scholarly journals Study on genetic variations of the D-loop region in three Vietnamese ethnic groups Kinh, Lolo and Lahu

2020 ◽  
Vol 18 (2) ◽  
pp. 231-238
Author(s):  
Nguyen Thuy Duong ◽  
Nguyen Van Phong ◽  
Nguyen Thy Ngoc ◽  
Nong Van Hai
Keyword(s):  
Ethnic Groups ◽  
Genetic Distances ◽  
Genetic Variations ◽  
Language Group ◽  
Nucleotide Polymorphisms ◽  
Loop Region ◽  
Minority Ethnic Groups ◽  
Mtdna Sequence ◽  
D Loop ◽  
History Of

Mitochondrial DNA (mtDNA) sequence analysis has been widely used to investigate population genetic and evolutional history of different ethnic groups worldwide. In this study, the D-loop region of 119 Vietnamese individuals belonging to three different ethnic groups was sequenced and compared with reference mtDNA on rCRS for genetic variations. Total 218 genetic polymorphisms were found in this population, among which 48 variations appeared with frequencies of more than 0.1. Further statistical analysis showed that there were 23, 13 and 24 single nucleotide polymorphisms (SNP) distributed differently between Kinh vs. Lolo, Kinh  vs. Lahu , and Lolo  vs. Lahu groups, respectively. The mean pairwise genetic distances between each pair of ethnic groups were 0.0101, 0.0098 and 0.0092 for Kinh - Lolo, Kinh - Lahu, Lolo - Lahu, respectively. This indicated that although the Lolo and Lahu ethnic groups both belong to the Tibeto-Burman language group, the genetic distance between them was no closer than the genetic distances between them and the Kinh group of the Viet-Muong (Austroasiatic) language group. This study was the first research on the D-loop region of the Lolo and Lahu populations in Vietnam. These results provided more data for exploring the genetic background and the history of those ethnic groups as well as other minority ethnic groups in Vietnam.

scholarly journals SINGLE NUCLEOTIDE POLYMORPHISMS IN THE D-LOOP REGION OF THE MITOCHONDRIAL GENOMES OF INDIVIDUALS FROM TWO ETHNIC GROUPS KINH AND MANG OF AUSTRO-ASIATIC LANGUAGE FAMILY

2018 ◽  
Vol 16 (2) ◽  
pp. 231-240
Author(s):  
Nguyen Thy Ngoc ◽  
Nguyen Bao Trang ◽  
Nguyen Quang Huy ◽  
Nguyen Dang Ton ◽  
Nguyen Thuy Duong
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Ethnic Group ◽  
Ethnic Groups ◽  
Mitochondrial Genomes ◽  
Nucleotide Polymorphisms ◽  
Language Family ◽  
Single Nucleotide ◽  
Loop Region ◽  
Pcr Products ◽  
D Loop

The two hypervariable regions HV-I and HV-II in the D-loop region are the most diverse region in the mitochondrial human genome. These DNA regions have an important role in population genetics and human evolution research. In this study, we identified single nucleotide polymorphisms (SNPs) in the D-loop region of the human mitochondrial DNA genomes of individuals in two Vietnamese ethnic groups: Kinh and Mang. 81 blood samples from 50 Kinh and 31 Mang unrelated individuals were collected for genomic DNA extraction. Using PCR and specific primers, we successfully amplified the two HV-I and HV-II regions with respective sizes of 693 bp and 689 bp. The PCR products then were purified and sequenced. After alignment to the reference mitochondrial genome rCRS (NC_012920.1), 96 SNPs were detected in the Kinh ethnic group, of which many polymorphisms were firstly found in this ethnic and 36 SNPs in the Mang ethnic group. Of the identified 132 SNPs, 16 SNPs were significantly different between the two ethnic groups (p < 0.05). Eight out of the 16 SNPs (T146C, T199C, A16182C, T16217C, T16297C, T16140C, A16183C, T16189C) were frequently found in the Kinh ethnic group but not or only rarely in the Mang ethnic group. On the other hand, 4 SNPs (C151T, A16162G, A16269G, T16271C) were commonly found in the Mang population but rarely in the Kinh population. These findings suggest that although Kinh and Mang belong to one language family (Austro-Asiatic), there is a noticeable diversity in the mitochondrial genomes between these two Vietnamese ethnic groups.

scholarly journals Genetic variations among selected wild Asian elephant populations in Peninsular Malaysia based on mitochondrial D-loop region DNA sequences

2019 ◽  
Vol 20 (9) ◽  
Author(s):  
KAYAL VIZI KARUPPANNAN ◽  
NOR AIFAT RAHMAN ◽  
KHAIRUL AMIRIN MOHAMED ◽  
NURUL FARAH DIYANA AHMAD TAHIR ◽  
FATIN MARDHIAH NORDIN ◽  
...  
Keyword(s):  
National Parks ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Haplotype Diversity ◽  
Mitochondrial Control Region ◽  
Genetic Variations ◽  
Peninsular Malaysia ◽  
Asian Elephant ◽  
Loop Region ◽  
D Loop

Abstract. Karuppannan KV, Aifat NR, Mohamed KA,  Ahmad-Tahir NFD,  Nordin FM, Yaakop S, Maldonado JE, Md-Zain BM. 2019. Genetic variations among selected wild Asian elephant populations in Peninsular Malaysia based on mitochondrial D-loop region DNA sequences. Biodiversitas 20: 2494-2502. Asian elephant (Elephas maximus) is an important large mammal in Peninsular Malaysia and is completely protected by the Wildlife Conservation Act 2010 (Act 716). The conservation of this species requires strong information-based research, such as genetic evaluations. The aim of this study was to compare mitochondrial control region variation among selected elephants from the Taman Negara National Parks (TNNP) population with other selected populations in Peninsular Malaysia. DNA materials were extracted from fecal samples and amplified using partial mitochondrial D-loop region. Total 13 haplotypes with haplotype diversity (Hd) of 0.7524 were observed. A total of 34 base pair (bp) segregation sites were formed in 547 bp sequences. Both phylogenetic trees showed that a few individual elephants from the TNNP formed a clade together with individuals from other populations. The remaining individual elephants from TNNP formed a monophyletic clade supported by a high bootstrap value. Low genetic distance was detected among the tested populations, which proved that both individuals from the TNNP and other selected populations have similar genetic patterns. High gene flow among tested populations would impact on fitness and long-term resilience of the populations. This highly significant outcome provides strong baseline data for Department of Wildlife and National Parks (DWNP) in monitoring elephant populations in order to reduce number of human-elephant conflicts which indirectly minimize translocating conflict elephants to TNNP.

scholarly journals A brief overview of GWAS: discover genetic variations of diseases and phenotypes

2020 ◽  
Vol 185 ◽  
pp. 03014
Author(s):  
Zhiying Peng
Keyword(s):  
Large Scale ◽  
Genome Wide Association Study ◽  
Genetic Variations ◽  
Nucleotide Polymorphisms ◽  
Information Discovery ◽  
Genome Wide ◽  
Whole Genomes ◽  
Statistical Analysis Method ◽  
History Of ◽  
Application Fields

GWAS, or Genome-wide association study, is a statistical analysis method to reveal specific genetic variations, usually single nucleotide polymorphisms, with particular phenotypes or diseases. The power to scan whole genomes from large scale samples made the method an efficient tool for information discovery. In the last decades, the application of GWAS has flourished, which benefited our understanding related to diseases, breeding and many other topics. In this review, we overviewed the history of GWAS, as well as different approaches to perform the analysis under different circumstances during different stages. Meanwhile, we also showed how different GWAS approaches benefited diverse research and application fields, and the potential limitations of the method.

scholarly journals Phylogeographic Structure of Freshwater Tor sp. in River Basins of Sabah, Malaysia

Fishes ◽  
2021 ◽  
Vol 6 (4) ◽  
pp. 44
Author(s):  
Helena Biun ◽  
Ahemad Sade ◽  
Rolando Robert ◽  
Kenneth Francis Rodrigues
Keyword(s):  
Isolation By Distance ◽  
In Situ Conservation ◽  
Haplotype Network ◽  
Phylogeographic Structure ◽  
Loop Region ◽  
Mtdna Sequence ◽  
Population Structuring ◽  
D Loop ◽  
Main Barrier

We characterized the genetic diversity, phylogeography, and demography of Tor sp. (Cyprinidae) from Sabah, Malaysian Borneo, by examining nucleotide variation in the D-loop region of the mtDNA. Sequence analysis of 18 populations (N = 173) yielded 35 unique mtDNA haplotypes with mean haplotype and nucleotide diversity of 0.833 and 0.023, respectively. Phylogenetic reconstructions using Bayesian, neighbor-joining, and maximum parsimony methods, as well as haplotype network, revealed four well-defined clades, namely, the eastern, central, northwestern, and southwestern clades, which corresponded to evolutionarily significant units (ESUs). These ESUs were estimated to have become separated since the late Miocene to Pliocene era (between 5 and 1 million years ago), with the central highlands of Sabah Crocker Trusmadi Range (CTR) constituting the main barrier to genetic exchange between clades. Analysis of molecular variance (AMOVA) and pairwise genetic differentiation showed significant population structuring (Φct = 0.575–1.000, p < 0.05). We further identified eight major groups of river systems harboring reproductively isolated Tor subpopulations. Neutrality statistics and Bayesian skyline plots (BSP) suggested constant population size over time for most Tor populations. Tor sp. in Sabah is comprised of four ESUs (eastern, central, northwestern, and southwestern ESUs), and that each ESU can be compartmentalized into 1–4 MUs. Due to isolation by distance, the highest number of MU occurs in the low-elevation drainages of Eastern Sabah, which is the largest in terms of land area. The evidence provided by this study supports the hypothesis that the four ESU represent genetically distinct subpopulations of Tor and highlight the urgent need for the in situ conservation of these subpopulations.

scholarly journals Genetic differentiation in the genus Characodon: implications for conservation and taxonomy

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11492
Author(s):  
Rosa G. Beltrán-López ◽  
Rodolfo Pérez-Rodríguez ◽  
Ofelia C. Montañez-García ◽  
Juan M. Artigas-Azas ◽  
Michael Köck ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Evolutionary History ◽  
Genetic Distances ◽  
Genetic Groups ◽  
Evolutionary Significant Units ◽  
Significant Genetic Structure ◽  
D Loop ◽  
History Of ◽  
The Subject ◽  
Phylogeographic Study

The subfamily Goodeinae is a group of fishes endemic to the Mexican highlands. Most of the species are restricted to small and isolated streams or springs. Within this subfamily, the genus Characodon is the earliest diverging lineage of which three species have been described: C. lateralis, C. audax, and C. garmani, with the latter, considered extinct. Characodon lateralis and C. audax are classed as endangered, and have been the subject of taxonomic controversy since their description: previous studies have recognized a genetic differentiation in two groups separated by the El Salto waterfall, but morphological analyses contradict these genetic results. We perform a phylogeographic study using the mitochondrial cytb gene and d-loop region to elucidate the evolutionary history of C. lateralis and C. audax. The results with both markers show the presence of two highly differentiated haplogroups; one distributed north and the other distributed south of the waterfall, with genetic distances of 1.7 and 13.1% with cytb and d-loop respectively, and divergence calculated to have occurred 1.41 Mya. Significant genetic structure was found within each haplogroup and suggests the existence of at least four Evolutionary Significant Units (ESUs) within the examined populations. The possible processes identified as contributing to the formation of differentiated genetic groups are isolation, low population size, recurrent bottlenecks, and the strong sexual selection exhibited by the genus.

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