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

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.

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Mitochondrial DNA D-loop sequence variability reveals high haplotype diversity and multiple maternal origins in twelve indigenous goat populations from Tanzania.

10.22541/au.161478201.16689055/v1 ◽

2021 ◽

Author(s):

Athumani Nguluma

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Haplotype Diversity ◽

Capra Hircus ◽

Maternal Origin ◽

High Genetic Diversity ◽

Ecological Zones ◽

Goat Population ◽

D Loop ◽

Indigenous Goats

The Small East African (SEA) goat (Capra hircus) breeds 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 goats populations, namely Fipa (n = 44), Songwe (n = 34), Tanga (n = 33), Pwani (n = 40), Newala (n = 49), Lindi (n = 46), Gogo (n = 73), Pare (n = 67), Maasai (n = 72), Sukuma (n = 67), and Ujiji (n = 67), based on the mitochondrial DNA (mtDNA) D-loop. High haplotype (Hd = 0.9619-0.9945) and nucleotide (π = 0.0120-0.0162) diversities were revealed from a total of 389 haplotypes. The majority of the haplotypes (h = 334) drawn from all the goat populations 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.

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Large-scale mitochondrial DNA analysis reveals new light on the phylogeography of Central and Eastern-European Brown hare (Lepus europaeus Pallas, 1778)

PLoS ONE ◽

10.1371/journal.pone.0204653 ◽

2018 ◽

Vol 13 (10) ◽

pp. e0204653 ◽

Cited By ~ 2

Author(s):

Mohammad Reza Ashrafzadeh ◽

Mihajla Djan ◽

László Szendrei ◽

Algimantas Paulauskas ◽

Massimo Scandura ◽

...

Keyword(s):

Mitochondrial Dna ◽

Large Scale ◽

Dna Analysis ◽

Lepus Europaeus ◽

Eastern European ◽

Brown Hare ◽

European Brown Hare ◽

Mitochondrial Dna Analysis

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The genetic profiles and maternal origin of local sheep breeds on Java Island (Indonesia) based on complete mitochondrial DNA D-loop sequences

Veterinary World ◽

10.14202/vetworld.2020.2625-2634 ◽

2020 ◽

Vol 13 (12) ◽

pp. 2625-2634

Author(s):

Alek Ibrahim ◽

I Gede Suparta Budisatria ◽

Rini Widayanti ◽

Wayan Tunas Artama

Keyword(s):

Mitochondrial Dna ◽

Genetic Relationships ◽

Haplotype Diversity ◽

Maternal Origin ◽

Loop Analysis ◽

High Genetic Diversity ◽

Sheep Breeds ◽

Loop Region ◽

D Loop ◽

Genetic Profiles

Background and Aim: Java Island is one of the islands in Indonesia which has local sheep breeds with specific characteristics and native development geography in certain regions. This study aimed to determine the genetic profiles and maternal origin of six local sheep breeds on Java Island. Materials and Methods: This study was conducted by identifying the profiles of complete mitochondrial DNA (mtDNA) displacement loop (D-loop) region sequences on a total of 22 individual in six local sheep breeds on Java Island, including Javanese thin-tailed (JTT), Javanese Fat-Tailed (JFT), Batur (BTR), Wonosobo (WSB), Garut (GRT), and Priangan (PRG) sheep. The D-loop region was amplified using specific primers, and the polymerase chain reaction (PCR) was performed. The PCR products were purified and sequenced. Results: The mtDNA D-loop analysis identified 21 haplotypes in the analyzed 22 animals with 123 polymorphic sites (V) consisting of 60 singleton variable sites (S) and 63 parsimony informative sites (P). Within all breeds tested, the haplotype diversity, the average number of pairwise differences (K), and nucleotide diversity (Pi) were 0.99567, 25.36364, and 0.02153, respectively. The genetic distance (D) within groups and between groups was 0.001-0.006 and 0.004-0.036, respectively. The phylogeny resulted in the presence of two haplogroups (Hap), which are 5 Hap A and 16 Hap B. All JTT, JFT, BTR, and WSB breeds were in the same cluster in Hap B, whereas GRT and PRG breeds were in clusters in both Hap A and Hap B. Conclusion: The high genetic diversity in six local sheep breeds on Java Island suggests that they originated from different genetic sources. JTT sheep have closer genetic relationships to JFT, BTR, and WSB sheep, and they are close to European sheep, whereas GRT sheep have closer genetic relationships to PRG sheep. Both are closer to Asian sheep than to European sheep.

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

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj21.055 ◽

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.

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

Scientific Reports ◽

10.1038/s41598-021-81589-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ayano Hata ◽

Mitsuo Nunome ◽

Thanathip Suwanasopee ◽

Prateep Duengkae ◽

Soontorn Chaiwatana ◽

...

Keyword(s):

Southeast Asia ◽

Evolutionary History ◽

Large Scale ◽

Large Population ◽

High Genetic Diversity ◽

Indigenous Chickens ◽

Red Junglefowl ◽

Loop Sequence ◽

Multiple Regions ◽

D Loop

AbstractIn 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.

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Preliminary results of the phylogenetic analysis of European hare (Lepus europaeus)

Acta Agraria Debreceniensis ◽

10.34101/actaagrar/61/2051 ◽

2014 ◽

pp. 99-104

Author(s):

Blanka Mező ◽

Szilvia Kusza

Keyword(s):

Genetic Structure ◽

Genetic Variants ◽

Dna Analysis ◽

Lepus Europaeus ◽

Brown Hare ◽

Agricultural Activities ◽

Wide Spread ◽

European Hare ◽

Mitochondrial Dna Analysis ◽

D Loop

Brown hare (Lepus europaeus) is one of the most wide spread mammal in Europe. Its genetic structure is affected not only by last glacial, even by human activities (hunting, agricultural activities), isolation of such areas or competing for food resources. According to literature datas brown hare populations has different genetic variants in Europe, however its evolution, phylogenetics has not studied well. The main goal of this work was to know genetic structure of some brown hare. Mitochondrial DNA analysis was performed in two regions (D-loop, 513 bp and cytochrome-b, 1183 bp). Genetic distance values and Network analysis were calculated. NCBI Genbank was used for further sequences. Our results showed that Italian samples differed from the Genbank samples. We found two main clades: 1: Greece without islands; Bulgaria, Italy and Central-Europe; 2: East-Macedonia,Greece with islands, Cyprus and North Israel.

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Mitochondrial Sequence Variation, Haplotype Diversity, and Relationships Among Dromedary Camel-Types

Frontiers in Genetics ◽

10.3389/fgene.2021.723964 ◽

2021 ◽

Vol 12 ◽

Author(s):

Randa Alaqeely ◽

Bader H. Alhajeri ◽

Faisal Almathen ◽

Hasan Alhaddad

Keyword(s):

Sequence Variation ◽

Haplotype Diversity ◽

Dromedary Camel ◽

Nuclear Markers ◽

Mitochondrial Region ◽

Hair Samples ◽

D Loop ◽

Almost All ◽

Future Work ◽

Tail Hair

Dromedary camels are outstanding livestock that developed efficient abilities to tolerate desert conditions. Many dromedary camel-types (i.e., named populations) exist but lack defined specific breed standards, registries, and breeders’ governing organizations. The breed status of dromedary camel-types can partly be assessed by exploring mitochondrial DNA (mtDNA) variation. Accordingly, this study aimed to examine the breed status and the inter-population relationships of dromedary camel-types by analyzing sequence variation in the mtDNA control region and in three coding genes [cytochrome b, threonine, and proline tRNA, and part of the displacement loop (D-loop)] (867 bp region). Tail hair samples (n = 119) that represent six camel-types from Kuwait were collected, extracted, sequenced, and compared to other publicly available sequences (n = 853). Within the sequenced mitochondrial region, 48 polymorphic sites were identified that contributed to 82 unique haplotypes across 37 camel-types. Haplotype names and identities were updated to avoid previous discrepancies. When all sequences were combined (n = 972), a nucleotide diversity of 0.0026 and a haplotype diversity of 0.725 was observed across the dromedary-types. Two major haplogroups (A and B) were identified and the B1 haplotype was predominant and found in almost all dromedary-types whereas the A haplotypes were more abundant in African regions. Non-metric multidimensional scaling revealed an increased similarity among Arabian Peninsula “Mezayen” camel-types, despite their defining coat colors. The relationships among dromedary camel-types can partly be explained by mtDNA. Future work aimed at a deeper understanding of camel-type breed status should focus on a high number of nuclear markers.

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