mtDNA D-loop Region Research Articles

Mitochondrial diversity and phylogeographic structure of native cattle breeds from Yunnan, Southwestern China

Little is so far known about genetic diversity and phylogeographic structure of native cattle breeds from Yunnan in Southwestern China, a frontier zone that connects China with South and Southeast Asia. Herein we analyzed a 910-bp fragment of mitochondrial DNA (mtDNA) D-loop region sequences of 280 individuals from 6 Yunnan native cattle breeds, of which 251 sequences were newly determined. There were 93 variable sites that defined 117 haplotypes among all sequences. Phylogenetic analysis of all haplotypes revealed that Yunnan native cattle had two distinct mtDNA lineages - taurine and zebu. The taurine sequences fell into four haplogroups T1a, T2, T3 and T4, whereas the zebu sequences grouped into two haplogroups I1 and I2. In addition, our results revealed patterns of gradient changes in frequencies of taurine and zebu mtDNA lineages across different geographic regions of Yunnan. Furthermore, three kinds of methods (haplotype network, analysis of molecular variance, and Mantel tests) consistently showed no significant phylogeographic structuring among Yunnan native cattle breeds. This might be attributed to historical strong gene flow and genetic admixture among native cattle breeds in different geographic regions.

Genetic diversity and origin of Namchi cattle breed inferred by matrilineage analyses

In animal genetic studies, mitochondrial DNA (mtDNA) analysis offers a way to detect changes in populations over time along with their maternal origin and migration routes. To determine these patterns in Namchi cattle breeds of Cameroon, analyses of 17 sequences of a 336 base pair fragment of the mtDNA D-loop region from two populations (Namchi Poli and Namchi Ngaoundere) were conducted in conjunction with previously published sequences from African, European, Japanese and Chinese subjects. As expected for an African taurine breed, all individuals in the study were found to be members of haplogroup T1. Due to the size of fragment analyzed, only one sub-haplogroup (T1c)could be detected, at a rate of 5.88%.This suggested that The Namchi cattle breed originated most probably from south west Asia and migrated to Cameroon through the Ismuth of Suez to Egypt and through Arabia to Somalia and Ethiopia. A relatively high nucleotide diversity (π) was found in Namchi Poli population (0.03421±0.00582) while in Namchi Ngaoundere a value of 0.00980±0.00185 was obtained, for a total nucleotide diversity of 0.01387±0.00234. The high genetic diversity observed in Namchi cattle breed reflects not only the presence of sub-haplogroups T1 but also an introgression from hybridization. This study provides new information regarding the sub haplogroups of the Namchi cattle, their origin and migration routes and their genetic diversity which seems to have been affected by gene flow with zebus like White Fulani or Red Fulani. To facilitate the preservation and the conservation of the Namchi cattle breed in Cameroon, it is therefore important to adopt effective breeding management practices.

From unknown to known: Identification of the remains at the mausoleum of fosse Ardeatine

During the Second World War, on 24th March 1944, 335 Italians were massacred near Rome by the occupying forces of Nazi Germany. Four months later forensic examination led to the identification of 323 out of 335 victims. After approximately 60 years, the identification of the remaining unidentified twelve victims began with anthropological and genetic analysis carried out by a team of Italian forensic experts. Anthropological analysis was performed in field in order to confirm the sex of each victim and verify the presence of only one individual in each grave for a correct sampling. Selected bone fragments for each individual were then collected and transferred to the laboratory for genetic analysis. Although the anthropological ante mortem information was limited, morphological and metrical data was collected for a possible future identification of the victims. Subsequently, the typing of autosomal loci, Y-STR and mtDNA D-loop region of all bone and available reference samples was conducted. LR and cumulative LRs obtained from autosomal STR and Y-STR results confirmed the alleged relationship between three victims and their relatives with values over 104 (one sample) and 106 (two samples). Therefore, the genetic analysis offered the families the possibility of replacing the number of the grave with the name of the victim.

DNMT1 mediates metabolic reprogramming induced by Epstein\u2013Barr virus latent membrane protein 1 and reversed by grifolin in nasopharyngeal carcinoma

Cancer cells frequently adapt fundamentally altered metabolism to support tumorigenicity and malignancy. Epigenetic and metabolic networks are closely interactive, in which DNA methyltransferases (DNMTs) play important roles. Epstein–Barr virus (EBV)-encoded latent membrane protein 1 (EBV-LMP1) is closely associated with nasopharyngeal carcinoma (NPC) pathogenesis because it can trigger multiple cell signaling pathways that promote cell transformation, proliferation, immune escape, invasiveness, epigenetic modification, and metabolic reprogramming. Our current findings reveal for the first time that LMP1 not only upregulates DNMT1 expression and activity, but also promotes its mitochondrial translocation. This induces epigenetic silencing of pten and activation of AKT signaling as well as hypermethylation of the mtDNA D-loop region and downregulation of oxidative phosphorylation (OXPHOS) complexes, consequently, leading to metabolic reprogramming in NPC. Furthermore, we demonstrate that grifolin, a natural farnesyl phenolic compound originated from higher fungi, is able to attenuate glycolytic flux and recover mitochondrial OXPHOS function by inhibiting DNMT1 expression and activity as well as its mitochondrial retention in NPC cells. Therefore, our work establishes a mechanistic connection between epigenetics and metabolism in EBV-positive NPC and provides further evidence for pathological classification based on CpG island methylator phenotype (CIMP) in EBV-associated malignancies. In addition, grifolin might be a promising lead compound in the intervention of high-CIMP tumor types. The availability of this natural product could hamper tumor cell metabolic reprogramming by targeting DNMT1.

Assessing the genetic diversity of the critically endangered Chinese sturgeon Acipenser sinensis using mitochondrial markers and genome-wide single-nucleotide polymorphisms from RAD-seq.

As a living fossil, the endangered Chinese sturgeon (Acipenser sinensis) has been considered a national treasure in China. Here, the famous Gezhouba Dam and Three Gorges Dam on the Yangtze River were built in 1988 and 2006, for economic purposes. The natural population of Chinese sturgeon has declined since then, as these dams block its migratory route to the original spawning grounds in the middle reaches of the Yangtze River. In 2013 and 2014, there was an absence of spawning where it typically happened near the Gezhouba Dam. Nevertheless, from April to June in 2015, over 1,000 larvae with different body lengths (10-35 cm) were detected along the Shanghai Yangtze Estuary; but only little is currently known about the population genetic structure of the Chinese sturgeon. Herein, we inferred population genetic parameters from 462 available Chinese sturgeon specimens based on a 421-bp fragment of the mitochondrial DNA (mtDNA) D-loop region and 1,481,620 SNPs (single-nucleotide polymorphisms) generated by restriction site-associated DNA sequencing (RAD-seq). For the D-loop dataset, 15 haplotypes were determined. Randomly picked 23 individuals, representing the 15 D-loop haplotype groups, were subsequently used for further RAD-seq validation. The average nucleotide diversity calculated from the mtDNA and RAD datasets was 0.0086 and 0.000478, respectively. The overall effective female population size was calculated to be 1,255 to 2,607, and the long-term effective population size was estimated to range from 11,950 to 119,500. We observed that the genetic variability and the effective female population size of the current population in the Yangtze River are severely low, which are similar to the data reported over 10 years ago. The deduced relatively small effective population of female fish, limiting the genetic connectivity among Chinese sturgeon, should be considered a serious threat to this endangered species.

Mutational Analysis of the Mitochondrial DNA Displacement-Loop Region in Human Retinoblastoma with Patient Outcome

Alteration in mitochondrial DNA plays an important role in the development and progression of cancer. The Displacement Loop (D-loop) region of mitochondrial DNA (mtDNA) is the regulatory region for its replication and transcription. Therefore, we aimed to characterize mutations in the D-loop region of mitochondrial DNA along with the morphological changes and analyzed their impact on survival in retinoblastoma patients. mtDNA D-loop region was amplified by Nested-Polymerase Chain Reaction (Nested-PCR) and mutations were analyzed in 60 tumor samples from retinoblastoma patients by DNA sequencing. Transmission electron microscopy was performed on 5 retinoblastoma specimens. Mutations were correlated with clinical, histopathological parameters and patient survival. D-loop mutations were found in total of 52/60 (86.6%) patients. The most common mutations were T to C and C to T followed by A to G. There were 5.81% mutations which were not previously reported in the MITOMAP database. A73G (83.33%) were the most frequent mutations found in our cases and it was statistically significant with poor tumor differentiation and age. In addition, this study was further analyzed for morphological changes in retinoblastoma that had disorganized, swollen and less numbers of mitochondria on electron microscopy. This is the first study showing high frequency of mtDNA mutation which might be due to abnormal morphology of mitochondria in retinoblastoma. Our results indicate that pathogenic mtDNA D-loop mutations may be involved in tumorigenesis of retinoblastoma tumor.

The mtDNA haplogroup P of modern Asian cattle: A genetic legacy of Asian aurochs?

BackgroundAurochs (Bos primigenius) were distributed throughout large parts of Eurasia and Northern Africa during the late Pleistocene and the early Holocene, and all modern cattle are derived from the aurochs. Although the mtDNA haplogroups of most modern cattle belong to haplogroups T and I, several additional haplogroups (P, Q, R, C and E) have been identified in modern cattle and aurochs. Haplogroup P was the most common haplogroup in European aurochs, but so far, it has been identified in only three of >3,000 submitted haplotypes of modern Asian cattle.MethodologyWe sequenced the complete mtDNA D-loop region of 181 Japanese Shorthorn cattle and analyzed these together with representative bovine mtDNA sequences. The haplotype P of Japanese Shorthorn cattle was analyzed along with that of 36 previously published European aurochs and three modern Asian cattle sequences using the hypervariable 410 bp of the D-loop region.ConclusionsWe detected the mtDNA haplogroup P in Japanese Shorthorn cattle with an extremely high frequency (83/181). Phylogenetic networks revealed two main clusters, designated as Pa for haplogroup P in European aurochs and Pc in modern Asian cattle. We also report the genetic diversity of haplogroup P compared with the sequences of extinct aurochs. No shared haplotypes are observed between the European aurochs and the modern Asian cattle. This finding suggests the possibility of local and secondary introgression events of haplogroup P in northeast Asian cattle, and will contribute to a better understanding of its origin and genetic diversity.

Analysis of Comparative Phylogenetic Story by Using Autosomal Markers and Mitochondrial Sequences

The current study aims at the molecular assessment of genetic diversity within and between Vietnamese local chicken populations. On average, a total of 32 individuals per Vietnamese local chicken population was randomly sampled. Nine Vietnamese chickens breeds and 2 The exotic chicken breeds originating from China were used. The DNA polymorphism was assessed using a set of 29 microsatellite markers recommended by FAO. A fragment of 455 bp from the mtDNA D-loop region was amplified. The results showed that at the autosomal level, the Vietnamese local chicken breeds from different agro-ecological zones represent genetically distinct populations. The northern breeds are clearly separated from breed of the South Central Coast and from breed of the Mekong Delta. The Vietnamese local chicken breeds are highly polymorphic and originated from eight maternal lineages. These lineages are present across the country. Two chicken breeds of Chinese origin, Tam Hoang and Luong Phuong, kept in the National Institute of Animal Sciences are genetically distinct from the Vietnamese local breeds. The Vietnamese chicken breeds are genetically separated from the Chinese chicken gene pool.

Estimating the distance of genetic domestic goats in Iran inferred from D-loop region of mitochondrial DNA analysis and origins of candidate native goat ancestor

The wild goat “bezoar”(Capra aegagrus) has been considered to be the strongest candidate for the ancestor of the domestic goats (C. hircus) . This article describes the complete sequences of the mitochondrial DNA displacement loop (D-loop) region from Mahabadi goats. The control region (D-loop) is the most variable and non-coding portion of the mitochondrial genome.The genetic diversity and phylogenetic structure was analyzed in Mahabadi goat population by mitochondrial DNA sequences. It is estimated genetic distance between native goat and goat ancestor based on mtDNA. Recent analysis of the most of domestic goat individuals revealed a total of six different monophyletic mitochondrial DNA (mtDNA) haplogroups A, B, C, D, F, and G, with the A haplogroup representing >90% of individuals . Phylogenetic analysis was carried out using hyper variable region 1 (896 bp) obtained form 30 animals. All Mahabadi haplotypes were classified into A haplotype group and revealed remarkably high genetic distances within the population when compared with other goat populations from several places, indicating high genetic variation in the Mahabadi goat. After extracting DNA, displacement loop (D-loop) region of mtDNA was amplified with specific primers using PCR and after purification was sequenced. The phylogenic tree was drawn with the consensus sequence of other similar sequences of different goats breeds and wild goat “bezoar”(Capra aegagrus) obtained from GenBank. InThe phylogenic tree, Mahabadi native goat was clustered with Switzerland, Romania, Austria, Cyprus, Jordan, Spain, Saudi Arabia, Albania , Turkey, Egypt, Kurdi Iran, Malaysia, Kyrgyzstan, Italya and ancestor of native goat breeds. The findings confirmed that Mahabadi goats was closed to Capra aegagrus compared to other domestic goats.

Can We Source the Origin of the Feral Tankwa Goat of South Africa?

Tankwa goats are feral animals initially identified from the Tankwa Karoo National Park in the Northern Cape, South Africa that is reported to be well adapted to their harsh environment. We assessed the genetic diversity of these goats by sequencing the hypervariable segment of the mitochondrial control region (mtDNA HVI D-loop). We additionally clarified genetic origin of the Tankwa goats relative to international breeds. A total of 40 blood samples were collected between 2012 and 2016 from individual unrelated Tankwa goats. Genomic DNA was extracted and the amplified mtDNA D-loop region was used for phylogenetic analysis. A total of 12 haplotypes were identified. Haplotype and nucleotide diversity of Tankwa goat’s population was identified to be low compared to the global goat populations including South African goats, which may be an indication of higher inbreeding in this population. The results obtained from analysis of the mtDNA region in Tankwa goats identified a unique population constructed of two lineages (A 42.5% and B 57.5%).

Genetic diversity, phylogeographic structure and effect of selection at the mitochondrial hypervariable region of Nigerian chicken populations.

In this study, the maternal genetic diversity, phylogenetic relationship and effect of natural selection on indigenous chickens from Nigeria were assessed. A total of 397-bp fragment of the mitochondrial DNA (mtDNA) D-loop region of 171 indigenous chickens from four populations of Nigeria and four commercial egg line strains (two Anak titan, one Giriraja and one Yaffa) as out-groups were analysed. Thirty-one haplotypes (28 from Nigerian chickens and three from commercial strains) and 34 polymorphic sites were identified. The mean haplotypic and nucleotide diversity were found to be 0.39 ± 0.05 and 0.02 ± 0.02, respectively. Majority of Nigerian chicken haplotypes observed were grouped into haplogroup D which originated from Indian subcontinent, suggesting a single maternal lineage. Genetic variation within and between populations accounted for 97.30 and 2.70% of the total genetic variation, respectively, which is in agreement with a recent and maternal founding effect. High number (4) of negatively selected sites observed based on single likelihood ancestral counting (SLAC) model indicated that the sampled Nigerian chicken populations were undergoing purifying selection. This study concluded that there was relatively high genetic diversity and differentiation, thus, this information will probably paveway for further evaluation studies, preservation and improvement of Nigerian chickens as genetic resources towards ensuring food security.

Assessing genetic diversity and phylogeographic structure of duck (<i>Anas platyrhynchos</i>) in Nigeria using mitochondrial DNA D-loop sequences

In this study, the maternal genetic diversity and phylogenetic relationship of Nigerian duck populations were assessed. A total of 591 base pair fragment of the mitochondrial DNA (mtDNA) D-loop region of 87 indigenous ducks from two populations in Nigeria were analyzed. Seven haplotypes and 70 polymorphic sites were identified. The mean haplotypic and nucleotide diversity were found to be 0.381±0.058 and 0.315±0.155 respectively. The phylogeny revealed two divergent haplotype clades, suggesting two possible maternal lineage in Nigerian duck population, with the most commonly shared haplotype belonging to Mallard ducks (Anas platyrhynchos). Genetic variation within and between populations accounted for 63.32% and 36.68% of the total genetic variation respectively. This study concluded that there was relatively high genetic diversity and differentiation, thus, this information will probably pave way for further evaluation studies, preservation and improvement of Nigerian ducks as genetic resources.Keywords: Genetic Diversity, MtDNA, Nigerian duck, phylogeny

Assessing genetic diversity and phylogeographic structure of duck (<i>Anas platyrhynchos</i>) in Nigeria using mitochondrial DNA D-loop sequences

In this study, the maternal genetic diversity and phylogenetic relationship of Nigerian duck populations were assessed. A total of 591 base pair fragment of the mitochondrial DNA (mtDNA) D-loop region of 87 indigenous ducks from two populations in Nigeria were analyzed. Seven haplotypes and 70 polymorphic sites were identified. The mean haplotypic and nucleotide diversity were found to be 0.381±0.058 and 0.315±0.155 respectively. The phylogeny revealed two divergent haplotype clades, suggesting two possible maternal lineage in Nigerian duck population, with the most commonly shared haplotype belonging to Mallard ducks (Anas platyrhynchos). Genetic variation within and between populations accounted for 63.32% and 36.68% of the total genetic variation respectively. This study concluded that there was relatively high genetic diversity and differentiation, thus, this information will probably pave way for further evaluation studies, preservation and improvement of Nigerian ducks as genetic resources.Keywords: Genetic Diversity, MtDNA, Nigerian duck, phylogeny

Genetic diversity of Geophagus brasiliensis from the South American Atlantic Rainforest

The Atlantic Rainforest is one of the global conservation hotspots, representing a seriously threatened area with high levels of endemism and species richness. The fishes from the Atlantic Rainforest are one of the most exploited vertebrate groups by the international aquarium commerce, with an annual trade volume of about U$15-25 billions, now aggravated by the Internet e-Commerce and playing a crucial role on the sales and distribution of these species. The Cichlidae is one of the most exploited groups with several species being commonly sold in several online sites and aquarium stores all around the world. In this sense, our aim is to study the genetic diversity of the native cichlid Geophagus brasiliensis from the South American Atlantic Rainforest in Brazil. We constructed a database including 75 sequences from Geophagus brasiliensis from the Ubatiba river with 540bp of the mtDNA D-loop region using primers H16498 and L15774M and conducted molecular analyses with Geneious v4.82, DnaSP v5, Arlequin v3.5 and PopART. Our results point show that although G. brasiliensis is considered as a territorialist species, which exhibits parental care and small movement rates, population genetic structure could not be observed along the sample area, suggesting the existence of considerable gene flow at least among the sampled populations.

Detection of somatic mutations in the mitochondrial DNA control region D‑loop in brain tumors: The first report in Malaysian patients

Although the role of nuclear-encoded gene alterations has been well documented in brain tumor development, the involvement of the mitochondrial genome in brain tumorigenesis has not yet been fully elucidated and remains controversial. The present study aimed to identify mutations in the mitochondrial DNA (mtDNA) control region D-loop in patients with brain tumors in Malaysia. A mutation analysis was performed in which DNA was extracted from paired tumor tissue and blood samples obtained from 49 patients with brain tumors. The D-loop region DNA was amplified using the PCR technique, and genetic data from DNA sequencing analyses were compared with the published revised Cambridge sequence to identify somatic mutations. Among the 49 brain tumor tissue samples evaluated, 25 cases (51%) had somatic mutations of the mtDNA D-loop, with a total of 48 mutations. Novel mutations that had not previously been identified in the D-loop region (176 A-deletion, 476 C>A, 566 C>A and 16405 A-deletion) were also classified. No significant associations between the D-loop mutation status and the clinicopathological parameters were observed. To the best of our knowledge, the current study presents the first evidence of alterations in the mtDNA D-loop regions in the brain tumors of Malaysian patients. These results may provide an overview and data regarding the incidence of mitochondrial genome alterations in Malaysian patients with brain tumors. In addition to nuclear genome aberrations, these specific mitochondrial genome alterations may also be considered as potential cancer biomarkers for the diagnosis and staging of brain cancers.

Decreased Methylation of the Mitochondrial D-Loop Region in Late-Onset Alzheimer's Disease.

Mitochondrial impairment is a feature of neurodegeneration and many investigators have suggested that epigenetic modifications of the mitochondrial DNA (mtDNA) might be involved in late-onset Alzheimer's disease (LOAD), but evidence in humans is limited. We assessed the methylation levels of the mtDNA D-loop region in blood DNA from 133 LOAD patients and 130 controls, observing a significant 25% reduction of DNA methylation levels in the first group (2.3 versus 3.1%). Overall, the present data indicate that there is a decreased methylation of the D-loop region in LOAD peripheral blood DNA, suggesting that mtDNA epimutations deserve further investigations in AD pathogenesis.

CAPABILITY OF MITOCHONDRIA DNA D-LOOP MARKERS FOR SHARK SPECIES IDENTIFICATION

ldentification of dry-fin shark was conducted by mitochondria DNA (mtDNA) D-loop markers. Eighteen of thiity samples have been successfully amplified the mtDNA D-loop region.

Historical gene flow and profound spatial genetic structure among golden pheasant populations suggested by multi-locus analysis

Major histocompatibility complex (MHC) is a good marker system for geographical genetics since they are functional genes in the immune system that are likely to affect the fitness of the individual, and the survival and evolutionary potential of a population in a changing environment. Golden pheasant (Chrysolophus pictus) is a wild Phasianidae distributed in central and north China. In this study, we used a locus-specific genotyping technique for MHC IIB genes of golden pheasant. Combining with microsatellites (simple sequence repeat, SSR) and mitochondrial DNA (mtDNA) D-loop region, we investigated the demographic history and illuminate genetic structure of this bird in detail. SYR (south of Yangtze river) – NYR (north of Yangtze river) lineages, separated by Yangtze River, were defined in genetic structure of MHC IIB. NYR was supposed as refuge during glacial period, suggested by diversity parameters and more ancient alleles in this region. Based on this hypothesis, there was gene flow from NYR to SYR, which was proved by three pieces of evidence: (1) distinct demographic histories of SYR (kept stable) and NYR (experienced expansion); (2) specific affiliation of LC in genetic structure of SSR and MHC genes; (3) significant gene flow from NYR to SYR. Moreover, we also found balancing selection by combination of three Grouping A2’s regions (SC, QL and North) into one in Grouping B4 (NYR) and no pattern of isolation by distance (IBD) found in MHC IIB, whereas for SSR we found a relatively strong and significant IBD. Several mechanisms in the evolution of MHC IIB genes, including recombination, historically positive selection, trans-species evolution and concerted evolution, were shown by molecular and phylogenetic analysis. Overall these results suggest the Yangtze River was inferred to be a geological barrier for this avian and NYR might experience population expansion, which invaded into a neighboring region. This study contributes to the understanding of the effects of geographic features on contemporary patterns of genetic variation in the golden pheasant in China, and helps us to define the adaptive unite (AU) for this avian.

The genetic diversity of chicken breeds from Jiangxi, assessed with BCDO2 and the complete mitochondrial DNA D-loop region.

The Jiangxi Province of China has numerous native domestic chicken breeds, including some black skin breeds. The genetic diversity of Jiangxi native chickens is largely unknown, and specifically, the genetic contribution of the grey junglefowl to black skin chickens is not well understood. To address these questions, the complete D-loop region of the mitochondrial DNA (mtDNA) and beta-carotene dioxygenase 2(BCDO2)gene was sequenced in a total of 209 chickens representing seven Jiangxi native breeds. Thirty-one polymorphic sites were identified across the complete mtDNA D-loop region sequence. Twenty-three haplotypes were observed in the seven breeds, which belonged to four distinct mitochondrial clades (A, B, C and E). Clade A and B were dominant in the chickens with a frequency of approximately 67.9%. There were five SNPs that defined two haplotypes, W and Y in BCDO2. Four breeds had one haplotype and three breeds had two. We conclude that Jiangxi native chicken breeds have relatively low genetic diversity and likely share four common maternal lineages from two different maternal ancestors of junglefowl. Furthermore, some Jiangxi chicken populations may have been mixed with chickens with exotic lineage. Further research should be established to protect these domestic chicken resources.

Maternal Phylogenetics of Some Anatolian Cattle Breeds

In the current study, the mtDNA D-Loop region was analyzed in South Anatolian Red (SAR, n=51), Anatolian Black (NB, n=50), Anatolian Grey (AG, n=54), Native Southern Anatolian Yellow (NSAY, n=51), East Anatolian Red (EAR, n=54) and Zavot (ZAV, n=19) cattle breeds (n=279) to reveal diversity of mitochondrial DNA, differentiation of breeds, and relevance between genetic differentiations and geographic distributions. Blood samples were collected from native cattle breeds. Genomic DNA was isolated using a standard phenol/chloroform method. MtDNA D-loop region was amplified by PCR. After mtDNA sequence analysis, sequence of the D-Loop region was aligned with reference sequence. Haplotypes were determined and phylogenetic tree was constructed using BioEdit version 5.0.6, DNAsp version 5.10.01, MEGA 4.0 Network, Arlequin, Phylip and TreeView software. The sequence data was examined for nucleotide and haplotypes diversity, genetic distance between breeds visualized with Neighbor Joining tree and Median Joining Network, evaluated with mismatch distribution analyses, neutrality tests and AMOVA analyses. As a result in comparison with cattle breeds throughout the world, the higher nucleotide (π=0.02240, ±0.0005) and haplotype diversity (H=0.9966, ±0.0006) higher haplotype number and also high genetic variation within and between the populations were determined in native Anatolian cattle breeds. These findings support the idea that Anatolia has been situated in a central position during the domestication process of the cattle species.