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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.

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.

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.

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.