Population structure, genetic diversity and phylogenetic analysis of different rural and commercial chickens of Pakistan using complete sequence of mtDNA D-loop

2018 ◽  
Vol 30 (2) ◽  
pp. 273-280
Author(s):  
Ayesha Nisar ◽  
Abdul Waheed ◽  
Sawar Khan ◽  
Xingang Feng ◽  
Abbas Hussain Shah
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Population Structure ◽  
Complete Sequence ◽  
D Loop ◽  
Commercial Chickens

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 Evaluation of the genetic diversity of six Chinese indigenous chickens

2020 ◽  
Vol 33 (10) ◽  
pp. 1566-1572
Author(s):  
Yuzhu Sha ◽  
Caixia Gao ◽  
Meimei Liu ◽  
Shengguo Zhao
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Indian Subcontinent ◽  
Coastal Region ◽  
Principal Component ◽  
Sharp Decrease ◽  
Haplotype Sharing ◽  
Indigenous Chickens ◽  
D Loop ◽  
Commercial Chickens

Objective: The extensive breeding of commercial chickens has led to a sharp decrease in the resources of many indigenous chickens, especially the indigenous chickens in the southeastern coastal region, which are on the verge of extinction, and the indigenous chickens in the northwestern region of China, which are also at risk. However, there are few reports on the evaluation of genetic diversity and conservation of genetic resources of indigenous chickens in remote areas in the Northwest of China.Methods: In the present study, the genetic diversity and phylogenetic relationship of six indigenous chickens from different regions were studied based on variation in mitochondrial DNA control region (D-loop), and the degree of introgression from commercial breeds into these chickens was determined by the amount of haplotype sharing between indigenous and commercial breeds.Results: Twenty-five polymorphic sites and 25 haplotypes were detected in 206 individuals. Principal component analysis showed that the Jingning chicken had the highest genetic diversity among the six indigenous chickens. According to the degree of introgression, the six indigenous breeds may be involved in haplotype sharing with commercial breeds, and the introgression from commercial chickens into the Haidong chicken is the most serious.Conclusion: The genetic uniqueness of indigenous chickens has been eroded, so it is necessary to consider the protection of their genetic resources. Phylogenetic analysis suggests that the six indigenous chickens have two major matrilineal origins: one from Yunnan or its surrounding areas in China and the other from the Indian subcontinent.

scholarly journals Origin and genetic diversity of Egyptian native chickens based on complete sequence of mitochondrial DNA D-loop region

2016 ◽  
Vol 95 (6) ◽  
pp. 1248-1256 ◽  
Author(s):  
Sayed A.-M. Osman ◽  
Takahiro Yonezawa ◽  
Masahide Nishibori
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Complete Sequence ◽  
Loop Region ◽  
D Loop ◽  
Native Chickens

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 Genetic diversity and population structure of Brycon nattereri (Characiformes: Bryconidae): a Neotropical fish under threat of extinction

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Bruno A. Galindo ◽  
Dhiego G. Ferreira ◽  
Caroline Apolinário-Silva ◽  
Mariana C. Terra ◽  
Nícollas G. O. Aprígio ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Paraná River ◽  
Neotropical Fish ◽  
Conservation Area ◽  
Restricted Area ◽  
Parana River ◽  
Mitochondrial Region ◽  
D Loop

ABSTRACT Brycon nattereri is an endangered Neotropical fish reported along conserved stretches of the upper Paraná, Tocantins and São Francisco rivers. Populations of this species have been very rare in some Paraná River sub basins. This study analyzes the genetic diversity and population structure of B. nattereri in a restricted area of occurrence recently identified in upper Paraná River basin. Seven microsatellite loci and 497 bp of D-Loop mitochondrial region were examined in 92 individuals from four points along the area of occurrence. Both molecular markers indicated a single population distributed along a stretch of the river approximately 80 km long. Although some of the data suggest an ancient bottleneck, current levels of genetic diversity (H E = 0.574 and h = 0.616) were similar to those of other species of the genus Brycon. The results suggest that the population of B. nattereri has been able to maintain satisfactory levels of genetic diversity, in spite of the small area of occurrence. These data have highlighted an important conservation area and action may prove essential to improve the quality of the environment, and especially the water and riparian plant life, if the area is to be managed and conserved efficiently.

Mitochondrial D-loop analysis for uncovering the population structure and genetic diversity among the indigenous duck (Anas platyrhynchos) populations of India

2017 ◽  
Vol 29 (2) ◽  
pp. 212-219 ◽  
Author(s):  
Uma Gaur ◽  
Madhu Sudan Tantia ◽  
Bina Mishra ◽  
Settypalli Tirumala Bharani Kumar ◽  
Ramesh Kumar Vijh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Anas Platyrhynchos ◽  
Loop Analysis ◽  
D Loop

scholarly journals Genetic diversity and gene flow decline with elevation in the Near Eastern fire salamander (Salamandra infraimmaculata) at Mount Hermon, Golan Heights

2020 ◽  
pp. 1-7
Author(s):  
Kathleen Preißler ◽  
Eliane Küpfer ◽  
Fabian Löffler ◽  
Arlo Hinckley ◽  
Leon Blaustein ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Altitudinal Gradient ◽  
Agricultural Landscape ◽  
Extinction Risk ◽  
Elevation Gradient ◽  
Near Eastern ◽  
Fire Salamander ◽  
D Loop

Abstract The Near Eastern fire salamander (Salamandra infraimmaculata) reaches its southern distribution range in Israel. Although the population structure has been analysed in central Israel and at the southern distribution limit, we lack knowledge on populations in the northern area, such as along Mount Hermon. S. infraimmaculata occurs at Mt. Hermon along an altitudinal gradient and appears to be fragmented by urban and agricultural landscape. We studied the genetic structure of four populations based on microsatellite loci and the mitochondrial D-loop to determine the genetic diversity and connectivity between populations. We observed moderate gene flow at lower parts, i.e. from Tel Dan and Nimrod Castle to Banias indicating extant but limited connectivity. Genetic diversity and gene flow declined along the altitudinal gradient at Mt. Hermon, reaching rock-bottom levels in the highest located population of Nimrod Pool. The observed isolation-by-elevation gradient might induce a higher extinction risk for the highland populations of S. infraimmaculata.

Sign in / Sign up

Export Citation Format

Share Document