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A detailed morphological and genetic characterization of honey bees from the Thrace and west Anatolian regions of Turkey was surveyed. A total of 1650 worker bee samples (110 colonies) were evaluated with the forty-one morphological characters and 217 honey bee samples were analyzed via DNA sequencing of the tRNA(leu)-cox2 region. In this study, three different populations, Thrace (Tekirdag, Kirklareli and Edirne provinces), Island Gokceada, and western Anatolia were formed based on morphometrics, since the Marmara Sea has taken a very strong barrier role in this formation. The morphological similarity of the Thrace population was supported by the genetic analysis. The sequencing of the tRNA(leu)-cox2 region revealed twenty-two different haplotypes, sixteen of which are novel. The C2d, macedonica-like haplotype, was the most widely found haplotype (48%) all around the Thrace region. Along with the C2d haplotype, previously published C2s, C2v, C2i, C2j, and C2h haplotypes, and the newly found haplotypes were also observed but less frequently. In this study, Thrace honey bees were found to more similar to A. m. macedonica through the mtDNA sequence analysis, whereas carnica-like honey bees were only found near the Istranca mountain ridges, Kirklareli province and macedonica-like honey bees all around the Thrace region. According to our results, some of the Thrace honey bee populations may be both A. m. carnica and A. m. macedonica but the assignment to the latter subspecies seems more likely due to its geographic range. Scientific and Technological Research Council of Turkey-TUBITAK [3001-TOVAG 114O883] The authors are deeply indebted to numerous people that have contributed to this study for providing honey bee reference samples; Ljubia Z. Stanisavljevi for providing A. m. carnica samples from Serbia and Leonidas Charistos for providing A. m. macedonica samples from Greece. Financial support for this research was provided by The Scientific and Technological Research Council of Turkey-TUBITAK through the Project 3001-TOVAG 114O883, Project Coordinator Fulya ozdil.

Çalışma, Türkiye’de Trakya bölgesinde yetiştirilen 90 eşekte MSTN genindeki varyasyonunu belirlemeyi amaçlamıştır. GDF-8 (growth differentiation factor 8) olarak da adlandırılan miyostatin (MSTN), farklılaşma büyüme faktörü β (TGF-β) süper ailesinin bir parçasıdır ve memeli türlerinde kas kütlesi, büyüme ve gelişme üzerinde negatif düzenleyici rolü bulunmaktadır. MSTN geni, iskelet kası büyümesini olumsuz yönde düzenler ve iskelet kaslarının homeostazında önemli bir role sahiptir. Ayrıca, kas liflerinde protein dengesi Myostatin faktörü tarafından desteklenmektedir. MSTN geninin toplam 866 bç uzunluğunda kısmi intron 1, 2 ve ekzon 2 bölgeleri çoğaltılmış ve PCR ürünleri DNA dizilimi kullanılarak analiz edilmiştir. Bu çalışmada MSTN geninin ikinci ekzon bölgesinde proteinde amino asit değişikliğine neden olmayan yeni bir sinonim SNP g.4183919 G>A belirlenmiştir. G>A değişimi, lösin amino asidinde sessiz bir mutasyona neden olmuştur. Sinonim mutasyonlar nedeniyle mRNA düzeyinde ve proteinin işlevselliğinde değişiklikler meydana gelebilmektedir. Lösin, kas kütlesi kaybını önleyebilen ve miyostatin ekspresyonunu engelleyen önemli bir amino asit olduğundan, bu çalışmada eşeklerde Leu'nun sessiz mutasyonunun eşeklerin kas kütlesini ve fiziksel yapısını değiştirebileceği söylenebilir. Mutant lösin, kas kaybını önlemede daha düşük bir etkiye sahip olduğundan, daha fazla Myostatin protein ekspresyonuna neden olabilmektedir. Türk eşeklerinde daha önce atlarda bulunan bu mutasyonlar tespit edilememiştir, bu da eşeklerin yarış kabiliyeti için daha az gereksinime sahip olduklarını göstermektedir. Tespit edilen SNP ilk olarak ortaya konmuş ve mevcut çalışma ile Türk eşeklerinde MSTN geninin DNA dizileri ilk kez ortaya çıkartılmıştır. MSTN geninin dizileri, MW970078-MW970079 erişim numarasıyla NCBI GenBank'a girilmiştir. Eşek ırklarında MSTN genindeki SNP'lerin ve bunların ekonomik öneme sahip morfolojik karakterlerle ilişkisinin protein ve moleküler düzeyde belirlenmesi amacıyla daha ileri çalışmalara ihtiyaç vardır., The study aimed to determine the MSTN gene variation in 90 donkeys reared in the Thrace region of Turkey. Myostatin (MSTN), also named GDF-8 (growth differentiation factor 8) is a part of the transforming growth factor β (TGF-β) superfamily and it has a negative regulator role on muscle mass, growth and development in mammalian species. MSTN gene regulates the skeletal muscle growth in a negative way and has a significant role in homeostasis of skeletal muscles. Also, in muscle fibers balance of protein has been promoted by Myostatin factor. The total of 866 bp long partial intron 1 and 2, whole exon 2 regions of MSTN gene was amplified and PCR products analysed using DNA sequencing. In this study, a novel synonymous SNP was determined as g.4183919 G>A in the second exon region of the MSTN gene which does not cause an amino acid change in the protein. The G>A transition caused a silent mutation in leucine (leu) amino acid. Alterations in mRNA level and functionality of protein can occur due to synonymous mutations. Since leucine is an important amino acid that can avoid muscle mass loss and inhibits the expression of Myostatin, it can be said that silent mutation of Leu in donkeys may have altered the muscle mass and physical factor of donkeys in this study. Mutant leucine may have a lower efficient effect on preventing loss of muscles and causes more Myostatin protein expression. The identified SNP was firstly released and the DNA sequences of the MSTN gene in Turkish donkeys was revealed for the first time with recent study. Turkish donkeys lacked these mutations that were identified before in horses, which cause for the less might require for race ability of donkeys. The sequences of MSTN gene were submitted to the NCBI GenBank with the accession number: MW970078- MW970079. Further studies are needed to conduct, on protein and molecular levels, SNPs on the MSTN gene and their association with the morphological characters that may affect economic traits in donkey breeds.

In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD) and nucleotide diversity (&pi, D), for the Turkish donkey populations ranged from 0.533 &plusmn, 0.180 (Tekirdağ&ndash, Malkara, MAL) to 0.933 &plusmn, 0.122 (Aydin, AYD), and from 0.01196 &plusmn, 0.0026 (Antalya, ANT) to 0.02101 &plusmn, 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries&rsquo, donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions.

This study presents the first insights to the genetic diversity and structure of the Turkish donkey populations. The primary objectives were to detect the main structural features of Turkish donkeys by microsatellite markers. A panel of 17 microsatellite markers was applied for genotyping 314 donkeys from 16 locations of Turkey. One hundred and forty-two alleles were identified and the number of alleles per locus ranged from 4 to 12. The highest number of alleles was observed in AHT05 (12) and the lowest in ASB02 and HTG06 (4), while ASB17 was monomorphic. The mean HO in the Turkish donkey was estimated to be 0.677, while mean HE was 0.675. The polymorphic information content (PIC) was calculated for each locus and ranged from 0.36 (locus ASB02) to 0.98 (locus AHT05), which has the highest number of alleles per locus in the present study. The average PIC in our populations was 0.696. The average coefficient of gene differentiation (GST) over the 17 loci was 0.020 &plusmn, 0.037 (p &lt, 0.01). The GST values for single loci ranged from &minus, 0.004 for LEX54 to 0.162 for COR082. Nei&rsquo, s gene diversity index (Ht) for loci ranged from 0.445 (ASB02) to 0.890 (AHT05), with an average of 0.696. A Bayesian clustering method, the Structure software, was used for clustering algorithms of multi-locus genotypes to identify the population structure and the pattern of admixture within the populations. When the number of ancestral populations varied from K = 1 to 20, the largest change in the log of the likelihood function (K) was when K = 2. The results for K = 2 indicate a clear separation between Clade I (KIR, CAT, KAR, MAR, SAN) and Clade II (MAL, MER, TOK, KAS, KUT, KON, ISP, ANT, MUG, AYD and KAH) populations.

In this study, the κ-casein (CSN3) and lactoferrin (LTF) genes which were found in association with milk production traits in different animal species were studied firstly in Turkish donkey populations. A total of 108 donkeys from different regions of Turkey were used in order to reveal the different genotypes of CSN3 and LTF genes by using polymerase chain reaction – restriction fragment length polymorphism (PCR-RFLP) and DNA sequencing methods. To determine the genetic polymorphism, we attempted to digest a fragment of 235 bp of the CSN3 gene and a fragment of 751 bp of the LTF gene using PstI, and DraII, EagI and MboI restriction enzymes, respectively. Neither the CSN3 gene nor the LTF gene had enzyme recognition sites with the PstI, DraII and MboI restriction enzymes in all of the studied samples. However, the LTF gene was only distinguished with the EagI restriction enzyme. Three genotypes were identified in the LTF gene with the EagI restriction enzyme: GG homozygotes (667, 84 bp), AG heterozygotes (751; 667, 84 bp) and AA homozygotes (751 bp). The transition from guanine to adenine in 89 bp of the LTF gene lacks the restriction site and different genotypes are obtained. This novel single nucleotide polymorphism (SNP) has been firstly detected in donkeys. According to the results, the G allele was predominant in the LTF-EagI gene in the studied Turkish donkey populations. In this study, all the genotype distributions of LTF-EagI were not found in Hardy–Weinberg equilibrium (P

In this study, the genetic characterization of Thrace honey bee populations of Turkey were identified using the mitochondrial gene region, 3′ end of cytochrome C oxidase I gene to 5′ end of cytochrome C oxidase II gene (inter CoxI-CoxII genes) by using XbaI PCR-RFLP and DNA sequencing. A total of 322 worker honey bees were collected from five different localities; 4 provinces (Tekirdağ, Kırklareli, Edirne and Çanakkale) and Gökçeada Island near Thrace. PCR RFLP and sequence data combined revealed three haplotypes. The most frequently observed haplotype (Type 1), revealed only one XbaI restriction site in inter CoxI-CoxII genes. Type 2 haplotype revealed additional XbaI restriction site and this digestion revealed three bands. The rarely seen third haplotype, which is first reported in this study, was only found in two of the samples that were collected from Gökçeada Island. According to Maximum Likelihood phylogenetic analysis which was constructed on the basis of the distance matrix, Type 1 haplotype was clustered in the same clade with A. m. caucasica and A. m. anatoliaca whereas Type 2 was clustered in the same clade with A. m. macedonica and A. m. carnica. These results may indicate that Carniolan or Macedonian honey bee subspecies or their ecotypes can be found in the Thrace region of Turkey, mainly in samples that were collected from Kırklareli and Edirne provinces near the borders with Greece and Bulgaria.

Diacylglycerol acyltransferase 1 (DGAT1) gene has become a potential candidate gene for milk composition and yield in cattle. A nonconservative lysine to alanine substitution (K232A) at position 10.433 and 10.434 in the eighth exon of DGAT1 gene has widely studied in cattle, goat, and sheep. This substitution conducted a considerable effect on milk fat, which was previously mapped to the centromeric end of bovine chromosome 14. Yet, no information has been found about DGAT1 gene in donkeys. In this study, the genetic variation of DGAT1 gene has been analyzed by CfrI (EaeI) restriction and DNA sequencing in 85 donkeys reared in Thrace region of Turkey. No digestion is found in the DGAT1 gene via CfrI restriction enzyme in the studied donkey populations. The DNA sequence of 437 bp of the DGAT1 gene in donkeys revealed only Alanine allele (K232A), which was reported in cattle with high milk fat content. But we found a novel polymorphism at position 10.435, from G to A, which also revealed Alanine allele. As a conclusion, CfrI digestion is not a diagnostic site in DGAT1 gene in donkeys. The DNA sequence of DGAT1 gene in donkeys is reported for the first time in this study, and this sequence is deposited to National Center for Biotechnology Information GenBank database with the accession number MK086162.

Leptin receptor is a fundamental regulator in physiological functions of the regulation of food intake, energy homeostasis, immune function, and reproduction as well as on ovarian follicular cells on the placenta and lactating mammary glands. The aim of this study was to investigate the LEPR gene polymorphism in 60 donkeys reared in Thrace region of Turkey. A 585 bp long partial intron 6, exon 7, intron 7, and exon 8 regions of LEPR gene were amplified, and polymerase chain reaction products analyzed via DNA sequencing. A novel single-nucleotide polymorphism (SNP) was identified as g.713668A>G in the seventh exon region of LEPR gene. This novel SNP was first identified, and the partial DNA sequence of LEPR gene in donkeys was reported for the first time in this study, and these sequences were deposited to NCBI Genbank database with the accession number: MK807114-MK807115. The A>G transition revealed a silent mutation (CAA-CAG) in glutamine amino acid. This nucleotide mutation could cause the changes of secondary structure of protein and expression level of LEPR hormone. For this reason, additional studies are needed to reveal new SNPs and in the LEPR gene that may affect economic traits and structure of protein in donkey breeds.

In this study, the κ-casein (CSN3) and lactoferrin (LTF) genes which were found in association with milk production traits in different animal species were studied firstly in Turkish donkey populations. A total of 108 donkeys from different regions of Turkey were used in order to reveal the different genotypes of CSN3 and LTF genes by using polymerase chain reaction – restriction fragment length polymorphism (PCR-RFLP) and DNA sequencing methods. To determine the genetic polymorphism, we attempted to digest a fragment of 235 bp of the CSN3 gene and a fragment of 751 bp of the LTF gene using PstI, and DraII, EagI and MboI restriction enzymes, respectively. Neither the CSN3 gene nor the LTF gene had enzyme recognition sites with the PstI, DraII and MboI restriction enzymes in all of the studied samples. However, the LTF gene was only distinguished with the EagI restriction enzyme. Three genotypes were identified in the LTF gene with the EagI restriction enzyme: GG homozygotes (667, 84 bp), AG heterozygotes (751; 667, 84 bp) and AA homozygotes (751 bp). The transition from guanine to adenine in 89 bp of the LTF gene lacks the restriction site and different genotypes are obtained. This novel single nucleotide polymorphism (SNP) has been firstly detected in donkeys. According to the results, the G allele was predominant in the LTF-EagI gene in the studied Turkish donkey populations. In this study, all the genotype distributions of LTF-EagI were not found in Hardy–Weinberg equilibrium (P

AcylCoA: diacylglycerol acyltransferase (DGAT1) gene has a considerable effect on milk content and yield in cattle with a substitution of lysine by alanine in the exon 8 of the gene. Moreover there are many other researches comprising the DGAT1 gene on different farm animals, such as buffalo, sheep and goat but there is no information about the DGAT1 gene in donkeys. In this study, the polymorphism of DGAT1 gene in donkey populations reared in Thrace region of Turkey has been investigated by restriction fragment length polymorphism (RFLP) via EaeI (CfrI) restriction enzyme. EaeI restriction site was found in cattle breeds which resulted after K232A substitution, Lysine (AAG) to Alanine (GCG) variant but this restriction site was not found in donkey populations. A novel single-nucleotide polymorphism (G -> A substitution) in the DGAT1 gene at position 10,435 lacks this restriction site which results only Alanine variant (GCA) instead of Lysine variant. This novel single-nucleotide polymorphism in the DGAT1 gene was found in the studied donkey breeds.

WOS: 000452379100003, PubMed: 32175456, 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-DRBI 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 Daglic 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., Selcuk University, The Scientific Research Projects Coordinating Office [12401025], We thank Selcuk University, The Scientific Research Projects Coordinating Office (project no: 12401025; principal investigator: Fulya Ozdil).

Bu calismada, Turkiye’nin Trakya bolgesinde bulunan bal arisi populasyonlarinda genetik varyasyon mitokondriyel genomda 16S rDNA ve ND5 gen bolgeleri kullanilarak arastirilmistir. PCR-RFLP ve DNA dizi analizi yontemlerinden yararlanilarak 16S rDNA ve ND5 gen bolgeleri Dra I , Mbo II ve Swa I restriksiyon enzimleri ile incelenmistir. Trakya bolgesinin Tekirdag, Edirne, Kirklareli illeri ile Canakkale ve Gokceada’nin farkli yorelerinden olmak uzere toplam 100 adet isci ari ornegi materyal olarak kullanilmistir. Bu calismada, 16S rDNA ve ND5 gen bolgelerinin Dra I ve Swa I restriksiyon enzimleri ile kesiminde iki farkli haplotip elde edilmistir. 16S rDNA/ Dra I kesimi bakimindan Tip 1 haplotipinde 6 kesim noktasi tespit edilmis ve 315, 212, 116, 116, 92, 70 ve 44 bc'lik kesim profili elde edilmistir. Tip 2 haplotipinde ise, C → T transizyonu sonucu 705. pozisyonda meydana gelen nokta mutasyonu sonucu ilave bir kesim noktasi daha olusmus ve bu haplotipte 8 bantlik kesim profili elde edilmistir (215, 212, 116, 116, 100, 92, 70 ve 44 bc). 16S rDNA/ Swa I kesimi bakimindan Tip 1 haplotipinde iki kesim noktasi sonucu 359, 324 ve 282 bc’lik kesim profili tespit edilmis, ayni gen bolgesinin 196. nukleotidinde meydana gelen A→T transversiyonu sonucu yeni bir kesim noktasi daha olusmus ve 359, 324, 195 ve 87 bc’lik 4 bant veren kesim profili elde edilmistir. Fakat bu bolgenin Mbo II restriksiyon enzimi ile kesimi sonucunda tum orneklerde 16S rDNA/ Mbo II bakimindan tek tip haplotip belirlenmistir. ND5 gen bolgesinde ise sadece Dra I restriksiyon enzimi ile kesim sonucunda varyasyon elde edilmistir. ND5/ Dra I kesimi bakimindan Tip 1 haplotipinde 440, 270 ve 112 bc’lik kesim profili elde edilirken, ayni gen bolgesinin 383. pozisyonda meydana gelen T→C transizyonu sonucu Dra I restriksiyon enzimi kesim noktasi kaybolmus ve 552 ve 270 bc’lik 2 banttan olusan kesim profili elde edilmistir. ND5 bolgesinin Mbo II ve Swa I restriksiyon enzimleri ile kesiminde varyasyon bulunmamis ve tum orneklerde tek tip haplotip elde edilmistir.

Previous studies have reported that a non-conservative substitution of lysine by alanine (K232A) in the 8th exon of acyl CoA:diacylglycerol acyltransferase (DGAT1) gene in cattle has a major effect on milk composition and yield. But yet little research has been utilized in this gene segment in buffalo. In this study the genetic differentiation of three indigenous Anatolian buffalo populations has been investigated in the 8th exon of DGAT1 gene. Fourteen out of the 24 restriction enzymes have a recognition site on the DGAT1 gene segment, generating a total of 26 restriction sites. AluI, HincII and HphI restriction enzymes out of these 14 enzymes were found to detect polymorphism. K232A substitution found in cattle breeds with CfrI restriction enzyme is not a diagnostic site in Anatolian buffalo. Only lysine variant (K allele) is found in all of the Anatolian buffalo tested. In this study, four different haplotypes were obtained and sequencing of this gene revealed three polymorphic nucleotide substitutions in the 8th exon of the buffalo DGAT1 gene. C→T, A→G and C→G base substitutions at positions 43, 154 and 373, respectively, each generated two different fragment patterns in Anatolian buffalo. Type 1 haplotype was the most common haplotype, found in 73.2% of the samples. Along with the polymorphic substitution sites in DGAT1 gene, this study provides evidence that all the Anatolian buffalo have fixed allele with respect to DGAT1 K allele reported to be responsible for high milk fat yield. Our study presents the first comprehensive sequencing analysis of Anatolian buffalo and it is the first time that sequencing data from DGAT1 gene segment have been obtained at the population level.

Mitochondrial DNA sequence variation can be used to infer honeybee evolutionary relationships. In this study, DNA sequence diversity of the mitochondrial 16s rDNA region was investigated in 112 honeybees from 15 populations in Turkey, which is mainly populated with Apis mellifera anatoliaca, A. m. caucasica, and A. m. meda. The study revealed 11 haplotypes for this segment, with 13 variable sites and nine parsimony informative sites. The haplotypes were not discriminated according to their geographical locations in a neighbor-joining dendrogram based on 16s rDNA sequences available in Genbank, but all the haplotypes obtained in this study are clustered with published haplotypes such as A. mellifera TAS (AF214666) and A. m. ligustica (EF116868) and with some unpublished Genbank records (HQ318928, HQ318934, and HQ318938). This study expands the knowledge of the mitochondrial 16s rDNA region, and it presents the first comprehensive sequence analysis of this region in Turkish honeybees.

BACKGROUND: The utilisation of molecular markers has increased in molecular research recently. Inter-simple sequence repeat (ISSR) markers allow the analysis of genomes without preliminary sequence information, since random primers are used. The purpose of the present study was to evaluate ISSR markers for assessing the genetic diversity of indigenous Anatolian Water Buffaloes reared in Afyon, Konya and Sivas provinces of Turkey, with a view to conservation of the gene resources. RESULTS: The 11 ISSR primers chosen for the analysis revealed a total of 110 bands, of which 76 (69.09%) were polymorphic. Also, genetic similarity, polymorphic information content (PIC), resolving power (Rp) and mean resolving power (Rp), heterozygosity (H) and Shannon index (I) were calculated as 0.9479–0.9562, 0.35 ± 0.20, 2.73, 0.27, 0.18 ± 0.07 and 0.28 ± 0.11, respectively. CONCLUSION: The ISSR markers were found to be promising for assessing the genetic diversity in buffalo populations. Potential genetic parameters such as PIC, Rp, Rp, H and I were effectively used in this study. Copyright © 2011 Society of Chemical Industry

The western honey bee, Apis mellifera L., is native to Africa, the Near and Middle East, and Europe. Based on morphometrics, the Near Eastern subspecies, Anatolian (A. m. anatoliaca), Caucasian (A. m. caucasica), and Iranian (A. m. meda), were grouped within the Middle Eastern O branch (Ruttner 1988; Kauhausen-Keller et al. 1997); however, mtDNA analysis has shown that they belong to the East Mediterranean C lineage (Smith et al. 1997; Palmer et al. 2000; Franck et al. 2000, 2001; Kandemir et al. 2006; Ozdil et al. 2009). According to Ruttner’s (1988) morphometric analysis, A. m. anatoliaca occupies nearly all of Turkey, A. m. caucasica is found in the northeastern part of Turkey, and A. m. meda is found primarily in Iran but also in the southeastern part of Turkey. Length and restriction site polymorphisms within the CoxI–CoxII intergenic region of the honey bee mitochondrial genome have been particularly useful in differentiating evolutionary lineages and groups of subspecies (Cornuet and Garnery 1991; Hall and Smith 1991; Garnery et al. 1992, 1993; Franck et al. 2000, 2001; Palmer et al. 2000). For example, DraI restriction of this region revealed more than 50 haplotypes in lineages A and M (Garnery et al. 1992, 1993; Franck et al. 2000, 2001) but only six haplotypes in lineage C (Franck et al. 2000; Kandemir et al. 2006; Ozdil et al. 2009), including one discovered recently (Ozdil et al. 2009).

WOS: 000305519600034, PubMed: 22614282, Mitochondrial DNA sequence variation can be used to infer honey bee evolutionary relationships. We examined DNA sequence diversity in the cytochrome C oxidase I (COI or Cox1) gene segment of the mitochondrial genome in 112 samples of Apis mellifera from 15 different populations in Turkey. Six novel haplotypes were found for the COI gene segment. There were eight variable sites in the COI gene, although only three were parsimony-informative sites. The mean pairwise genetic distance was 0.3% for the COI gene segment. Neighbor-joining (NJ) trees of the COI gene segment were constructed with the published sequences of A. mellifera haplotypes that are available in GenBank; the genetic variation was compared among the different honeybee haplotypes. The NJ dendogram based on the COI sequences available in GenBank showed that Eastern European races were clustered together, whereas the Mellifera and Iberian haplotypes were clustered far apart. The haplotypes found in this study were clustered together with A. mellifera ligustica and some of the Greek honey bees (accession Nos. GU056169 and GU056170) found in NCBI GenBank database. This study expands the knowledge about the mitochondrial COI region and presents the first comprehensive sequence analysis of this region in Turkish honeybees.

WOS: 000302587400004, In this study, the genetic structure of Turkish honey bee (Apis mellifera L.) populations, mainly obtained from the Central Anatolian region, were investigated at three different mitochondrial regions. A total of 165 worker bees were collected from 15 different populations in ten different locations. Portions of the mitochondrial 16S ribosomal RNA (16S rDNA), cytochrome C oxidase I (COI) and NADH dehydrogenase 5 (ND5) genes were amplified by PCR and then subjected to RFLP pattern analysis using 18 restriction enzymes (these having at least one recognition site in each region were used). Nucleotide polymorphisms were revealed using restriction enzymes Bsp1431, DraI and SspI in 16S rDNA and TaqI in the COI gene segment. The polymorphisms were subsequently confirmed by direct DNA sequencing with sequences thereafter deposited in Genbank. In this study, six novel composite genotypes (haplotypes) were found in Turkish honey bee populations. The most common haplotype, type 1, was found in 12 of the sampled populations and overall accounted for 85.5% of the samples. TCS spanning network of haplotypes revealed that type 1 was the basal haplotype. Genetic distance (D) values were found to be low (0.0-0.0112) within Turkish honey bee populations. The average haplotype diversity (h) within populations was 0.082. Molecular phylogenetic analysis revealed that Konya/Sizma, Antalya/Elmali and Konya/Selcuklu populations were the most distant from all the other Turkish honey bee populations surveyed., Scientific Research Projects (BAP) Coordinating Office of Selcuk University, TurkeySelcuk University [08401051], The authors thank Mehmet Ali Yildiz (Ankara University, Faculty of Agriculture) for providing insights and guidance during the various phases of this project. The project was supported by a grant from the Scientific Research Projects (BAP) Coordinating Office of Selcuk University, Turkey (Project No: 08401051).

WOS: 000270406000009, To identify the evolutionary lineage of honey bee colonies in Turkey, the mtDNA of 244 colonies from 20 locations was analyzed. Several polymorphic restriction sites showed that they belonged to the Mediterranean C lineage. DraI digestion of the CoxI-CoxII intergenic region produced four fragment patterns, one first seen in this study. From 37 colonies from 16 different locations in Turkey and two colonies from Iran, the intergenic region was sequenced. Previously, from among all honey bee populations of the C lineage, eight haplotypes had been described from this mtDNA region, three of which were found here. In addition, eight new haplotypes were found. A deletion in one of these haplotypes accounts for the novel DraI RFLP pattern. Most of the novel haplotypes were in a subgroup of lineage C, yet none of these had been found in previous studies of Turkish honey bees. The geographical distribution of some haplotypes suggests that they may be characteristic of subspecies native to Turkey., T. R. Prime Ministry State Planning Organization [DPT-2003K12019015-5]; Scientific and Technological Research Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [TOVAG-103V070/VHAG-2046, TUBITAK TOVAG-108O200], This work was performed by Fulya Ozdil in partial fulfillment of the Ph.D. degree in Biometry and Genetics at University of Ankara, Turkey. The authors would like to thank Dr. Cetin Firatli ( Ankara University), Dr. H. Vasfi Gencer ( Ankara University) and Dr. Cengiz Erkan (Yuzuncu Yil University) for providing honey bee samples and Raquel McTiernan, Hasan Meydan and Yasemin Gedik for their help with the laboratory work. This project was supported by three grants: DPT-2003K12019015-5 from T. R. Prime Ministry State Planning Organization ( Project coordinator: Dr. M. A. Yildiz), TUBITAK TOVAG-103V070/VHAG-2046 and TUBITAK TOVAG-108O200 from the Scientific and Technological Research Council of Turkey (Project coordinator: Dr. M. A. Yildiz).

Mitochondrial DNA sequence variation can be used to infer honey bee evolutionary relationships. In this study, DNA sequence diversity in the ND5 region of the mitochondrial genome was investigated in 93 samples of Apis mellifera from 15 different populations in Turkey. Five novel haplotypes were revealed for the ND5 gene segment of Turkish honeybees. The number of variable sites found was 6 for this region while 2 were parsimony informative sites. The average pairwise genetic distances were 0.3% for ND5 gene. In this study, the NJ tree of ND5 gene segment were constructed with the published sequences of Apis mellifera haplotypes. This study expands the knowledge about the mitochondrial ND5 region in Apis mellifera and it is also the first comprehensive sequencing analysis of ND5 region in Turkish honeybees.

Bu çalışmada, Ankara Üniversitesi Ziraat Fakültesi Zootekni Bölüm İşletmesinde yetiştirilen Saanen–Kilis melezi Akkeçi’lerden ve Konya–Ermenek yöresi özel işletmelerdeki Kıl keçi’lerden temin edilen toplam 30 adet süt örneğinden genomik DNA izolasyonu yapılmıştır. Genomik DNA izolasyonu, fenol–kloroform ile Chelex® 100 ekstraksiyon yöntemleri kullanılarak yapılmıştır. Her iki yöntemle elde edilen genomik DNA’nın konsantrasyonu ve saflık derecesi, 260 ve 280 nm UV ışığı altında absorbans değerlerinden hesaplanmış ve karşılaştırılmıştır. Fenol–kloroform ekstraksiyon yöntemi ile elde edilen DNA konsantrasyonu ortalama, 2406±322 µg/mL ve saflık derecesi A260/A280oranında ortalama, 1.816±0.038 olarak bulunmuştur. Bu durum fenol-kloroform ekstraksiyon yöntemiyle genomik DNA’nın saf olarak elde edildiğini göstermektedir. Chelex® 100 ekstraksiyon yönteminde ise DNA konsantrasyonu ortalama, 590.0±54.9 µg/mL ve elde edilen genomik DNA’nın saflık derecesi ortalama, 1.311±0.012 olarak bulunmuştur. Bu sonuç Chelex® 100 ekstraksiyonu ile elde edilen DNA örneklerinde protein kontaminasyonu olduğunu göstermekte ve DNA’ların çok saf elde edilemediğini ifade etmektedir. Fenol–kloroform ekstraksiyon yöntemi ile elde edilen genomik DNA, % 1.0 ’lik agaroz jelinde tek bant olarak görülmüştür. Ancak Chelex® 100 ekstraksiyon yöntemi ile elde edilen DNA miktarı az olduğu için agaroz jelinde görüntü alınamamıştır, In this study, the isolation of genomic DNA was carried out by using a total of 30 Akkeçi and native hair goat milk samples that were collected from Konya-Ermenek region and University of Ankara, Faculty of Agriculture, Department of Animal Science. The isolation of genomic DNA was performed by using phenol–chloroform and Chelex® 100 extraction methods. The concentration and the purity of genomic DNA obtained with both methods, were determined by spectrophotometric absorption of UV light at 260 nm and 280 nm wave length and the results were compared. The mean DNA concentration obtained from phenol–chloroform extraction method was 2406±322 µg/mL and the mean purity of genomic DNA A260/A280 ratio was 1.816±0.038. These results indicate good deproteinisation in phenol–chloroform extraction method. The mean DNA concentration obtained from Chelex® 100 extraction method was 590.0±54.9 µg/mL and the mean purity of genomic DNA was 1.311±0.012. These results showed that there were some protein contaminations in DNA samples by using Chelex® 100 extraction method. The genomic DNA obtained from phenol–chloroform extraction method, appeared to be a single band on 1 % agarose gel but due to the less amount of genomic DNA obtained in Chelex® 100 extraction method, there was no signal on agarose gel

WOS: 000263951400001, PubMed: 19161609, Background: Factor XI (FXI) is a plasma protein that participates in the formation of blood clots. Factor XI deficiency is autosomal recessive hereditary disorder that may be associated with excess bleeding in Holstein cattle. Methods: In this study, 225 Holstein cows reared in Turkey were screened in order to identify FXI genotypes. DNA extractions were obtained from the fresh blood of the cows. Amplicons of FXI exon 12 were obtained by Polymerase Chain Reaction (PCR), and analyzed by 2% agarose gel electrophoresis stained with ethidium bromide. Additionally, all cows were confirmed by DNA sequencing to determine whether or not there was a mutant allele. Results: Carriers of the FXI deficiency have two DNA fragments of 320 bp and 244 bp in size. The results of our study demonstrated that only four out of the 225 Holstein cows tested in Turkey carried the FXI deficiency. The frequency of the mutant FXI allele and the prevalence of heterozygous cows were found as 0.9% and 1.8%, respectively. Conclusion: The DNA-based test determines all genotypes, regardless of phenotype or FXI activity. The mutation responsible for the FXI deficiency had not been detected in Holstein cattle in Turkey before prior to this study. The frequency of the mutant FXI allele needs to be confirmed by carrying out further analyses on cattle in Turkey and the selection programs should be developed to eliminate this genetic disorder., Scientific and Technological Research Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [TOVAG-107O914], We are indebted to Dr. Jonathan E. Beever of the Department of Animal Sciences, University of Illinois, Urbana-USA, for providing the control DNA samples. This study was partially supported by a grant, TOVAG-107O914, from The Scientific and Technological Research Council of Turkey (Project coordinator: Dr. M. A. YILDIZ). We are also grateful to Dr. Hans H. Cheng of the USDA, Agricultural Research Service, Avian Disease and Oncology Laboratory, Michigan State University, and anonymous reviewers for their comments on an earlier version of the manuscript.