Phylogenetic analysis of Myanmar indigenous chickens using mitochondrial D‐loop sequence reveals their characteristics as a genetic resource

2021 ◽  
Vol 92 (1) ◽  
Author(s):  
Su Lai Yee Mon ◽  
Moe Lwin ◽  
Aye Aye Maw ◽  
Lat Lat Htun ◽  
Saw Bawm ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Resource ◽  
Indigenous Chickens ◽  
Loop Sequence ◽  
D Loop

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 Origin and evolutionary history of domestic chickens inferred from a large population study of Thai red junglefowl and indigenous chickens

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ayano Hata ◽  
Mitsuo Nunome ◽  
Thanathip Suwanasopee ◽  
Prateep Duengkae ◽  
Soontorn Chaiwatana ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Evolutionary History ◽  
Large Scale ◽  
Large Population ◽  
High Genetic Diversity ◽  
Indigenous Chickens ◽  
Red Junglefowl ◽  
Loop Sequence ◽  
Multiple Regions ◽  
D Loop

AbstractIn this study, we aimed to elucidate the origin of domestic chickens and their evolutionary history over the course of their domestication. We conducted a large-scale genetic study using mitochondrial DNA D-loop sequences and 28 microsatellite DNA markers to investigate the diversity of 298 wild progenitor red junglefowl (Gallus gallus) across two subspecies (G. g. gallus and G. g. spadiceus) from 12 populations and 138 chickens from 10 chicken breeds indigenous to Thailand. Twenty-nine D-loop sequence haplotypes were newly identified: 14 and 17 for Thai indigenous chickens and red junglefowl, respectively. Bayesian clustering analysis with microsatellite markers also revealed high genetic diversity in the red junglefowl populations. These results suggest that the ancestral populations of Thai indigenous chickens were large, and that a part of the red junglefowl population gene pool was not involved in the domestication process. In addition, some haplogroups that are distributed in other countries of Southeast Asia were not observed in either the red junglefowls or the indigenous chickens examined in the present study, suggesting that chicken domestication occurred independently across multiple regions in Southeast Asia.

scholarly journals A Phylogenetic Analysis of Otters (Lutra lutra) Inhabiting in the Gyeongnam Area Using D-Loop Sequence of mtDNA and Microsatellite Markers

2011 ◽  
Vol 21 (3) ◽  
pp. 385-392
Author(s):  
Moon-Sung Park ◽  
Hyun-Tae Lim ◽  
Ki-Cheol Oh ◽  
Young-Rok Moon ◽  
Jong-Gap Kim ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Microsatellite Markers ◽  
Lutra Lutra ◽  
Loop Sequence ◽  
D Loop

scholarly journals Genetic diversity of Myanmar cattle breeds using complete mitochondrial D-loop sequence

2018 ◽  
Vol 46 (2) ◽  
pp. 57-67 ◽  
Author(s):  
Moe LWIN ◽  
Su Lai Yee MON ◽  
Yukio NAGANO ◽  
Kotaro KAWABE ◽  
Hideyuki MANNEN ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cattle Breeds ◽  
Loop Sequence ◽  
D Loop

scholarly journals Phylogenetical Relationships between Kejobong Goat and Other Goats Based on Mt-DNA D-loop Sequence Analysis

2018 ◽  
Vol 41 (2) ◽  
pp. 85-93 ◽  
Author(s):  
D. A. Lestari ◽  
E. Purbowati ◽  
S. Sutopo ◽  
E. Kurnianto
Keyword(s):  
Sequence Analysis ◽  
Mt Dna ◽  
Loop Sequence ◽  
D Loop

scholarly journals Geographic Origin and Genetic Characteristics of Japanese Indigenous Chickens Inferred from Mitochondrial D-Loop Region and Microsatellite DNA Markers

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2074
Author(s):  
Ayano Hata ◽  
Atsushi Takenouchi ◽  
Keiji Kinoshita ◽  
Momomi Hirokawa ◽  
Takeshi Igawa ◽  
...  
Keyword(s):  
Dna Markers ◽  
Microsatellite Dna ◽  
Genetic Relationships ◽  
Indigenous Chicken ◽  
Genetic Characteristics ◽  
Indigenous Chickens ◽  
Loop Region ◽  
Microsatellite Dna Markers ◽  
D Loop ◽  
Chicken Breeds

Japanese indigenous chickens have a long breeding history, possibly beginning 2000 years ago. Genetic characterization of Japanese indigenous chickens has been performed using mitochondrial D-loop region and microsatellite DNA markers. Their phylogenetic relationships with chickens worldwide and genetic variation within breeds have not yet been examined. In this study, the genetic characteristics of 38 Japanese indigenous chicken breeds were assessed by phylogenetic analyses of mitochondrial D-loop sequences compared with those of indigenous chicken breeds overseas. To evaluate the genetic relationships among Japanese indigenous chicken breeds, a STRUCTURE analysis was conducted using 27 microsatellite DNA markers. D-loop sequences of Japanese indigenous chickens were classified into five major haplogroups, A–E, among 15 haplogroups found in chickens worldwide. The haplogroup composition suggested that Japanese indigenous chickens originated mainly from China, with some originating from Southeast Asia. The STRUCTURE analyses revealed that Japanese indigenous chickens are genetically differentiated from chickens overseas; Japanese indigenous chicken breeds possess distinctive genetic characteristics, and Jidori breeds, which have been reared in various regions of Japan for a long time, are genetically close to each other. These results provide new insights into the history of chickens around Asia in addition to novel genetic data for the conservation of Japanese indigenous chickens.

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