Karayaka sheep

In the current study, we investigated the existence of population substructure in the Karayaka sheep breed from Turkey. A fragment of the mitochondrial D-loop region has been successfully sequenced in 69 Karayaka sheep sampled in the districts of Çarsamba, Bafra and Ladik. Though the B haplogroup was the most abundant in these three subpopulations, haplogroup frequencies and nucleotide diversities were remarkably different. The analysis of molecular variance (AMOVA) showed the existence of a significant (P-value = 0.019) between-subpopulations component representing 5.14% of the total variation. Moreover, phylogenetic analyses showed that the fixation index (FST) and the GammaST genetic distance between Karayaka subpopulations are similar to those observed between certain Turkish sheep breeds. We conclude that there is a significant population substructure in Karayaka sheep. Since breeds do not behave as single panmictic populations, this result could probably be extrapolated to other ovine breeds. Noteworthy, population substructure can have adverse effects on the maintenance of breed diversity and it is an important confounder effect in genome-wide-association studies.

Genetic Polymorphisms of Cyp19 and Myostatin Genes in Turkish Indigenous Sheep Breeds

Growth and meat production traits are very important in sheep breeding. Cyp19 gene has a major role in reproductive activity and growth due to its function in estrogen synthesis. Another gene affecting growth traits is Myostatin (MSTN) gene, which mainly regulates skeletal muscle growth. In this study allele frequencies of genetic polymorphism in Cyp19 and Myostatin genes were identified by PCR-RFLP method in five indigenous Turkish sheep breeds, Chiose, Imroz, Kivircik, Zom and Morkaraman. Digestion of Cyp19 gene with HaeIII only revealed uncut AA genotype and digestion of MSTN with DraI also revealed only uncut AA genotype. Both loci analyzed in this study were found to be monomorphic in five Turkish indigenous sheep breeds. These highly conserved parts of the two genes can be useful for molecular evolutionary studies in sheep. Further studies regarding association analysis of Cyp19 and MSTN in sheep should be conducted.

Identification of genetic variation in the major histocompatibility complex gene region in Turkish sheep breeds

The major histocompatibility complex (MHC) in sheep, Ovar-Mhc, remains poorly characterized relative to other domestic animals. However, its basic structure is similar to that of other mammals, comprising class I, II and III regions. In this study, the Ovine MHC class II DRB1 and DRB3 genes were amplified by polymerase chain reaction in eight sheep breeds reared in Turkey. Informative restriction fragment length polymorphisms (RFLPs) were obtained with five restriction enzymes for DRB1 and with two restriction enzymes for DRB3 . The digestion of DRB1 exon 2 with Nci I, Sac I, Sac II, Hin 1I each produced three genotypes and two alleles (viz., a and b) with frequencies of 0.69 and 0.31; 0.65 and 0.35; 0.91 and 0.09; 0.57 and 0.43, respectively. The digestion of DRB1 exon 2 with Dde I produced four genotypes and three alleles (viz., a, b and c) with frequencies of 0.62, 0.28 and 0.10, respectively. On the other hand, the digestion of DRB3 exon 2 with Nde II and Bsa I each produced three genotypes and two alleles (viz., a and b) with frequencies of 0.72 and 0.28; 0.96 and 0.04, respectively. This study presents the genetic profiles of the exon 2 region of the MHC DRB1 and DRB3 genes in native Turkish sheep breeds. Keywords: DRB1, DRB3 , polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP)

Genetic relationships among four Turkish sheep breeds using microsatellites

The genetic structure of 4 Turkish breeds of sheep, Gokceada, Kivircik, Karacabey Merino, and Sakiz (SZ), was analyzed by genotyping with 17 microsatellite markers in 250 individuals. The microsatellites showed high levels of polymorphism, with means for total and effective number of alleles per locus of 20.71 and 7.04, respectively. The average observed and expected heterozygosity values were 0.66 and 0.87, respectively. It was found that a higher level of breed admixture existed in the 4 breeds, which was an important finding. It was also found that 7.9% of genetic variation resulted from difference between the populations, whereas 92.1% resulted from difference between individuals. Our results showed that the used microsatellite markers were adequately polymorphic and can be successfully used for investigating genetic diversity in the 4 breeds studied. The genetic variation in Turkish breeds was not significantly higher than that of European breeds, which might be a consequence of the recent sharp decrease in sheep numbers.

Investigation of PrP locus polymorphisms in some native Turkish sheep breeds

Investigation of PrP locus polymorphisms in some native Turkish sheep breeds

Genetic diversity in nine native Turkish sheep breeds based on microsatellite analysis.

The genetic variability of 204 sheep from nine breeds (Awassi, Çine Çaparı, Karakaş, Karya, Karayaka, Morkaraman, Norduz, Sakız and Tuj) growing in four different regions (western, northern, eastern and south-eastern Anatolia) was assessed using 18 microsatellite loci. High mean number of alleles, allelic richness and factorial correspondence analysis showed the degree of admixture between native sheep breeds of Turkey. The Karya and Çine Çaparı breeds were observed as the most distinct of the breeds, and possible introgressions were detected in other breeds. It was found that 8.9% of genetic variation resulted from the difference between the populations. The genetic variation in Turkish breeds was not much higher than that of European breeds, which might be a consequence of the recent sharp decrease in sheep numbers.

A study on gastrointestinal tract characteristics of ram lambs at the same weights from six Turkish sheep breeds

A study was conducted, first, to compare the gastrointestinal tract (GIT), reticulo-rumens and intestinal capacities (relative to body weight) of ram lambs from six Turkish sheep breeds: Turkish Merino (TM, Anatolia Merino), Akkaraman (AK), Kıvırcık (KV), Awassi (AW), Karayaka (KY) and Morkaraman (MK), and second, to examine the influence of sheep breed on the pH of the digesta in the various segments (rumen, jejunum and caecum) of the GIT. Six ram lambs from each breed were slaughtered at 40.2 ± 0.80 kg liveweight. Lambs from the AK breed had a heavier GIT weight than the AW, KY or MK breeds. The weight of the full stomach was higher in AK lambs compared with the other lambs, except for KV lambs, while the relative weight of the empty stomachs was heavier in MK ram lambs than in TM, AW and KY lambs. The AK lambs had the highest relative empty intestinal weight. The relative weight of empty intestines was heavier in KV lambs than in KY lambs. The pH of the rumen content was higher in TM and AK lambs compared with KY and MK lambs, while the pH of the caecum content of KV lambs was higher than those of KY and MK lambs. In conclusion, significant differences were found among the six breeds in terms of some variables that were studied, although a higher proportional GIT weight in the fat-tail breeds such as the MK, AK and AW was not reflected in all components or in the pH of the GIT content.Keywords: Native sheep breed, digestive system, rumen, small and large intestine, pH value

Polymorphism of the ovine calpastatin gene in some Turkish sheep breeds

The calpastatin (CAST) gene has a major effect on muscle growth and meat tenderness after slaughter; it is located on the fifth chromosome in sheep. Blood samples were collected from 720 animals in total from Kivircik (KIV), Sakiz (SZ), Karacabey Merino (KM), and Gokceada (GA) sheep populations raised in West Anatolia. The PCR products were digested by the restriction endonuclease MspI. Allele frequencies for M and N alleles of the gene were found to be 0.85 and 0.15 in KIV, 0.80 and 0.20 in KM, 0.99 and 0.01 in GA, and 0.34 and 0.66 in SZ sheep, respectively. It was determined that NN genotype frequency was quite lower in KIV (0.04) and KM (0.07) populations than in the SZ breed (0.40). On the other hand, the NN genotype was not observed in the GA population. Populations other than KM were found to be in Hardy–Weinberg equilibrium. In general, allele and genotype frequencies of CAST were similar to those in other studies on different sheep populations. This research is a beginning step for finding candidate genes’ effects on meat quantity and quality.

Aromatase Cytochrome P450 (CYP19) ve Melatonin Receptor 1A (MTRN1A) Genlerinin Farklı Allelerinin Türkiye Yerli Koyun Irkları Arasındaki Dağılımı

Aromatase Cytochrome P450 (CYP19) ve Melatonin Receptor 1A (MTRN1A) Genlerinin Farklı Allelerinin Türkiye Yerli Koyun Irkları Arasındaki Dağılımı

Investigation of the genetic diversity among native Turkish sheep breeds using mtDNA polymorphisms

A total of 135 unrelated sheep from nine Turkish native sheep breeds (Daglıc, Kivircik, Imroz, Chios, Morkaraman, Ivesi, Hemsin, Karayaka and Akkaraman) were investigated to determinate the maternal genetic diversity using a sequence of a 531-bp segment of the mtDNA control region. Analysis of the mtDNA control region sequence revealed 63 haplotypes and 53 polymorphic sites. Haplotype diversity, nucleotide diversity and the average number of nucleotide differences were estimated to be 0.9496 ± 0.011, 0.01407 ± 0.00060 and 7.456, respectively. The sequence analysis also revealed high level of genetic diversity among the native Turkish breeds. These breeds were grouped into three major maternal haplogroups: A, B and C, with one animal belonging from the Akkaraman breed to the rare haplogroup E. Irregular shape of mismatch distribution of haplogroup C could be an indicator that haplogroup C may represent different haplogroups. Contrarily to previous studies carried out on Turkish native breeds, majority of animals grouped in haplogroup A in the present study. This result and the irregular shape of mismatch curve of haplogroup C indicate that genetic structure of Turkish native sheep breeds could be more complicated than it is thought.