scholarly journals Status and origin of Egyptian local rabbits in comparison with Spanish common rabbits using mitochondrial DNA sequence analysis

2020 ◽  
Vol 28 (2) ◽  
pp. 93
Author(s):  
Ahmed Mostafa Emam ◽  
Sandra Afonso ◽  
Pedro González-Redondo ◽  
G.M.K. Mehaisen ◽  
A.A.A. Azoz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Haplotype Diversity ◽  
Wild Rabbit ◽  
Cyt B ◽  
The Status ◽  
European Rabbits ◽  
Cyt B Gene ◽  
Cluster 2 ◽  
Haplotype A

<p>Mitochondrial DNA (mtDNA) and cytochrome b (cyt b) gene sequences were used to determine the status of genetic diversity and phylogeny for 132 individuals from local rabbit breeds in Egypt and Spain. The Egyptian local rabbit breeds were Egyptian Red Baladi (ERB), Egyptian Black Baladi (EBB) and Egyptian Gabali Sinai (EGS). However, the Spanish local rabbit breed was Spanish common rabbit (SCR). Previous breeds were compared with European Wild Rabbit taken from Albacete, Spain (EWR). A total of 353 mutations, 290 polymorphic sites, 14 haplotypes, 0.06126 haplotype diversity and -1.900 (&lt;em&gt;P&lt;/em&gt;&lt;0.05) for Tajima’s D were defined in this study. Haplotype A mostly occurred in 83.3% of Egyptian rabbits and 11.7% of EWR, while haplotype B occurred in 63.8% of Spanish rabbits and 36.2% of  the EGS breed. A total of 47 domestic and wild &lt;em&gt;Oryctolagus cuniculus&lt;/em&gt; published sequences were used to investigate the origin and relation among the rabbit breeds tested in this study. The most common haplotype (A) was combined with 44.7% of published sequences. However, haplotype B was combined with 8.5%. Haplotypes of Egyptian, SCR and EWR were scattered in cluster 1, while we found only one EGS haplotype with two haplotypes of EWR in cluster 2. Our results assumed that genetic diversity for ERB, EBB and SCR was very low. Egyptian breeds and SCR were introduced from European rabbits. We found that ERB and EBB belong to one breed.</p>

scholarly journals Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences

2018 ◽  
Vol 20 (1) ◽  
pp. 17-22
Author(s):  
TETY HARTATIK ◽  
DWI NUR HAPPY HARIYONO ◽  
YUDI ADINATA
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Cytochrome B ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Cytochrome B Gene ◽  
Cyt B ◽  
Gene Sequences ◽  
Cattle Breeds ◽  
Cyt B Gene

Hartatik T, Hariyono DNH, Adinata Y. 2019. Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas 20: 17-22. Genetic diversity and phylogenetic relationships of two Indonesian local cattle breeds (Pasundan and Pacitan cattle) were investigated using mitochondrial DNA (mtDNA) cytochrome b (cyt b) gene analysis. Partial sequences of cyt b gene, 404 bp in length, were determined for 21 individuals from the two breeds. Genetic diversity of the breeds was assessed based on the number of polymorphic sites, number of haplotypes, haplotype diversity, nucleotide diversity and average number of differences. In addition, a neighbour-joining (NJ) haplotype tree was constructed based on Kimura’s two-parameter model. Among the two breeds, haplotype and nucleotide diversity of Pacitan cattle were the highest with values of 0.3778 and 0.00099, respectively. In contrast, Pasundan cattle had the lowest value for haplotype (0.1818) and nucleotide (0.00045) diversity. Four haplotypes (Hap_16, Hap_17, Hap_18 and Hap_19) were found across the two breeds and around 85.71% of investigated individuals were classified as Hap_16. Phylogenetic analysis with the inclusion of the cyt b sequences from 39 cattle breeds from Genbank database, showed that Indonesian cattle made a separated lineage together with Bos javanicus, B. bison, and B. bonasus. Pasundan and Pacitan cattle were considered from the same lineage based on haplotype distribution as well as phylogenetic analysis. This study may help the future researchers and livestock breeders for designing a breeding program based on a better understanding of the genetic diversity and history of local breeds.

scholarly journals Substitution and Haplotype Diversity Analysis on The Partial Sequence of The Mitochondrial DNA Cyt b of Indonesian Swamp Buffalo (Bubalus bubalis)

2015 ◽  
Vol 3 (2) ◽  
pp. 59
Author(s):  
Akhmad Sukri ◽  
Mohamad Amin ◽  
Aris Winaya ◽  
Abdul Gofur
Keyword(s):  
Mitochondrial Dna ◽  
Gene Sequence ◽  
Genetic Relationships ◽  
Haplotype Diversity ◽  
Bubalus Bubalis ◽  
Cyt B ◽  
Substitution Pattern ◽  
Silent Substitution ◽  
Swamp Buffalo ◽  
Cyt B Gene

<p>This research aims to investigate the substitution pattern of nucleotide base and haplotype diversity of Indonesian swamp buffalo (<em>Bubalus bubalis)</em> based on the mitochondrial DNA cyt b partial gene sequence. 17 samples were chosen from 7 different regions with each uniquely represents Indonesian biogeography which comprise Aceh, Riau, Madiun, Blitar, Lombok, South Borneo and Tana Toraja. The result of cyt b gene sequence alignment showed the presence of transition and transversion substitutions and the absence of insertion and deletion. The amount of transitions was found to be higher than that of transversions and the amount of substitution in pyrimidine was also higher than that in purine. The highest amount of transitions happened in base TàC which is a silent substitution. The result of median joining network analysis showed that Indonesian haplotype<em> Bubalus bubalis</em> could be classified into 16 haplotypes which form different haplogroups unique to their geographical region. The result of median joining network<em> </em>analysis also indicated that the genetic relationships of swamp buffaloes (<em>Bubalus bubalis) </em>in Indonesia are highly influenced by their geographical locations.</p>

scholarly journals Partial sequence analysis of mitochondrial cytochrome B gene of Labeo calbasu of Bangladesh

2019 ◽  
Vol 5 (1) ◽  
pp. 25-30
Author(s):  
RA Begum ◽  
MT Alam ◽  
H Jahan ◽  
MS Alam
Keyword(s):  
Genetic Diversity ◽  
Cytochrome B ◽  
Tissue Sample ◽  
Sequence Similarity ◽  
Cytochrome B Gene ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Multiple Sequence ◽  
Mitochondrial Cytochrome B ◽  
Cyt B Gene

Labeo calbasu (Family Cyprinidae) was studied at DNA level to know genetic diversity within and between species. The mitochondrial cytochrome b (cyt-b) gene of L. calbasu was sequenced and compared to the corresponding sequences of other Labeo species. DNA was isolated from the tissue sample of L. calbasu using phenol: chloroform extraction method. Forward and reverse primers were designed to amplify the target region of cytochrome b gene. A standard PCR protocol was used for the amplification of the desired region. Then, the forward and reverse sequences obtained were aligned and edited to finalize a length of 510 nucleotides which was submitted to NCBI genbank database. Nucleotide BLAST of this sequence at NCBI resulted 100% sequence similarity with L. calbasu sequence of the same region of cyt-b gene. Multiple sequence alignment of the sequence with seven more Labeo species sequences revealed 120 polymorphic sites, which have been mark of diversity among the species and might be used in molecular identification of the Labeo species. A constructed phylogenetic tree has shown relationship among the Labeo species. This research demonstrated the usefulness of mitochondrial DNA-based approach in species identification. Further, the data will provide appropriate background for studying genetic diversity within-species of the Labeo species in general and of L. calbasu in particular. J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(1): 25-30

Haplotype diversity in the mtDNA cyt b gene in round goby (Neogobius melanostomus (Pallas)) from the northwestern part of the Black Sea basin

2014 ◽  
Vol 50 (3) ◽  
pp. 274-279 ◽  
Author(s):  
Yu. V. Slynko ◽  
V. V. Stolbunova ◽  
S. V. Chebotar ◽  
V. V. Zamorov ◽  
A. N. Gurovskiy
Keyword(s):  
Black Sea ◽  
Round Goby ◽  
Haplotype Diversity ◽  
Neogobius Melanostomus ◽  
The Black Sea ◽  
Northwestern Part ◽  
Cyt B ◽  
Cyt B Gene

Genetic diversity and phylogenetic analysis of eight Cyprinoid aquaculture breeds based on mitochondrial Cyt b gene

2013 ◽  
Vol 37 (3) ◽  
pp. 344 ◽  
Author(s):  
Tongqian XIAO ◽  
Cuiyun LU ◽  
Chao LI ◽  
Mingzhao ZHANG ◽  
Ying GU ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Cyt B ◽  
Cyt B Gene

Mitochondrial DNA study of Mongolian horses

2018 ◽  
Vol 22 (03) ◽  
pp. 12-16
Author(s):  
Bolor-Oyut B ◽  
Ochirkhuyag B ◽  
Khulan J
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Nucleotide Diversity ◽  
Sequence Variation ◽  
Maternal Inheritance ◽  
Haplotype Diversity ◽  
Research Field ◽  
Important Research ◽  
Evolutionary Studies ◽  
High Level

Studies of population genetic diversity is important research field in conservation and restoration of animal breeds and genetic resources. The control region of mitochondrial DNA is widely used for population and evolutionary studies because of its‘ maternal inheritance and high level of sequence variation as well as its‘ much less recombination rate. To determine genetic diversity and maternal inheritance, we collected 10 blood samples of Tes horses from Zavkhan, Mongolia. In this study, 8 haplotypes and 44 polymorphic sites were detected. Haplotype diversity was 0.9333 and nucleotide diversity was 0.0224. 4 haplogroups (A, C, F, I) were identified among 8 haplotypes.

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

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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