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

Growth hormone (GH), prolactin (PRL), and diacylglycerol acyltransferase (DGAT1) gene polymorphisms in Turkish native cattle breeds

The aim of this study was to determine the genetic diversity of 4 native Turkish cattle breeds, based on the growth hormone (GH), prolactin (PRL), and diacylglycerol acyltransferase (DGAT1) genes. In order to study the polymorphisms in these genes, the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) method was performed. A 329-bp fragment and a 223-bp fragment of GH, a 156-bp fragment of PRL, and a 411-bp fragment of DGAT1, thus 4 loci of 3 genes, were amplified via PCR. These fragments were then restricted with the enzymes MspI, Alu1, RsaI, and CfrI, respectively. In this study, 2 types of alleles, (+) and (-) for the GH-MspI, L and V for the GH-Alu1, A and B for the PRL, and K and A for the DGAT1 loci, were observed. The results of the present study will contribute to the polymorphism data on the world's cattle breeds. Furthermore, the above-mentioned allele frequencies of Turkish native breeds are evaluated in relation to their genetic relatedness, and to infer their milk production properties on the basis of the available literature. In turn, these results can be utilized for future breeding programs of dairy cattle in Turkey

Türkiye'nin Akdeniz ve Ege Denizi'ndeki kılıçbalığı populasyonlarının mitokondriyal Dna (Mtdna) kullanılarak incelenmesi

TÜBİTAK KBAG15.07.2014Kılıç balığı (Xiphias gladius) hem dünya hem de Türkiye için önemli besin kaynaklarından biridir. Çeşitli moleküler belirteçler kullanılarak yapılan genetik çalışmalar, kılıç balıklarının Kuzey Atlantik, Güney Atlantik, Akdeniz ve Hint-Pasifik olmak üzere 4 ana stoktan oluştuğunu göstermektedir. Şu ana kadar tek bir stok olarak kabul edilen Akdeniz için tek bir koruma ve yönetim senaryosu önerilmiştir. Türkiye’deki kılıç balığı popülasyonları Akdeniz stoğunun bir parçası olarak kabul edilir. Fakat Türkiye’nin Ege ve Akdeniz kıyılarını içeren herhangi bir genetik çalışma yapılmamıştır. Bu projede, Türkiye’nin Akdeniz (Antalya Körfezi civarından) ve Kıbrıs’ın Karşıyaka kıyısından, Kuzey Levant Denizi’ni temsilen, (n= 42) ve Türkiye’nin Ege Denizi kıyısından Gökçeada ve Çanakkale civarından (n=26) kılıç balığı örnekleri toplanmıştır. Bu örneklerden DNA izole edilerek, mtDNA kontrol bölgesinin 450 baz çiftlik (bç) dizi analizi yapılmıştır. Ayrıca Yenikapı kazılarından çıkartılan örneklerden antik DNA (aDNA) izole edilmiş ve 450 bç’lik bölgesi 5 parça halinde analiz edilmiştir. Sonuçlar birbirleri ve literatürdeki dizi örnekleri ile karşılaştırılarak incelendiğinde Akdeniz’de batıdan doğuya gidildikçe genel olarak genetik çeşitliliğin ve etkin popülasyon sayısının düştüğü ve soy I diye tanımlanan soya ait alt soyların frekansları açısından Ege Denizi kılıç balıklarının Kuzey Levant havzasından değil ama diğer Akdeniz örneklerinden düşük anlamlılık (p0.05). Again, based on clade I, there is no implicit differentiation between east and west populations that overlap with two spawning areas (around South Italy- Sardinia Island and Crete Island-Fethiye) in the Mediterranean, but it is very likely that these two groups are mixed around the middle of the Mediterranean. The frequencies of the clades observed in ancient samples are similar to modern swordfish populations. Production of swordfish in Turkey has been increasing every year since 1980s. İt is observed that, this increase and disappearance of swordfish from Marmara and Black Sea has not been expressed as a decline in the population size, yet. Data obtained from this study can contribute to conservation and management of swordfish populations inhabiting Turkish coasts

"Türkiye ve Pakistan yerli koyun ırklarında prion protein geni polimorfizmleri taranması"

TÜBİTAK TOVAG01.01.2012Koyun ve keçilerin inkübasyon süresi uzun, ölümcül, merkezi sinir sistemini etkileyen (nörodejeneratif) bir hastalığı olan skrapi; birçok memeli türünü etkileyen bulaşıcı süngerimsi ensefalopatilerden (Transmissible Spongyform Encephalopathy -TSE) yani prion protein hastalıklarından biridir. Koyunda üç ekzon ve iki introndan oluşan prion protein geninde üçüncü ekzon bölgesinde halen 50’den fazla nokta mutasyonu polimorfizmi (TNP) gözlenmiştir. Ancak, skrapiye direnç / hassasiyeti belirleyen prion protein gen bölgesindeki mutasyonların 136, 141, 154 ve 171. kodonlarına dayalı genotiplerin olduğu bildirilmektedir. Avrupa-Asya yelpazesinde birikmiş verilerin çoğunlukla Avrupa’dan olduğu dikkat çekicidir. Halbuki arkeolojik ve genetik veriler Orta Doğu’nun koyun evcilleştirme merkezi olduğunu göstermektedir. Ancak, yapılan çalışmalar incelendiğinde bu bölgeden verilerin daha sınırlı olduğu görülmektedir. Bu çalışmada, skrapi vakasının rapor edilmediği Türkiye yerli koyun ırklarında prion protein gen polimorfizminin 15 farklı populasyonda incelemesi yapılmıştır. Çalışmada prion protein gen bölgesinin 3’üncü ekzon bölgesine ait 745 bç (baz çifti) uzunluğundaki bölgesi 655 bireyde sekanslanarak çalışılmıştır. Elde edilen veriler, Türkiye’de skrapiyi önlemeden sorumlu otoriteler, hayvan yetiştirme birlikleri ve üniversitelerin araştırma birimlerince kullanılması açısından yararlıdır. Ayrıca veriler, Dünya’daki PrP protein polimorfizm verilerinin coğrafi dağılımındaki büyük boşluğu önemli ölçüde doldurmuştur. Çalışmada elde edilen detaylı veriler fonksiyonu tam olarak bilinmeyen PrP protein bölgesinin hangi evrimsel güçler etkisinde olabileceği ile ilgili bilgilere katkılarda bulunmaktadır.Scrapie is an infectious fatal disease of sheep and it is a member of Transmissible Spongiform Encephalopathies (TSE) (or a prion disease) and affects the central nervous system. Susceptibility to scrapie is associated with polymorphisms in sheep prion protein (PrP) gene, based on their genotypes at codons 136, 141, 154 and 171. In Europe-Asia spectrum, accumulated data is mostly from Europe. Whereas, archeological and genetic evidences indicated that Middle East is the heart of sheep domestication and all of the sheep breeds must have went out from this region. Yet, data from this region is preliminary. The main purpose of the study is to collect an extensive data,covering 14 breeds 15 different populations represented by 655 individuals where each of which are sequenced for 745 base pairs of PrP 3rd exon region. It will be a data where individuals were from Turkey from which scrapie incidence was not reported. This data is important and useful for the authorities responsible from the risk management of scrapie in Turkey, for animal breeders association and for research units of universities. At the same time, it will, considerably, fill the big gap which is present in the data of geographic distribution of PrP polymorphisms in the world. The detailed data obtained by the study will contribute to the understanding of evolutionary mechanisms operating on the PrP gene of which the function is unknown

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

Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean

The Neolithic transition in west Eurasia occurred in two main steps: the gradual development of sedentism and plant cultivation in the Near East and the subsequent spread of Neolithic cultures into the Aegean and across Europe after 7000 cal BCE. Here, we use published ancient genomes to investigate gene flow events in west Eurasia during the Neolithic transition. We confirm that the Early Neolithic central Anatolians in the ninth millennium BCE were probably descendants of local hunter-gatherers, rather than immigrants from the Levant or Iran. We further study the emergence of post-7000 cal BCE north Aegean Neolithic communities. Although Aegean farmers have frequently been assumed to be colonists originating from either central Anatolia or from the Levant, our findings raise alternative possibilities: north Aegean Neolithic populations may have been the product of multiple westward migrations, including south Anatolian emigrants, or they may have been descendants of local Aegean Mesolithic groups who adopted farming. These scenarios are consistent with the diversity of material cultures among Aegean Neolithic communities and the inheritance of local forager know-how. The demographic and cultural dynamics behind the earliest spread of Neolithic culture in the Aegean could therefore be distinct from the subsequent Neolithization of mainland Europe.WoSScopu

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

Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication

Yurtman, ozer, Yuncu et al. provide an ancient DNA data set to demonstrate the impact of human activity on the demographic history of domestic sheep. The authors demonstrate that there may have been multiple domestication events with notable changes to the gene pool of European and Anatolian sheep since the Neolithic. Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central and west Anatolian sheep dating from Epipaleolithic to late Neolithic, comparatively with modern-day breeds and central Asian Neolithic/Bronze Age sheep (OBI). Analyzing ancient nuclear data, we found that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds relative to Asian breeds, a conclusion supported by mtDNA haplogroup frequencies. In contrast, OBI showed higher genetic affinity to present-day Asian breeds. These results suggest that the east-west genetic structure observed in present-day breeds had already emerged by 6000 BCE, hinting at multiple sheep domestication episodes or early wild introgression in southwest Asia. Furthermore, we found that ANS are genetically distinct from all modern breeds. Our results suggest that European and Anatolian domestic sheep gene pools have been strongly remolded since the Neolithic

The effects of hybridization on developmental stability in the housefly(Musca domestica L.).

Ph.D. - Doctoral Progra