scholarly journals Variability of mitochondrial DNA D-loop sequences in Zabaikalskaya horse breed

2021 ◽  
Vol 25 (5) ◽  
pp. 486-491
Author(s):  
L. A. Khrabrova ◽  
N. V. Blohina ◽  
B. Z. Bazaron ◽  
T. N. Khamiruev
Keyword(s):  
Mitochondrial Dna ◽  
Hypervariable Region ◽  
Composite Likelihood ◽  
Dna Polymorphisms ◽  
Nucleotide Position ◽  
Horse Breed ◽  
Bootstrap Analysis ◽  
Genetic Characteristics ◽  
Hair Samples ◽  
D Loop

The Zabaikalskaya horse is an indigenous breed of horses from Siberia with diverse use. It is characterized by e durance 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 identified 31 haplotypes representing 8 haplogroups: B, C, G, H, L, M, Q and R according to modern classification. 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.

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

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 155
Author(s):  
Kefena Effa ◽  
Sonia Rosenbom ◽  
Jianlin Han ◽  
Tadelle Dessie ◽  
Albano Beja-Pereira
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Differentiation ◽  
Sequence Divergence ◽  
Dna Polymorphisms ◽  
Base Pairs ◽  
Feral Horses ◽  
Domestic Horses ◽  
D Loop ◽  
Diversity Estimates

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.

scholarly journals Mitochondrial DNA-based diversity study of Hungarian brown hares (Lepus europaeus Pallas 1778)

2016 ◽  
pp. 23-29
Author(s):  
Noémi Soós ◽  
Szilvia Kusza
Keyword(s):  
Mitochondrial Dna ◽  
Large Scale ◽  
Haplotype Diversity ◽  
Lepus Europaeus ◽  
Brown Hare ◽  
High Genetic Diversity ◽  
Ongoing Research ◽  
European Continent ◽  
Hair Samples ◽  
D Loop

The brown hare being an important game species which is widespread across the European continent has been in focus of many population genetic studies. However only a few comprising researches can be found on the diversity of Central-European populations. The aim of our large scale long term ongoing study is to fill this gap of information on the species by describing the genetic history and structure of the brown hare populations of the area using both mitochondrial DNA markers and genomic skin and hair colour regulating genes. This article gives forth a part of our results concerning the mitochondrial DNA diversity of Hungarian brown hares based on amplification of a 512 bp long D-loop sequence. N=39 tissue or hair samples have been collected from 15 sampling sites on the Hungarian Great Plain. We have described a high level of haplotype diversity (Hd=0.879±0.044) based on a 410 bp alignment of our sequences. We have found 17 haplotypes within our sample set with the nucleotid diversity of π=0.01167±0.0022. Our ongoing research shows high genetic diversity for the brown hare in the studied region and a second alignment with 156 sequences downloaded from GenBank indicates a geographic pattern of haplotypes among the studied populations though these results need confirmation by our further analyses.

scholarly journals Coincidences between molecular genetic and studbook data of gidrán mare families on the basis of mtDnA

2015 ◽  
pp. 69-73
Author(s):  
Nikolett Sziszkosz ◽  
Szilvia Kusza ◽  
András Jávor ◽  
Sándor Mihók
Keyword(s):  
Molecular Genetic ◽  
Point Of View ◽  
Horse Breed ◽  
Bottleneck Effect ◽  
Hair Samples ◽  
D Loop ◽  
Loop Regions ◽  
Show Jumping ◽  
Mtdna Markers ◽  
Made In

The traditional Hungarian horse breed, Gidran has been close to the edge of extinction several times. Despite the multiple bottleneck effect, the breed has retained a part of its genetic variability, and performed prominently in carriage driving and show-jumping competitions. Maintaining of the Gidran breed is important in the point of view of world heritage; because besides Hungary, smaller Gidran populations exist only in Bulgaria and Romania. Taking advantage of the special inheritance features of mtDNA, our study focused on two mtDNA regions of Gidran mares. Altogether, 251 hair samples from various Hungarian studs were examined. The analysis was successfully made in case of 251 samples of the cytochrome b and in case of 246 samples of D-loop regions. Because of the distinct mutation rates of the two mtDNA markers, the number of the haplotypes and the way of grouping samples into haplotypes was different. Our key finding was that most haplotypes may be compatible with mare families of the stud book; however incidental mistakes in stud book have occurred only in a few cases. Our results indicate the importance of the preservation and breeding those mare families, which are molecular genetically more diverse than the others, and are in the edge of extinction.

scholarly journals Effects of Hair dyes on Sequence Analysis of Hair Mitochondrial DNA Hypervariable Region 1

2017 ◽  
Vol 11 (1) ◽  
pp. 61-66
Author(s):  
Halah Al-summarraie ◽  
Mohammed Al-Zubaidi ◽  
Dhuha Salim نعمة ◽  
Sura Nabeel Hameed ◽  
Thooalnoon Younes Saleh ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Sequence Analysis ◽  
Dna Extraction ◽  
Hypervariable Region ◽  
Hair Shaft ◽  
Hair Follicles ◽  
Hair Dyes ◽  
Hypervariable Region 1 ◽  
Hair Samples ◽  
The Impact

Hair can be a valuable source of DNA especially in forensic casework and for noninvasive studies of human, when blood samples not available. This study emphasizes the impact of hair dyes on DNA sequence analysis. Samples collected from forty Iraqi families; each sample was divided in to two parts hair follicles and hair shaft. DNA extracted by using two different techniques, Phenol-chloroform (organic) method and prepFiler forensic DNA extraction kit. After quantification of DNA by real time PCR to confirm the exact DNA yield, Mitochondrial DNA (MtDNA) hypervariable region 1 successfully amplified from (50% of samples include hair follicle and 20% samples include shaft only), which all extracted  by organic method. Whereas by using prepFiler kit the ratio of amplification success reach to 95% of samples included hair follicles, but there wais no DNA outcome from hair shaft by using this kit. Our results demonstrate that treated hair by dyed or henna had a significant influence on the sequence analysis results. Organic method was an appropriate method for extraction DNA from hair shaft, since this method used for extracting the old and degraded samples. While prepFiler DNA extraction kit was more convenient for isolation DNA from, hair samples included follicles only with excellent result.

Genetic characteristics of endangered Japanese golden eagles (Aquila chrysaetos japonica) based on mitochondrial DNA D-loop sequences and karyotypes

Zoo Biology ◽  
1998 ◽  
Vol 17 (2) ◽  
pp. 111-121 ◽  
Author(s):  
Ryuichi Masuda ◽  
Miyuki Noro ◽  
Naoko Kurose ◽  
Chizuko Nishida-Umehara ◽  
Hideo Takechi ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Aquila Chrysaetos ◽  
Genetic Characteristics ◽  
Golden Eagles ◽  
D Loop

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

TREUBIA ◽  
2020 ◽  
Vol 47 (2) ◽  
pp. 99-110
Author(s):  
Jarulis Jarulis ◽  
Dedy Duryadi Solihin ◽  
Ani Mardiastuti ◽  
Lilik Budi Prasetyo
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Distance ◽  
Captive Breeding ◽  
Genetic Distances ◽  
Nucleotide Polymorphisms ◽  
Genetic Characteristics ◽  
Group I ◽  
Loop Sequence ◽  
Spin Column ◽  
D Loop

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.  

scholarly journals Genetic relationships between local Brazilian goat breeds based on mtDNA D-loop region similarity

2020 ◽  
Vol 17 (4) ◽  
pp. e0407 ◽  
Author(s):  
Núbia M. V. Silva ◽  
Edgard C. Pimenta-Filho ◽  
Janaina K. G. Arandas ◽  
Rosália B. N. Medeiros ◽  
Aderbal Cavalcante-Neto ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Population Structure ◽  
Genetic Relationships ◽  
Hypervariable Region ◽  
Genetic Composition ◽  
Mitochondrial Lineage ◽  
Breeding Programs ◽  
Loop Region ◽  
Population Structure Analysis ◽  
D Loop

Aim of study: Our objective was to investigate the mitochondrial DNA of local Brazilian goats to gain insights into the genetic composition of this precious genetic resource.Area of study: The study was developed in BrazilMaterial and methods: We analyzed a hypervariable region of the mitochondrial DNA of 83 goats belonging to four local Brazilian breeds, including Canindé (CAN-RN), Moxotó (MOX-CE), Marota (MAR-PI) and Azul (AZU-PE) as well as of exotic breeds raised in different states of the Federation. Sequences related to local Brazilian goats showed a dispersed distribution throughout the median-joining network, and clustering with sequences of exotic breeds occurred in some haplotypes. The obtained sequences were analyzed and compared with different haplogroups (A, B1, B2, C, D, F, and G) available on GenBank.Main results: The local Brazilian goat breeds showed significant diversity, with 16 (0.8240) haplotypes. Population structure analysis revealed substantial differences among breeds (p < 0.05). Mitochondrial lineage A was observed in Brazilian goats. Phylogeny showed European goats as the dominant stock for Brazilian goats, but there weare some haplotypes within haplogroup A, clustering with African and Asian haplotypes.Research highlights: These results could be suitable for creating a strategic conservation program, potentially benefitting future breeding programs.

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