Mitochondrial DNA D-loop Research Articles

Mitochondrial DNA D-loop sequence analysis reveals high variation and multiple maternal origins of indigenous Tanzanian goat populations.

The Small East African (SEA) goat are widely distributed in different agro‐ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goat populations, namely Fipa, Songwe, Tanga, Pwani, Iringa, Newala, Lindi, Gogo, Pare, Maasai, Sukuma, and Ujiji, based on the mitochondrial DNA (mtDNA) D‐loop. High haplotype (H d = 0.9619–0.9945) and nucleotide (π = 0.0120–0.0162) diversities were observed from a total of 389 haplotypes. The majority of the haplotypes (n = 334) belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B, and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro‐ecological regions of the country.

Rapid authenticity testing of artificially bred green turtles (Chelonia mydas) using microsatellite and mitochondrial DNA markers.

Sea turtles are threatened by climate change and human activity, and their global populations continue to decline sharply. The Chinese government encourages artificial breeding of sea turtles to reduce the use of wild populations. However, artificial breeding of sea turtles is still fairly difficult, and some facilities may illegally purchase wild turtle eggs and then sell incubated turtles by marketing them as artificially bred turtles, which adds another threat to an already endangered species. Therefore, it is necessary to find a reliable method to distinguish the authenticity of artificially bred individuals. In this study, we investigated a turtle farm in southern China, that contained more than 400 green turtles, which were claimed to have been bred in captivity. Parentage testing of turtles from this farm was successfully conducted using two nuclear microsatellites combined with a mitochondrial D-loop DNA marker. Genetic matching of all 19 adults and randomly selected 16 juvenile turtles revealed that none of the juvenile turtles had a matching parent combination among the adult turtles. Therefore, we speculated that the green turtles in this farm were from the wild and that their origin of birth was mainly the Sulu Sea. The methods and molecular markers used in this study could be a reference for rapid authenticity testing of green turtles in future forensic enforcement and population management.

Genetic Diversity of Nepalese Indigenous Cattle Breeds Based on D-Loop Mitochondrial DNA

Nepalese cattle are known for their genetic potentiality concerning inhabitant in extreme climatic conditions, surviving in the scarce food supply, and resistant to several diseases. We aimed to assess Nepal’s ancestral origin and genetic diversity of indigenous cattle breeds based on hyper-variable D loop mtDNA sequences. Three cattle breeds (Siri, Achammi, & Lulu) comprising the total sample population (n= 75) were employed in the study where the mt DNA information of two breeds (Achammi & Lulu) were retrieved from the published source. Hyper-variable D loop (910bp) of Siri cattle was PCR amplified and sequenced. This study claims that the possible ancestral origin of Bos taurus and Bos indicus mtDNA lineage in the Nepalese cattle population is majorly influenced by China and India, respectively. This study suggests that Nepalese cattle can be divided into two major groups: Bos taurus and Bos indicus, where most of the cattle population was of Bos indicus origin. The sampled population can be classified into three significant haplogroups: T3 (25%), I1 (48%), and I2 (27%) revealing a higher genetic diversity among the Nepalese cattle population. Only T3 taurine haplogroup was found in the sampled population. It was consistent with the fact that the absence of T1 haplogroup in North-East Asian cattle. In terms of Bos indicus, the I1 haplogroup was dominant over I2. Higher genetic diversity can be appropriate reasoning for Nepalese cattle’s survival in a harsh environment and low food conditions.

Вариабельность последовательности D-петли митохондриальной ДНК у лошадей забайкальской породы.

The Zabaikalskaya horse is an indigenous breed of horses from Siberia with diverse use. It is characterized by endurance and good adaptability to year-round herd maintenance in the harsh conditions of the Baikal steppes. To determine the genetic characteristics of the maternal lineage of the Zabaikalskaya horse breed based on mitochondrial DNA polymorphisms, we collected hair samples from 31 horses belonging to breeding farms in the Trans-Baikal Territory. Analysis of the 530 bp sequence of the mtDNA D-loop was performed using the maximum composite likelihood (MCL) model in combination with bootstrap analysis. When studying the polymorphism of the hypervariable region of the mtDNA D- loop in Zabaikalskaya horses, we identif ied 31 haplotypes representing 8 haplogroups: B, C, G, H, L, M, Q and R according to modern classif ication. The sequenced fragment of the D-loop from nucleotide position 15471 to 16000 contained 17 polymorphic sites, mainly represented by the A→G, G→A and T→C transitions. The haplogroups Q (25.81 %), B (19.35 %), G (16.13 %) and H (12.90 %) were prevailing in the mtDNA structure of this breed. Genetic analysis of the mitochondrial genome of the Zabaikalskaya horse revealed a high level of diversity of haplotypes and haplogroups, which are typical for the horse populations of Eurasia.

Phylogenetic analysis of combined lobular and ductal carcinoma of the breast.

Breast cancer manifests in diverse forms, with particular reference to various cell types harboring different mutations and gene expression profiles. To elucidate the clonal relationship between cancer cells in tumors composed of both ductal and lobular phenotypes, two combined lobular and ductal carcinoma (CLDC) cases were analyzed, including one mixed ductal-lobular carcinoma (MDL) lesion, by direct sequencing of the mitochondrial DNA D-loop, digital PCR targeting of chromosomes 1q and 16q, as well as next-generation sequencing. DNA was extracted from formalin-fixed paraffin-embedded tissue sections of different histological types, including invasive ductal carcinoma, invasive lobular carcinoma, ductal carcinoma in situ, lobular carcinoma in situ, flat epithelial atypia, non-neoplastic mammary gland and extramammary organs, using laser-assisted microdissection. Mutations detected by the comprehensive cancer panel were validated by SYBR green allele-specific quantitative PCR (RRM1, AKT1, PIK3CA, RALGDS, EGFR, TP53, IL21R, DPYD, SGK1, CDH1, TIMP3 and KMT2C). CLDC, which shared the basic genetic alterations of 1q gain or 16q loss, progresses to invasive lobular or ductual carcinoma with the accumulation of further mutations. Cancer cells contained in an MDL lesion shared closely related genetic alterations, suggesting that these cells have the same origin, despite different histological features, namely ‘lobular’ or ‘ductal’. By contrast, multiple lesions located away from the main tumor, diagnosed as CLDC (excluding an MDL lesion) were not always identical with different genetic alterations, despite being diagnosed as ductal carcinoma in situ. Thus, MDL should be defined as a distinct category separate from CLDC, whose components of ‘lobular’ and ‘ductal’ may have the same cellular origin.

Maternal Phylogenetic Relationships and Genetic Variation among Rare, Phenotypically Similar Donkey Breeds.

The mitochondrial DNA (mtDNA) D-loop of endangered and critically endangered breeds has been studied to identify maternal lineages, characterize genetic inheritance, reconstruct phylogenetic relations among breeds, and develop biodiversity conservation and breeding programs. The aim of the study was to determine the variability remaining and the phylogenetic relationship of Martina Franca (MF, with total population of 160 females and 36 males), Ragusano (RG, 344 females and 30 males), Pantesco (PT, 47 females and 15 males), and Catalonian (CT) donkeys by collecting genetic data from maternal lineages. Genetic material was collected from saliva, and a 350 bp fragment of D-loop mtDNA was amplified and sequenced. Sequences were aligned and evaluated using standard bioinformatics software. A total of 56 haplotypes including 33 polymorphic sites were found in 77 samples (27 MF, 22 RG, 8 PT, 19 CT, 1 crossbred). The breed nucleotide diversity value (π) for all the breeds was 0.128 (MF: 0.162, RG: 0.132, PT: 0.025, CT: 0.038). Principal components analysis grouped most of the haplogroups into two different clusters, I (including all haplotypes from PT and CT, together with haplotypes from MF and RG) and II (including haplotypes from MF and RG only). In conclusion, we found that the primeval haplotypes, haplogroup variability, and a large number of maternal lineages were preserved in MF and RG; thus, these breeds play putative pivotal roles in the phyletic relationships of donkey breeds. Maternal inheritance is indispensable genetic information required to evaluate inheritance, variability, and breeding programs.

Limited Heredity Diversity of the Critically Endangered Guizhou Golden Monkeys

Guizhou golden monkey (Rhinopithecus brelichi) was a unique, endangered and endemic primate species in Guizhou Province. It was an isolated population caused by habitat loss and fragmentation due to the human disturbance in the recently 30 years in China, only distributed in Fanjingshan National Natural Reserve, Guizhou Province. To know the background with demonic population structure, we sequenced 867 bp of the mitochondrial DNA D-loop from 312 fresh fecal samples, results showed there 11 haplotypes among these samples, h was 0.517, π was 0.00413. It indicated that this species had the lowest genetic diversity among four golden monkeys in China and need strengthen the conversation concern for this species immediately.

A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?

There are particular challenges in defining the taxonomic status of recently radiated groups due to the low level of phylogenetic signal. Members of the Salmo trutta species-complex, which mostly evolved during and following the Pleistocene, show high morphological and ecological diversity that, along with their very wide geographic distribution, have led to morphological description of 47 extant nominal species. However, many of these species have not been supported by previous phylogenetic studies, which could be partly due to lack of significant genetic differences among them, the limited resolution offered by molecular methods previously used, as well as the often local scale of these studies. The development of next-generation sequencing (NGS) and related analytical tools have enhanced our ability to address such challenging questions. In this study, Genotyping-by-Sequencing (GBS) of 15,169 filtered SNPs and mitochondrial DNA (mtDNA) D-loop sequences were combined to assess the phylogenetic relationships among 166 brown trouts representing 21 described species and three undescribed groups collected from 84 localities throughout their natural distribution in Europe, west Asia, and North Africa. The data were analysed using different clustering algorithms (admixture analysis and discriminant analysis of principal components-DAPC), a Bayes Factor Delimitation (BFD) test, species tree reconstruction, gene flow tests (three- and four-population tests), and Rogue taxa identification tests. Genomic contributions of the Atlantic lineage brown trout were found in all major sea basins excluding the North African and Aral Sea basins, suggesting introgressive hybridization of native brown trouts driven by stocking using strains of the Atlantic lineage. After removing the phylogenetic noise caused by the Atlantic brown trout, admixture clusters and DAPC clustering based on GBS data, respectively, resolved 11 and 13 clusters among the previously described brown trout species, which were also supported by BFD test results. Our results suggest that natural hybridization between different brown trout lineages has probably played an important role in the origin of several of the putative species, including S. marmoratus, S. carpio, S. farioides, S. pellegrini, S. caspius (in the Kura River drainage) and Salmo sp. in the Danube River basin. Overall, our results support a multi-species taxonomy for brown trouts. They also resolve some species in the Adriatic-Mediterranean and Black Sea drainages as members of very closely related genomic clusters that may need taxonomic revision. However, any final conclusions pertaining to the taxonomy of the brown trout complex should be based on an integrative approach combining genomic, morphological, and ecological data. To avoid challenges in taxonomy and conservation of species complexes like brown trouts, it is suggested to describe species based on genomic clusters of populations instead of describing species based only on morphologically differentiated single type populations.

Genetic diversity of the Nubian ibex in Oman as revealed by mitochondrial DNA.

The Nubian ibex (Capra nubiana) is patchily distributed across parts of Africa and Arabia. In Oman, it is one of the few free-ranging wild mammals found in the central and southern regions. Its population is declining due to habitat degradation, human expansion, poaching and fragmentation. Here, we investigated the population's genetic diversity using mitochondrial DNA (D-loop 186 bp and cytochrome b 487 bp). We found that the Nubian ibex in the southern region of Oman was more diverse (D-loop HD; 0.838) compared with the central region (0.511) and gene flow between them was restricted. We compared the genetic profiles of wild Nubian ibex from Oman with captive ibex. A Bayesian phylogenetic tree showed that wild Nubian ibex form a distinct clade independent from captive animals. This divergence was supported by high mean distances (D-loop 0.126, cytochrome b 0.0528) and high FST statistics (D-loop 0.725, cytochrome b 0.968). These results indicate that captive ibex are highly unlikely to have originated from the wild population in Oman and the considerable divergence suggests that the wild population in Oman should be treated as a distinct taxonomic unit. Further nuclear genetic work will be required to fully elucidate the degree of global taxonomic divergence of Nubian ibex populations.

Subspecies Identification of Captive Gentoo Penguins in Japan, Using Mitochondrial DNA Phylogeny for Their Pedigree Management

The Gentoo Penguins Pygoscelis papua has been classified into two subspecies, Northern P. papua papua and Southern P. papua ellsworthi. In Japan, where a breeding program exists for Gentoo Penguins, the Japanese Association of Zoos and Aquariums (JAZA) has recognized three categories of species in its pedigree ledger: Northern (from the islands of South Georgia), Southern (from the South Shetland Islands), and Unknown (when their origins are not clear). Phylogenetic analyses of the mitochondrial DNA (mtDNA) D-loop region of Gentoo Penguins in their natural habitat have differentiated them as belonging to the Kerguelen Islands (Indian Ocean), Falkland Islands (Atlantic Ocean), and South Georgia (Atlantic Ocean), and categorized some as Northern and others as Southern subspecies. However, the identification of a third subspecies has been suggested. Therefore, reclassification of captive Gentoo Penguins using phylogenetic analysis is necessary for domestic subspecies pedigree management. In this study, we determined five mtDNA haplotype sequences using seven Gentoo Penguins (considered morphologically as three Northern, three Southern, and one Unknown) and characterized their phylogenetic relationships among subspecies and among geographical distributions including 56 published mtDNA sequences. The phylogenetic tree showed three major lineages, Kerguelen Islands, Falkland Islands, and Scotia Arc/Antartica. The five haplotype sequences of the seven captive Gentoo Penguins were classified unexpectedly to one lineage, the Scotia Arc/Antartica, which contains the nucleotide sequences derived from Southern P. papua ellsworthi. Therefore, the mtDNA phylogeny of the seven captive penguins suggests that all captive Gentoo Penguins in Japan belong to the Southern subspecies. If so, then more comprehensive genetic testing of Gentoo Penguins in Japanese aquariums and zoos is required for the management of successful breeding programs.

Mitochondrial DNA diversity and demographic history of Black-boned chickens in China

Black-boned chickens (Gallus domesticus, herein abbreviated BBCs) are well known for their unique appearance and medicinal properties and have a long breeding history in China. However, the genetic diversity and demographic history of BBCs remain unclear. In this study, we analyzed 844 mitochondrial DNA D-loop sequences, including 346 de novo sequences and 498 previously published sequences from 20 BBC breeds. We detected a generally high level of genetic diversity among the BBCs, with average haplotype and nucleotide diversities of 0.917 ± 0.0049 and 0.01422, respectively. Nucleotide diversity was highest in populations from Southwest China (0.01549 ± 0.00026), particularly in Yunnan Province (0.01624 ± 0.00025). Significant genetic divergence was detected between most breeds, particularly between Yunnan chickens and those from all other provinces. Haplogroups F and G had the highest levels of genetic diversity and were restricted to Southwest China, particularly Yunnan Province. Based on neutrality tests and mismatch distribution analyses, we did not obtain evidence for rapid population expansions and observed similar demographic histories in BBCs and local non-BBCs. Our results suggest that Chinese BBCs have complex breeding histories and may be selected in situ from local domestic chickens. These results improve our understanding of the genetic heritage and breeding histories of these desirable chickens.

Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers.

The African cattle provide unique genetic resources shaped up by both diverse tropical environmental conditions and human activities, the assessment of their genetic diversity will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the genetic diversity of cattle samples from Nigeria using both maternal and paternal DNA markers. Nigerian cattle can be assigned to 80 haplotypes based on the mitochondrial DNA (mtDNA) D-loop sequences and haplotype diversity was 0.985 + 0.005. The network showed two major matrilineal clustering: the dominant cluster constituting the Nigerian cattle together with other African cattle while the other clustered Eurasian cattle. Paternal analysis indicates only zebu haplogroup in Nigerian cattle with high genetic diversity 1.000 ± 0.016 compared to other cattle. There was no signal of maternal genetic structure in Nigerian cattle population, which may suggest an extensive genetic intermixing within the country. The absence of Bos indicus maternal signal in Nigerian cattle is attributable to vulnerability bottleneck of mtDNA lineages and concordance with the view of male zebu genetic introgression in African cattle. Our study shades light on the current genetic diversity in Nigerian cattle and population history in West Africa.

Investigation of the D-loop sequence of mitochondrial DNA of the Volgograd sheep breed

The paper presents the results of studies of the sequence of the D-loop of mitochondrial DNA of the Volgograd sheep breed. Mitochondrial DNA has a number of unique features that make it possible to effectively use markers based on it in phylogenetic studies of a wide range of organisms.

Genetic diversity analysis of Topmouth Culter (Culter alburnus) based on microsatellites and D-loop sequences

Topmouth culter (Culter alburnus) is an economically important fish species distributed in rivers, lakes and reservoirs throughout China. This study focused on the genetic diversity and genetic germplasm resources of C. alburnus populations. We developed a set of 14 polymorphic multi-nucleotide repeat microsatellites using specific locus amplification fragment sequencing (SLAF-seq). Based on microsatellites and mitochondrial DNA D-loop sequences analysis, we identified six C. alburnus populations that had a high level of genetic diversity. Among them, the Xingkai Lake (XKL) population had the lowest genetic diversity, so it might require strengthened protection measures. XKL and Danjiangkou Reservoir (DJKR) populations were relatively closely related, and genetically distant from the remaining four populations. These results shall help us effectively monitor the germplasm resources of C. alburnus and provide scientific guidance for its resource development, utilization and protection.

Genetic Diversities and Historical Dynamics of Native Ethiopian Horse Populations (Equus caballus) Inferred from Mitochondrial DNA Polymorphisms

Matrilineal genetic diversity and relationship were investigated among eight morphologically identified native Ethiopian horse populations using polymorphisms in 46 mtDNA D-loop sequences (454 base pairs). The horse populations identified were Abyssinian, Bale, Borana, Horro, Kafa, Kundido feral horses, Ogaden and Selale. Mitochondrial DNA D-loop sequences were characterized by 15 variable sites that defined five different haplotypes. All genetic diversity estimates, including Reynolds’ linearized genetic distance, genetic differentiation (FST) and nucleotide sequence divergence (DA), revealed a low genetic differentiation in native Ethiopian horse populations. However, Kundido feral and Borana domestic horses were slightly diverged from the rest of the Ethiopian horse populations. We also tried to shed some light on the matrilineal genetic root of native Ethiopian horses from a network constructed by combining newly generated haplotypes and reference haplotypes deposited in the GenBank for Eurasian type Turkish Anatolian horses that were used as a genetic conduit between Eurasian and African horse populations. Ninety-two haplotypes were generated from the combined Ethio-Eurasian mtDNA D-loop sequences. A network reconstructed from the combined haplotypes using Median-Joining algorithm showed that haplotypes generated from native Ethiopian horses formed separate clusters. The present result encourages further investigation of the genetic origin of native African horses by retrieving additional mtDNA sequences deposited in the GenBank for African and Eurasian type horses.

Origin and evolutionary history of domestic chickens inferred from a large population study of Thai red junglefowl and indigenous chickens

In this study, we aimed to elucidate the origin of domestic chickens and their evolutionary history over the course of their domestication. We conducted a large-scale genetic study using mitochondrial DNA D-loop sequences and 28 microsatellite DNA markers to investigate the diversity of 298 wild progenitor red junglefowl (Gallus gallus) across two subspecies (G. g. gallus and G. g. spadiceus) from 12 populations and 138 chickens from 10 chicken breeds indigenous to Thailand. Twenty-nine D-loop sequence haplotypes were newly identified: 14 and 17 for Thai indigenous chickens and red junglefowl, respectively. Bayesian clustering analysis with microsatellite markers also revealed high genetic diversity in the red junglefowl populations. These results suggest that the ancestral populations of Thai indigenous chickens were large, and that a part of the red junglefowl population gene pool was not involved in the domestication process. In addition, some haplogroups that are distributed in other countries of Southeast Asia were not observed in either the red junglefowls or the indigenous chickens examined in the present study, suggesting that chicken domestication occurred independently across multiple regions in Southeast Asia.

Dispersal history of Miniopterus fuliginosus bats and their associated viruses in east Asia.

In this study, we examined the role of the eastern bent-winged bat (Miniopterus fuliginosus) in the dispersion of bat adenovirus and bat alphacoronavirus in east Asia, considering their gene flows and divergence times (based on deep-sequencing data), using bat fecal guano samples. Bats in China moved to Jeju Island and/or Taiwan in the last 20,000 years via the Korean Peninsula and/or Japan. The phylogenies of host mitochondrial D-loop DNA was not significantly congruent with those of bat adenovirus (m2XY = 0.07, p = 0.08), and bat alphacoronavirus (m2XY = 0.48, p = 0.20). We estimate that the first divergence time of bats carrying bat adenovirus in five caves studied (designated as K1, K2, JJ, N2, and F3) occurred approximately 3.17 million years ago. In contrast, the first divergence time of bat adenovirus among bats in the 5 caves was estimated to be approximately 224.32 years ago. The first divergence time of bats in caves CH, JJ, WY, N2, F1, F2, and F3 harboring bat alphacoronavirus was estimated to be 1.59 million years ago. The first divergence time of bat alphacoronavirus among the 7 caves was estimated to be approximately 2,596.92 years ago. The origin of bat adenovirus remains unclear, whereas our findings suggest that bat alphacoronavirus originated in Japan. Surprisingly, bat adenovirus and bat alphacoronavirus appeared to diverge substantially over the last 100 years, even though our gene-flow data indicate that the eastern bent-winged bat serves as an important natural reservoir of both viruses.

Genetic diversity in maternal lines of cognate Mongolian horses of Mongolia, China and Russia

Analysis of D-loop of mitochondrial DNA of 4 populations of Mongolian horses from different origin was conducted. Nowadays Mongolian horses massive is divided to several countries. Among them there are Mongolia, Inner Mongolia part of China, and Kalmyk Republic of Russia. D-loop of mitochondrial DNA gives an inside into the maternal lines of population of horses. I was stated, that maternal lines of 4 populations from different territories have their similarities, as well as differences. More investigations are in need to understand, if similarities can be explained by the same origin of the populations, or due to other horse breeds, involved into the breed’s genesis.

CHARACTERS OF MITOCHONDRIAL DNA D-LOOP HYPERVARIABLE III FRAGMENTS OF INDONESIAN RHINOCEROS HORNBILL (BUCEROS RHINOCEROS) (AVES: BUCEROTIDAE)

The rhinoceros hornbill (Buceros rhinoceros) genetic characteristics consist of nucleotide polymorphisms, haplotypes, genetic distances, and relationships which are important for their conservation effort in Indonesia. We sequenced mitochondrial DNA D-loop hypervariable III fragments from five rhinoceros hornbill individuals at Safari Park Indonesia I and Ragunan Zoo, which were isolated using Dneasy® Blood and Tissue Kit Spin-Column Protocol, Qiagen. D-loop fragment replication was done by PCR technique using DLBuce_F (5'-TGGCCTTTCTCCAAGGTCTA-3') and DLBuce_R (5'-TGAAGG AGT TCATGGGCTTAG-3') primer. Thirty SNP sites were found in 788 bp D-loop sequences of five rhinoceros hornbill individuals and each individual had a different haplotype. The average genetic distance between individuals was 3.09% and all individuals were categorized into two groups (Group I: EC6TS, EC1RG, EC2TS and Group II: EC9TS, EC10TS) with a genetic distance of 3.99%. This result indicated that the two groups were distinct subspecies. The genetic distance between Indonesian and Thai rhinoceros hornbills was 10.76%. Five Indonesian rhinoceros hornbill individuals at Safari Park Indonesia I and Ragunan Zoo probably came from different populations, ancestors, and two different islands. This study can be of use for management consideration in captive breeding effort at both zoos. The D-loop sequence obtained is a useful character to distinguish three rhinoceros hornbill subspecies in Indonesia.

Polymorphisms and haplotype of mitochondrial DNA D-loop region are associated with polycystic ovary syndrome in a Chinese population

Polymorphisms in mitochondrial DNA (mtDNA) have been linked to a range of diseases. Here we investigate the relationship between mtDNA D-loop region polymorphisms, mtDNA haplotype and polycystic ovary syndrome (PCOS), as well as the correlation of D-loop variants and clinical characteristics of PCOS, in a Chinese population. The mtDNA D-loop of whole blood samples from 421 PCOS patients and 409 controls underwent next generation sequencing. The variants G207A (PBH＜0.05), 16036GGins (PBH＜0.05) and 16049Gins (PBH＜0.001) were associated with decreased risk of PCOS. No variants were associated with PCOS, and within the PCOS group, no statistical significance was found between D-loop polymorphisms and clinical characteristics. Patient haplotype was identified from D-loop single nucleotide polymorphisms and analysis suggested that haplotype A15 (P adjusted ＜0.01) was significantly associated with decreased risk of PCOS. In conclusion, mtDNA D-loop alterations and haplotype appear to confer resistance to PCOS in Chinese women.