Genetic relationship between Kangal, Akbash and other dog populations

Kangal and Akbash dogs are the two well-known shepherd dog breeds in Turkey. In order to contribute to the understanding of the genetic relationship between Kangal dogs, Akbash dogs and the dogs from different regions of Eurasia, 585 base pair (bp) segment of mitochondrial DNA (mtDNA) control region was sequenced from Kangals and Akbashes. Sequences of the Kangal and Akbash dogs examined in the present study were comparatively examined with those of previous studies on dogs. Consensus neighbour-joining tree with bootstrapping, which is constructed based on pairwise Fst values between populations, indicated that Kangal dogs and Akbash dogs are on different branches of the tree. Furthermore, the nodes of these branches were supported with high bootstrap values. In conclusion, the present study indicated that Kangal and Akbash dogs might have descended maternally from different origins along the evolutionary history of domestic dogs

Yerli koyun ırklarında bulunan genetik çeşitlilik

TÜBİTAK TBAG01.12.2004Bu çalışmada, Türk koyun ırklarında mevcut genetik çeşitlilik 5 mikrosatelit lokusu kullanılarak incelenmiştir. Devlet üretim çiftlikleri, üniversite üretim çiftlikleri ve yerel yetiştiricilerin elinde bulunan sürülerden yerli ve melez onbir Türk ırkı (Akkaraman, Morkaraman, Kıvırcık, İvesi, Dağlıç, Karayaka, Hemşin, Norduz, Kangal, Konya Merinosu, Türkgeldi) ile bireyleri Irak'tan getirilmiş yabancı bir ırkı (Hamdani) temsil eden toplam 423 birey bu çalışmada kullanılmıştır. Bazı ırklar icin birden fazla örnekleme yapılmıştır. Genetik varyasyonun ölçütlerinden beklenen heterozigotluk (HE) 0.686 ile 0.793 arasında, ortalama gözlenen allel sayıları (OAS) ise 5.8 ile 11.8 arasında değişmiştir. Türkiye üzerinde allel frekans dağılımları, evcilleşme merkezlerinden olmuş olabilecek göçlerle beklenen, dogudan batıya geçişli bir değişim göstermemiştir. FST indeksi Akkaraman, Karayaka ve Dağlıç'ta aynı ırkın farklı örneklemelerindeki farklılaşmayı ölçmek için kullanılmıştır ve yetiştirme çiftliğinden alınan Akkarman1'in diğer iki Akkaraman populasyonundan istatistiki önemle (P<0.001) farklı olduğu bulunmuştur. FIS indeksi ile ırklar Hardy-Weinberg (H-W) dengesi açısından test edilmiş, Akkaraman1, İvesi, Morkaraman ve Hemşin'de H-W'den sapma tespit edilmiştir. AMOVA analizi toplam genetik varyasyonun büyük bir kısmının (~% 95) ırk içi bireyleri arasında olduğunu göstermiştir. Parallel sonuçlar ırk ve bireyleri arası genetik ilişkinin incelendiği faktöriyel benzerlik analizi ve allel paylaşım uzaklığı ile de elde edilmiş ve genellikle, ırklar arası belirgin bir fark görülmemiştir. DA genetik uzaklığı ile çizilen komşu birleştirme ağacı ve temel öğeler analizi ise ırklar ve çeşitli örnekleri arası farklılaşmayı incelemek için kullanılmıştır. Özellikle ilk analiz çiftlik örneklerinin farklı olduğunu göstermiştir. Delaunay ağı ırklar arasında 4 adet (ikisi coğrafi bariyer ile paralel) genetik sınır belirlemiştir. Sonuçların hepsi Kıvırcık ırkının diğerlerinden çok farklı olduğu yönündedir. Mantel testi ve Darboğaz testi istatistiksel olarak anlamlı bir sonuç ortaya koymamıştır. Avrupa ırklarının çoğuna genetik olarak en yakın bulunan Kıvırcık örneği olmuştur. Türk ırklarında Avrupa ırklarından yüksek fakat çok da farklı olmayan bir genetik çeşitlilik belirlenmiştir. Bunda son yıllarda koyun sayısında, Türkiye’de, yaşanan hızlı düşüş etkili olmuş olabileceği düşünülmüştür.In this study the genetic diversity in Turkish native sheep breeds was investigated based on fıve microsatellite loci. In total, 423 individuals from 11 native and crossbred Turkish sheep breeds (Akkaraman, Morkaraman, Kıvırcık, İvesi, Dağlıç, Karayaka, Hemşin, Norduz, Kangal, Konya Merinosu, Türkgeldi) and one Iraqi breed (Hamdani) were analyzed by sampling from breeding farms and local breeders. For some of the breeds sampling was done more than once. Genetic variation within breeds was estimated by expected heterozygosity (HE), which ranged between 0.686 and 0.793 and by the mean number of observed alleles (MNA), it ranged between 5.8 and 11.8. The allele frequency distribution across Turkey showed no gradient from east to west, gradient was expected in accordance with the migrations from the domestication centers. The differentiation between different samples of Akkaraman, Dağlıç and Karayaka breeds was tested by FST index. Akkaraman1 sample from the breeding farm was significantly (P<0.001) different from the other two Akkaraman samples. Deviation from Hardy-Weinberg expectations observed for Akkaraman1, İvesi, Morkaraman and Hemşin breeds. AMOVA analysis revealed that most of the total genetic variation (~95%) was within the individuals of the breeds. In parallel to this observation, when factorial correspondence analysis and shared alleles distances were used to analyze the relationship between the breeds and their individuals, generally, there were no clear discriminations between the breeds. Moreover, neighbour joining tree constructed based on DA genetic distance, and principle component analysis were used to analyze among breed differentiation. The former one emphasized the genetic distinctness of the farm samples. Delaunay network drew 4 genetic boundaries (two of them being parallel to geographic boundaries) between the breeds. All the results indicated that Kıvırcık was the most differentiated breed. Finally, Mantel Test and Bottleneck analysis did not reveal a significant result. Kıvırcık breed, among all native Turkish breeds, was found to be the genetically closest to the European breeds based on the loci analyzed. 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 number, in Turkey

Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

In the last decades, several endangered breeds of livestock species have been re-established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO-recommended microsatellites of these landraces and three phenotypically similar Nordic-type landraces and compared these breeds with central European, Mediterranean and south-west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south-west Asian domestication site with a south-east-to-north-west cline that is clearly steeper than the Mediterranean east-to-west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land-races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long-horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately

Anadolu yerli ve melez ırklarının genetik çeşitliliği

In this study the genetic diversity in Turkish native sheep breeds was investigated based on microsatellite DNA loci. In total, 423 samples from 11 native and crossbreed Turkish sheep breeds (Akkaraman, Morkaraman, Kivircik, Ivesi, Dagliç, Karayaka, Hemsin, Norduz, Kangal, Konya Merinosu, Türkgeldi) and one Iraqi breed (Hamdani) were analyzed by sampling from breeding farms and local breeders. After excluding close relatives by Kinship analysis, the genetic variation within breeds was estimated as gene diversities (HE), which ranged between 0.686 and 0.793. The mean number of observed alleles (MNA) ranged between 5.8 and 11.8. The allele frequency distribution across Turkey showed no gradient from east to west expected in accordance with the Neolithic Demic Diffusion model. The differentiation between different samples of Akkaraman, Dagliç and Karayaka breeds was tested by FST index. Akkaraman1 sample from the breeding farm was significantly (P<0.001) different from the other two Akkaraman samples. Deviation from HW expectations observed for Akkaraman1, Ivesi, Morkaraman and Hemsin breeds. AMOVA analysis revealed that most of the total genetic variation (~90%) was partitioned within the individuals. In parallel to this observation, when factorial correspondence analysis and shared alleles distances were used to analyze the relationship between the individuals of the breeds, there was no clear discrimination between breeds. Moreover, NJ tree constructed based on DA genetic distance, and PC analyses were used to analyze among breed differentiation. Delaunay Network drew 4 genetic boundaries (two of them being parallel to geographic boundaries) between breeds. All the results indicated that Kivircik was the most differentiated breed. Finally, Mantel Test and Bottleneck analysis did not reveal a significant result. Kivircik breed, among all native Turkish breeds, wasPh.D. - Doctoral Progra

Blood Protein Polymorphism of Horse Types Being Bred by Public at Villages in Three Different Regions of Turkey

Different breeds and types of horses are raised in different regions of Turkey. The numbers and types of native horses have declined steadily over time because of increased agricultural mechanization. The blood samples of 85 native Turkish horses of different types from different geographical regions (Kars-Erzurum 30, Sanliurfa 20 and Adapazari 35) were analysed for blood protein polymorphism. Starch gel electrophoresis, polyacrylamide gel electrophoresis and polyacrylamide isoelectric focusing were used to identify genotypic variants of albumin (ALB), transferrin (TF), hemoglobin alpha (HBA), vitamin D-binding protein (GC), serum carboxylesterase (ES), A1B-glycoprotein (A1B), 6-phosphogluconate dehyrogenase (6-PGD) and phosphoglucomutase (PGM) loci. The direct counting method was used to calculate the frequency of genes for blood protein systems. Homozygosity degrees and chi-square were calculated with the frequency of genes for blood protein systems. According to the results of chi-square testing on eight systems of three different regions, 6-PGD system was significant P<0.001 in the eastern population (Kars-Erzurum). Among the local horses in the south-east region (Sanliurfa) 6-PGD system (P<0.001) and HBA system (P<0.05) were found to be significant. On the other hand, in the western region (Adapazari), chi-square analyses of 6-PGD and HBA systems were found to be significant at P<0.05. In this study, it was found that the three different local horse types in the three regions descended from the same origin

Beta-casein A1/A2, kappa-casein and beta-lactoglobulin polymorphisms in Turkish cattle breeds

In this study, the genetic diversity of three milk protein genes namely beta-casein, kappacasein and beta-lactoglobulin was estimated in Turkish cattle breeds. Based on these genes, breeds in Turkey have been grouped as: 1) Eastern Anatolian Red, Anatolian Black and Southern Anatolian Red and 2) Turkish Grey, Turkish Holstein and Holstein Candidate Bulls. B alleles of the three studied genes, which were reported to be positively related with cheese yield and quality, seemed to be low-intermediate for beta-casein and kappa-casein but relatively high for beta-lactoglobulin in the first group of Turkish breeds compared to other breeds of the world. The kappa-casein E allele, which has a negative effect on cheese quality, is absent in Turkish cattle breeds, except in Holstein Candidate Bulls. Therefore, the results suggest that milk of Turkish native breeds is suitable for cheese making. Based on observations of the Turkish breeds, some suggestions were made regarding breeding practices in Turkey.Scientific and Technological Research Council of Turkey (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [TOVAG 104V137]We thank Prof. Dr. Ihsan Soysal for his help in the collection of the samples. This work was supported by grant TOVAG 104V137 from The Scientific and Technological Research Council of Turkey (TUBITAK)

First Molecular Record of the Pacific Oyster (Crassostrea gigas, Thunberg 1793) in the Marmara Sea, Turkey

The Pacific oyster (Crassostrea gigas) has a very important economic potential for aquaculture, but on the other hand, is among the highly invasive species in the world and within the Mediterranean ecosystem. In the 1960s, C. gigas was brought to Europe for aquaculture in the Mediterranean and Black Sea regions from Japan and Canada. The Turkish waters are the part of the Mediterranean Sea, which is the world’s most invaded sea. The invasion of alien species results from marine transportation and aquaculture activities of non-native species. A heavy maritime traffic is also present in the Marmara Sea, which connects the Black Sea and Mediterranean Sea. The identification of the invasive species and their distributions is very prominent in terms of protecting natural habitat and monitoring the effects of invasive species. In this study, 30 individuals, morphologically identified as C. gigas, were collected from Bandırma bay. The genomic DNAs were extracted from each sample’s muscle tissue using universal salt extraction method. Partial sequences of COI and 16S Mitochondrial DNA loci of the sample DNAs were obtained for species identification. The sequences were searched against the database and results were retrieved from BLAST. All the sequences obtained in this study showed significant similarity with the C. gigas sequences present in the database (E=0). The sample sequences resulted in 9 different haplotypes for the COI locus (hd: 0.5296 and variance: 0.01256±0.112) and 5 different haplotypes for the 16S rDNA locus (hd: 0.2529, Variance: 0.01076±0.104). The results of this study provided the first molecular evidence for the presence of non-native Pacific oyster individuals in the Marmara Sea