Sequence analysis of the mitochondrial D-loop region throws a new light on the origin of Hungarian Nonius, Danubian Horse and Serbian Nonius

2021 ◽  
Author(s):  
Georgi Yordanov ◽  
Nebojsa Zlatanovic ◽  
Nadezhda Palova ◽  
Ivan Mehandjyiski ◽  
Boyko Neov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Middle Eastern ◽  
Genetic Profile ◽  
Loop Region ◽  
Central Asian ◽  
High Prevalence ◽  
D Loop ◽  
Genetic Profiles ◽  
G 13

AbstractThe objective of our study was to investigate the genetic structure of yet uninvestigated populations of three closely related horse breeds – the Danubian Horse, the Hungarian Nonius and the Serbian Nonius – in order to clarify their origin and genetic diversity. A 640-bp-long fragment of the mtDNA D-loop region was amplified and sequenced. The results showed that the investigated breeds have different genetic profiles although they share some common characteristics. We identified nine of the 17 haplogroups described in modern horses. Most of the obtained sequences fall into the M, L, G, and O’P lineages, which is indicative of the genetic profile of the ancestral mares that had probably been used at the initial stages of the formation of the breeds. The population of the Danubian Horse is characterised by a high prevalence of the Anatolian specific haplogroup G (45%), followed by the Western Eurasian specific haplogroups L and M (both about 21%). In the Hungarian Nonius breed we found the highest frequency of the Western Eurasian haplogroup M (44%), followed by the Middle Eastern O’P (26%) and the Central Asian specific E (13%) and G (13%). The Serbian Nonius showed a distinct genetic profile, characterised by a high prevalence of the rare European haplogroup D (67%), followed by the Central Asian specific haplogroup G (17%). The high percentage of haplogroups shared especially between the Danubian and the Hungarian Nonius indicates the possibility of a common origin of the two breeds. In contrast, the Serbian Nonius showed a specific genetic profile, which can be explained by a different and independent origin.

scholarly journals Genetic Diversity of Maternal Lineage in the Endangered Kiso Horse Based on Polymorphism of the Mitochondrial DNA D-Loop Region

2014 ◽  
Vol 76 (11) ◽  
pp. 1451-1456 ◽  
Author(s):  
Masaki TAKASU ◽  
Namiko ISHIHARA ◽  
Teruaki TOZAKI ◽  
Hironaga KAKOI ◽  
Masami MAEDA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Maternal Lineage ◽  
Loop Region ◽  
D Loop

Genetic diversity in mitochondrial DNA D-loop region of indigenous pig breeds of India

2022 ◽  
Vol 101 (1) ◽  
Author(s):  
Rongala Laxmivandana ◽  
Yoya Vashi ◽  
Dipjyoti Kalita ◽  
Santanu Banik ◽  
Nihar Ranjan Sahoo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Pig Breeds ◽  
Loop Region ◽  
D Loop

scholarly journals Origin, Genetic Diversity, and Population Structure of Rabbits (Oryctolagus cuniculus) in Kenya

2019 ◽  
Vol 2019 ◽  
pp. 1-6 ◽  
Author(s):  
Sharon Auma Owuor ◽  
Edward George Mamati ◽  
Remmy Wekesa Kasili
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Western Region ◽  
Eastern Region ◽  
Low Genetic Diversity ◽  
Loop Region ◽  
Agriculture Industry ◽  
D Loop ◽  
Breeding Programmes ◽  
Geographic Regions

To evaluate the origin, genetic diversity, and population structure of domesticated rabbits in Kenya, a 263-base pair region of mtDNA D-loop region of 111 rabbits sampled from Kakamega, Vihiga, and Bungoma counties in the western region, Laikipia and Nyandarua counties in the central region, and Kitui, Machakos, and Makueni in the eastern region of the country were analyzed. The average haplotype (0.40702) and nucleotide (0.01494) diversities observed were low, indicating low genetic diversity of domesticated rabbits in Kenya. This study resolved 5 unique haplotypes in the mtDNA D-loop region. A population genetic structure distinguishing Europe grouping and domesticated rabbits in Kenya was obtained on incorporating 32 known haplotypes. Domesticated rabbits in Kenya clustered together with rabbits from other geographic regions, suggesting common origin. The results suggested that the Kenyan domesticated rabbits may have originated from Europe. Integration of exotic breeds into breeding programmes could have contributed to the low genetic diversity. These results provide useful information for breeding and conservation decisions by the relevant stakeholders in the agriculture industry in Kenya.

scholarly journals Mitochondrial DNA-based genetic evaluation of autochthonous cattle breeds in Croatia

2014 ◽  
Vol 59 (No. 11) ◽  
pp. 519-528 ◽  
Author(s):  
A. Ivanković ◽  
S. Paprika ◽  
J. Ramljak ◽  
P. Dovč ◽  
M. Konjačić
Keyword(s):  
Genetic Diversity ◽  
Conservation Management ◽  
Large Fraction ◽  
Base Pairs ◽  
Cattle Breeds ◽  
Loop Region ◽  
D Loop ◽  
Mtdna Diversity ◽  
High Level ◽  
Relationship Of

Genetic diversity and phylogenetic relationship of three Croatian autochthonous cattle breeds was analyzed using a sequence of the mtDNA D-loop region. Among Busha, Istrian, and Slavonian Syrmian Podolian cattle 146 unrelated animals were tested. The sequencing of 780 base pairs of the mtDNA D-loop region revealed 39 polymorphic sites representing 28 different haplotypes. The highest numbers of haplotypes were observed in the Busha population and the lowest in the population of Slavonian Syrmian Podolian cattle, while the highest level of sequence diversity within a population was observed in the Istrian cattle. Our results indicate a high level of mtDNA diversity in the populations of Busha and Istrian cattle and a low level of preserved diversity in the population of Slavonian Syrmian Podolian cattle. The sequence analysis showed substantial subdivision between the breeds (F<sub>ST</sub> = 0.1434), and a large fraction of variation within the breeds. Although the dominant haplotypes are classified as the T3 haplogroup, some of the haplotypes are classified as the rarer T2 and T5 haplogroups. Genetic information based on mtDNA typing has a great importance for the future conservation management and preservation of genetic diversity in autochthonous cattle breeds. &nbsp;

Genomic characterization of three Vietnamese indigenous chicken varieties using mitochondrial D-loop sequences

2019 ◽  
Vol 99 (4) ◽  
pp. 833-839
Author(s):  
Son Quang Do ◽  
Lan Thi Phuong Nguyen ◽  
Thinh Hoang Nguyen ◽  
Trung Quoc Nguyen
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Diversity Indices ◽  
Fixation Index ◽  
Indigenous Chicken ◽  
Loop Region ◽  
Red Junglefowl ◽  
D Loop ◽  
Genomic Characterization

In this study, partial mitochondrial DNA (mtDNA) D-loop sequences of three Vietnamese indigenous chicken varieties, including Mong Tien Phong, To, and Sau Ngon, were analyzed to access genetic diversity and the maternal lineages of origin. A 525 bp fragment of the mtDNA D-loop region was sequenced from a total of 61 chickens of the three varieties. A neighbor-joining phylogenetic tree was assembled from the haplotypes obtained and reference sequences of mtDNA D-loop sequences of Red Junglefowl and domestic chickens from National Center for Biotechnology Information database. Genetic diversity indices and analysis of molecular variance were performed. Evaluation of genetic relationships between the three varieties was carried out with pairwise fixation index (FST). In total, 16 haplotypes were identified in the chickens studied. These haplotypes were classified in three haplogroups (A, B, and E) with the majority grouped in haplogroup B and haplogroup E. All three chicken varieties studied were distributed into 2–3 haplogroups and all three haplogroups found in this study are also represented by Red Junglefowl. In conclusion, all three Vietnamese indigenous chicken varieties have likely originated from multiple maternal lineages and potentially descended from the Red Junglefowl.

mtDNA D-loop sequence analysis of Kalang, Krayan, and Thale Noi buffaloes (Bubalus bubalis) in Indonesia and Thailand reveal genetic diversity

2021 ◽  
Vol 46 (2) ◽  
pp. 93-105
Author(s):  
S. Suhardi ◽  
P. Summpunn ◽  
S. Wuthisuthimethavee
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Bubalus Bubalis ◽  
Relationship Patterns ◽  
Loop Region ◽  
Loop Sequence ◽  
D Loop

Kalang (KBuf), Krayan (KrBuf), and Thale Noi buffaloes (TBuf) are swamp buffalo genetic resources in Indonesia and Thailand. The maternally inherited mitochondrial DNA (mtDNA), particularly D-loop region is an important material for phylogenetic inference and analyzing genetic diversity. Therefore, the objectives of the present study were to evaluate genetic diversity and to reconstruct the phylogenetic tree within buffalo breeds in Kalimantan, Indonesia, and Phatthalung, Thailand using mtDNA D-loop sequences. A total of one hundred forty buffaloes (70 males and 70 females) were observed including 40 buffaloes from North (NK), 40 from East (EK), and 40 from South Kalimantan (SK) provinces Indonesia and 20 from Phatthalung (PT) province, Thailand. DNA samples were isolated from buffalo tail hairs. DNA sequences were manually assembled using BioEdit program with consideration of gaps and ambiguous sequences. The phylogenetic tree of buffalo was generated by PHYLIP software. The observed variables included haplotype diversity, genetic distance, and genetic tree. The 956 bp of amplified mtDNA D-loop fragment presented a total of 24 haplotypes with several mutations that included transitions (293), transversions (60), deletions (15), and insertions (20). The neighbor-joining tree using the Kimura 2 parameter model demonstrated two local buffalo clusters among buffalo from Kalimantan and Thailand with four buffalo relationship patterns observed from buffaloes in Kalimantan Island (KBuf and KrBuf), Indonesia. The Results of the present study demonstrated that the buffaloes sequence analysis revealed relatively high diversity and is a good basis to perform selection and modern buffalo breeding development.

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