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.

scholarly journals Genetic Relationships of Cattle Breeds Assessed by PCR-RFLP of the Bovine Mitochondrial DNA D-loop Region

2005 ◽  
Vol 18 (10) ◽  
pp. 1368-1374 ◽  
Author(s):  
Du Hak Yoon ◽  
Hak Kyo Lee ◽  
Sung Jung Oh ◽  
Ki Chang Hong ◽  
Gwang Joo Jeon ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Relationships ◽  
Cattle Breeds ◽  
Loop Region ◽  
Pcr Rflp ◽  
D Loop

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

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.

scholarly journals Mitochondrial DNA Methylation and Human Diseases

2021 ◽  
Vol 22 (9) ◽  
pp. 4594
Author(s):  
Andrea Stoccoro ◽  
Fabio Coppedè
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Nuclear Dna ◽  
Epigenetic Modification ◽  
Nuclear Genome ◽  
Epigenetic Modifications ◽  
Human Diseases ◽  
Loop Region ◽  
D Loop

Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.

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

scholarly journals Protein binding to a single termination-associated sequence in the mitochondrial DNA D-loop region.

1993 ◽  
Vol 13 (4) ◽  
pp. 2162-2171 ◽  
Author(s):  
C S Madsen ◽  
S C Ghivizzani ◽  
W W Hauswirth
Keyword(s):  
Mitochondrial Dna ◽  
Protein Binding ◽  
Loop Formation ◽  
Sequence Element ◽  
Conserved Sequence ◽  
Loop Region ◽  
In Organello ◽  
Close Proximity ◽  
D Loop

A methylation protection assay was used in a novel manner to demonstrate a specific bovine protein-mitochondrial DNA (mtDNA) interaction within the organelle (in organello). The protected domain, located near the D-loop 3' end, encompasses a conserved termination-associated sequence (TAS) element which is thought to be involved in the regulation of mtDNA synthesis. In vitro footprinting studies using a bovine mitochondrial extract and a series of deleted mtDNA templates identified a approximately 48-kDa protein which binds specifically to a single TAS element also protected within the mitochondrion. Because other TAS-like elements located in close proximity to the protected region did not footprint, protein binding appears to be highly sequence specific. The in organello and in vitro data, together, provide evidence that D-loop formation is likely to be mediated, at least in part, through a trans-acting factor binding to a conserved sequence element located 58 bp upstream of the D-loop 3' end.

scholarly journals The AAA+ protein ATAD3 has displacement loop binding properties and is involved in mitochondrial nucleoid organization

2007 ◽  
Vol 176 (2) ◽  
pp. 141-146 ◽  
Author(s):  
Jiuya He ◽  
Chih-Chieh Mao ◽  
Aurelio Reyes ◽  
Hiroshi Sembongi ◽  
Miriam Di Re ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Uncharacterized Protein ◽  
Supercoiled Dna ◽  
Recombinant Fragment ◽  
Loop Region ◽  
Mitochondrial Nucleoids ◽  
Marked Preference ◽  
D Loop ◽  
Aaa Protein

Many copies of mammalian mitochondrial DNA contain a short triple-stranded region, or displacement loop (D-loop), in the major noncoding region. In the 35 years since their discovery, no function has been assigned to mitochondrial D-loops. We purified mitochondrial nucleoprotein complexes from rat liver and identified a previously uncharacterized protein, ATAD3p. Localization studies suggested that human ATAD3 is a component of many, but not all, mitochondrial nucleoids. Gene silencing of ATAD3 by RNA interference altered the structure of mitochondrial nucleoids and led to the dissociation of mitochondrial DNA fragments held together by protein, specifically, ones containing the D-loop region. In vitro, a recombinant fragment of ATAD3p bound to supercoiled DNA molecules that contained a synthetic D-loop, with a marked preference over partially relaxed molecules with a D-loop or supercoiled DNA circles. These results suggest that mitochondrial D-loops serve to recruit ATAD3p for the purpose of forming or segregating mitochondrial nucleoids.

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
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