scholarly journals Mitochondrial D-loop sequence variation among autochthonous horse breeds in Croatia

2009 ◽  
Vol 54 (No. 3) ◽  
pp. 101-111 ◽  
Author(s):  
A. Ivanković ◽  
J. Ramljak ◽  
M. Konjačić ◽  
N. Kelava ◽  
P. Dovč ◽  
...  
Keyword(s):  
Proximal Part ◽  
Conservation Strategy ◽  
Selection Strategy ◽  
Horse Population ◽  
Mitochondrial Haplotypes ◽  
Loop Region ◽  
Loop Sequence ◽  
D Loop ◽  
Endangered Breed ◽  
Two Populations

Genetic variation in three Croatian coldblood horse populations was analysed using a sequence analysis of the proximal part (nt 15 498–15 821) of the D-loop region of mtDNA. Twenty unrelated horses were chosen from the Posavina horse and the Croatian Coldblood breeds and fifteen horses from the Murinsulaner horse population. Sequencing of the proximal part of the mtDNA D-loop region revealed 26 polymorphic sites representing thirty haplotypes which were clustered into eight haplogroups. A wide variety of mitochondrial haplotypes of the analysed horse breeds were clustered into eight different haplogroups. Two haplogroups (D and F) were specific to Posavina horse, five haplogroups were shared among the Croatian Coldblood and Murinsulaner horse, the fact that can be explained by selection strategy at the beginning of the 20<sup>th</sup> century and possible gene flow between the two populations. These results indicate the presence of many ancient maternal lineages with high diversity in mtDNA. The genetic information based on mtDNA typing has a great importance for the future breed conservation strategy, especially for the critically endangered breed such as Murinsulaner horse.

scholarly journals Mitochondrial D-loop sequence variation among Hucul horse

2013 ◽  
Vol 58 (No. 10) ◽  
pp. 437-442 ◽  
Author(s):  
V. Czerneková ◽  
T. Kott ◽  
I. Majzlík
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Information ◽  
Sequence Variation ◽  
Dna Typing ◽  
Conservation Strategies ◽  
Base Pairs ◽  
Horse Population ◽  
Loop Region ◽  
Loop Sequence ◽  
D Loop

Genetic variation in the Czech Hucul horse population was analyzed using a sequence analysis of the D-loop region of mitochondrial DNA. One hundred and sixty-five Hucul horses were tested. Sequencing of the 700-base pairs fragment of the mitochondrial DNA D-loop region revealed 38 mutation sites representing 14 haplotypes, which were clustered into six haplogroups. The genetic information obtained from the mitochondrial DNA typing is of utmost importance for the future breed-conservation strategies. &nbsp;

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.

Genetic diversity among Canadienne, Brown Swiss, Holstein and Jersey cattle based on mitochondrial D-loop sequence variation

2003 ◽  
Vol 83 (1) ◽  
pp. 39-44 ◽  
Author(s):  
C. Hansen ◽  
J. N. B. Shrestha ◽  
R. J. Parker ◽  
G. H. Crow ◽  
P. J. McAlpine ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Bos Taurus ◽  
Sequence Divergence ◽  
Single Nucleotide ◽  
Brown Swiss ◽  
Jersey Cattle ◽  
Loop Region ◽  
Loop Sequence ◽  
D Loop

Polymorphisms creating 36 unique haplotypes were observed with in breeds at 55 sites in the displacement loop (D-loop) region of the mitochondrial DNA (mtDNA) consisting of 814 bp. The majority (56%) of the differences observed were the result of nucleotide substitution events with 19 transitions, 12 transversions, 11 deletions, 12 insertions and 1 inversion. In all cases, the insertions and deletions were of a single nucleotide. Canadienne cattle were found to have 60% unique haplotypes within the population compared to 89% in Brown Swiss, 90% in Holstein and 100% in Jersey cattle, possibly reflecting the narrow genetic base in the Canadienne breed. The degree of sequence divergence in the D-loop region of mtDNA was based on samples from 20 Canadienne, 9 Brown Swiss, 10 Holstein and 10 Jersey cattle and a phylogenetic analysis showed that these cattle (Bos taurus) were not evolutionarily distinct. All four breeds grouped together when a strict consensus tree was generated. Intra-breed variability proved to be high for the Canadienne, Holstein and Jersey breeds (57–73%) but not the Brown Swiss breed (29%). The Canadienne and Brown Swiss (45%), and Brown Swiss and Holstein (43%) showed the lowest degree of inter-breed variability. The greatest variability among the four breeds was between Canadienne and Jersey (80%) cattle. These findings question the validity of phenotypic assessment of genetic diversity, such as Canadienne cattle being described as “Black Jersey”. Key words: Genetic distance, phylogenetic analysis, D-loop sequence, cattle

scholarly journals The very low genetic variability on Aceh Tamiang’s (Indonesia) population of Painted Terrapin (Batagur borneoensis) inferred by cytochrome oxidase I (CO I) and D-loop (control region)

2020 ◽  
Vol 21 (6) ◽  
Author(s):  
JOKO GUNTORO ◽  
WIRDATETI ◽  
AWAL RIYANTO
Keyword(s):  
Genetic Variability ◽  
Cytochrome Oxidase ◽  
Control Region ◽  
Haplotype Diversity ◽  
Cytochrome Oxidase I ◽  
Conservation Strategy ◽  
Wild Populations ◽  
Loop Control ◽  
Loop Region ◽  
D Loop

Abstract. Guntoro J, Wirdateti, Riyanto A. 2020. The very low genetic variability on Aceh Tamiang’s (Indonesia) population of Painted Terrapin (Batagur borneoensis) inferred by cytochrome oxidase I (CO I) and D-loop (control region). Biodiversitas 21: 2514-2520. Populations of Batagur borneoensis have been rapidly decreasing due to the harvesting of adults and eggs for food and the construction of beachfront property causing the loss of nesting areas. By the new Indonesian regulation, since 2018 this turtle listed in the protected animal. Meanwhile, IUCN placed as critically endangered which indicating a high risk of extinction in the wild in the near future (www.iucnredlist.org). We used cytochrome oxidase I (COI) and control region D-loop region to investigate intraspecific variations on Aceh Tamiang’s population of painted terrapin, Batagur borneoensis. DNA material was gathered from saliva collected from 90 juveniles in the reaching facility of Sukacita Lestari Indonesia Foundation which hatched from eggs collected from December 2015 to April 2016 from 30 nests on beach area at Aceh Tamiang. The population showed very low genetic variability (haplotype diversity, Hd = 0.457 based on COI and 0.405 based on D-loop; nucleotide diversity, π = 0.00089 based on COI and 0.00076 based on D-loop). So, we suggested that further study such as more exploration to find new wild populations and genetic study across wild populations should be done to reveal genetic variability and genetic structure which important to decide the conservation strategy. At the time for Aceh Tamiang's population, the ranching conservation program should be maintained at least to keep the successful hatchling from hunters and natural predators both during eggs laying and hatching.

scholarly journals Genetic variability of Akhal-Teke horses bred in Italy

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4889
Author(s):  
Maria C. Cozzi ◽  
Maria G. Strillacci ◽  
Paolo Valiati ◽  
Elisa Rogliano ◽  
Alessandro Bagnato ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Haplotype Diversity ◽  
Principal Component ◽  
Italian Population ◽  
Horse Population ◽  
Loop Region ◽  
Marker Loci ◽  
D Loop ◽  
Inbreeding Level ◽  
Almost All

Background The Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences. Methods Seventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on other eight AKH populations. In addition, 397 bp of mtDNA D-loop region were sequenced on a sub-group of 22 unrelated AKH out of the 95 sampled ones, and on 11 unrelated Arab horses. The haplotypes identified in the Italian population were aligned to sequences of AKH (56), Arab (five), Caspian Pony (13), Przewalskii (two) and Barb (15) horses available in GenBank. The Median Joining Network (MJN), Principal Component Analysis (PCA) and Neighbor-joining (NJ) tree were calculated on the total 126 sequences. Results Nucleic markers showed a high degree of polymorphism (Ho = 0.642; He = 0.649) and a low inbreeding level (FIS = 0.016) in Italian horses, compared to other AKH populations (ranged from −0.103 AKH from Estonia to 0.114 AKH from Czech Republic). High variability was also recorded in the D-Loop region. 11 haplotypes were identified with haplotype diversity (hd), nucleotide diversity (π) and average number of nucleotide differences (k) of 0.938, 0.021 and 6.448, respectively. When all the 126 D-Loop sequences were compared, 51 haplotypes were found, and four were here found only in the Italian AKH horses. The 51 haplotypes were conformed to eight recognized mtDNA haplogroups (A, C, F, G, L, M, P and Q) and confirmed by MJN analysis, Italian horses being assigned to five haplogroups (A, C, G, L and M). Using a PCA approach to the same data, the total haplotypes were grouped into two clusters including A+C+M+P and G+F haplogroups, while L and Q haplogroups remained ungrouped. Finally, the NJ algorithm effectively discretizes only the L haplogroup. All the above data univocally indicate good genetic variability and accurate management of the Akhal-Teke population in Italy.

scholarly journals 220 Mitochondrial DNA polymorphism as a measure of genetic diversity in African tilapia fish

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 47-48
Author(s):  
Ekei Ikpeme ◽  
Ekerette Ekerette ◽  
Michael Ozoje
Keyword(s):  
Genetic Diversity ◽  
Genetic Analysis ◽  
Cytochrome B ◽  
Fixation Index ◽  
Cyt B ◽  
Important Species ◽  
Loop Region ◽  
South West ◽  
D Loop ◽  
Two Populations

Abstract This study focused on the assessment of genetic diversity in African tilapia fish (Oreochromis niloticus) obtained from two populations (Domita in South-South and Odeda in South-West, Nigeria) using the displacement loop (D-loop) and cytochrome B region of the mitochondrial deoxyribonucleic acid (mtDNA). A total of 28 samples (15 from South-South and 13 from South-West) were used for the genetic analysis. DNA was extracted from the tissue of all the samples using Quik-gDNATM miniPrep kit. The D-loop region was sequenced for all samples from the two populations, while cytochrome b (cyt b) region of mtDNA was only sequenced for samples from South-South population Multiple sequence alignment was carried out using molecular evolutionary genetic analysis (MEGA) software before subsequent genetic analyses. There were 176, 162 and 144 polymorphic sites for D-loop of South-South, South-West and cyt b of South-South populations, respectively. Haplotype diversities (Hd) were 1.00 ± 0.024 and 1.00 ± 0.030 while nucleotide diversities were 0.168 ± 0.086 and 0.161 ± 0.084 for D-loop of South-South and South-West populations, respectively. For the cyt b, haplotype and nucleotide diversities were 0.91 ± 0.003 and 0.051 ± 0.016. The genetic distance inferred between D-loop regions of South-South and South-West populations was 0.243. Phylogenetic analysis grouped the samples into two clusters based on population. Analysis of molecular variance (AMOVA) revealed 37.32% variation within population and 62.68% variation among population with a significant fixation index of 0.627 (P &lt; 0.05). The findings of this study revealed high level of genetic diversity among the tilapia populations and may serve as pivot information for the genetic improvement of this important species.

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