scholarly journals Genetic diversity among two native Indian chicken populations using cytochrome c oxidase subunit I and cytochrome b DNA barcodes

2021 ◽  
pp. 1389-1397
Author(s):  
Ankit R. Dave ◽  
Dhaval F. Chaudhary ◽  
Pooja M. Mankad ◽  
Prakash G. Koringa ◽  
D. N. Rank
Keyword(s):  
Genetic Diversity ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Cytochrome B ◽  
Haplotype Analysis ◽  
Haplotype Diversity ◽  
Cyt B ◽  
Oxidase Subunit ◽  
Commercial Chicken ◽  
Chicken Breeds

Background and Aim: India has large varieties (recognized, unrecognized) of native chickens (Desi) scattered throughout the country, managed under scavenging system different from commercial chicken breeds. However, they are less investigated for genetic diversity they harbor. The present study was planned to evaluate genetic diversity among two native chicken populations of North Gujarat (proposed Aravali breed) and South Gujarat (Ankleshwar breed). Aravali chicken, a distinct population with unique characters different from the registered chicken breeds of India is under process to be registered as a new chicken breed of Gujarat, India. Materials and Methods: Two mitochondrial markers, namely, cytochrome c oxidase subunit I (COX I) and cytochrome b (Cyt b) genes were studied across 10 birds from each population. Methodology included sample collection (blood), DNA isolation (manual), polymerase chain reaction amplification of mitochondrial genes, Sanger sequencing, and purification followed by data analysis using various softwares. Results: Haplotype analysis of the COX I gene unveiled a total eight and three haplotypes from the Aravali and Ankleshwar populations, respectively, with haplotype diversity (Hd) of 92.70 % for the Aravali and 34.50% for the Ankleshwar breed. Haplotype analysis of the Cyt b gene revealed a total of four haplotypes from the Aravali population with 60% Hd and no polymorphism in Ankleshwar breed. The phylogenetic analysis uncovered Red Jungle Fowl and Gray Jungle Fowl as prime roots for both populations and all domestic chicken breeds. Conclusion: Study findings indicated high genetic variability in Aravali chicken populations with COX I mitochondrial marker being more informative for evaluating genetic diversity in chickens.

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 Genetic diversity of Bemisia tabaci species colonizing cassava in Central African Republic characterized by analysis of cytochrome c oxidase subunit I

PLoS ONE ◽  
2017 ◽  
Vol 12 (8) ◽  
pp. e0182749 ◽  
Author(s):  
Brice Kette Tocko-Marabena ◽  
Semballa Silla ◽  
Christophe Simiand ◽  
Innocent Zinga ◽  
James Legg ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Bemisia Tabaci ◽  
Central African Republic ◽  
Oxidase Subunit

scholarly journals Genetic diversity analysis of brown marmorated stink bug, Halyomorpha halys based on mitochondrial COI and COII haplotypes

2020 ◽  
Author(s):  
Juncong Yan ◽  
Chandan Pal ◽  
Diane Anderson ◽  
Gábor Vétek ◽  
Péter Farkas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Genetic Difference ◽  
Management Strategies ◽  
Haplotype Diversity ◽  
Halyomorpha Halys ◽  
Brown Marmorated Stink Bug ◽  
Stink Bug ◽  
China And Japan

Abstract Background: In the past decade, the brown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera: Pentatomidae) has caused extensive damage to global agriculture. As a high-risk pest for many countries, including New Zealand, it is important to explore its genetic diversity to enhance our knowledge on and devise management strategies for BMSB populations. In this study, two mitochondrial genes, Cytochrome c oxidase I (COI) and Cytochrome c oxidase II (COII) were used to explore the genetic diversity among 463 BMSB individuals collected from 12 countries. Result: In total, 51 COI and 29 COII haplotypes of BMSB were found, which formed 59 combined haplotypes (5 reported and 54 novel). Of these, H1h1 was the predominant haplotype. The haplotype diversity (Hd) and nucleotide diversity (π) were high while the neutrality (Fu's Fs) values were negative for the BMSB populations in the native countries, China, and Japan. For the BMSB populations from the invaded countries, the Fu's Fs values were negative for populations from Chile, Georgia, Hungary, Italy, Romania, Turkey, and USA, indicating that those populations are under demographic expansion. In comparison, the Fu's Fs values were positive for the populations from Austria, Serbia, and Slovenia, revealing a potential population bottleneck. Analysis of molecular variance (AMOVA) suggested that significant genetic difference exist between groups of populations: China, Japan, and the invasive populations. Conclusion: This study revealed that the haplotype diversity of the BMSB populations was high in those two studied countries where BMSB is native to (China and Japan) but low in those countries which have been invaded by the species. The analysis indicated that multiple invasions of BMSB occurred and a new stable genetic cluster has established in Europe and the USA. The study also revealed that three ancestral lines and most of the novel haplotypes were evolved from them. Moreover, we observed two genetic clusters in the invasive populations that are formed during different invasion events. Our study provided a comprehensive overview on the global haplotypes distribution thus expanding the existing knowledge on BMSB genetic diversity that potentially could play an important role in formulating feasible pest management strategies, especially biocontrol.

scholarly journals The last Pleistocene glaciations phylogeography episode of Phaneroptera falcata (Poda, 1761) (Orthoptera: Tettigoniidae) in the Volga River basin based on the mtDNA Cytochrome C Oxidase subunit 1 (COI) gene fragment

2020 ◽  
Vol 6 ◽  
pp. 279-291
Author(s):  
Inessa O. Karmazina ◽  
Stanislav K. Korb ◽  
Andrey P. Mikhailenko ◽  
Alexander B. Ruchin ◽  
Nikolai V. Shulaev ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
River Basin ◽  
Haplotype Diversity ◽  
Coi Gene ◽  
Gene Fragment ◽  
Volga River ◽  
Volga River Basin ◽  
Oxidase Subunit ◽  
Middle Volga

This study is to research the phylogeography of Phaneroptera falcata (Poda, 1761) in the Volga river basin based on the mtDNA Cytochrome C Oxidase subunit 1 (COI) gene fragment at the last Pleistocene glaciation episode. The studied location is the Volga river basin, a territory within the central and partially southern parts of European Russia; it includes the rivers Volga, Oka, Khoper and Don basins. We used the traditional molecular phylogeography methods: mtDNA COI gene fragment from the key locations within the studied area was sequenced and then analyzed (cladogram topology, haplotype diversity, cladogram calibration etc.). The phylogenetic tree shows the dispersion of our samples over the following regions: Lower Volga, Middle Volga, Lower Oka, Middle Oka, Upper Oka, Don basin, Khoper basin. Nine haplotypes determined from our samples; they are grouped into 7 haplogroups. Six of them are in the basins of the main rivers of the Volga region: three haplogroups - on the Oka (Upper, Middle and Lower Oka respectively), haplogroups of the Khoper and Don basins, and the haplogroup of the Middle Volga combining two subgroups – Lower and Middle Volga basins. The distribution of found haplogroups correlates with big river basins in the Volga area (Volga, Oka, Khoper, Don).

scholarly journals Genetic diversity analysis of brown marmorated stink bug, Halyomorpha halys based on mitochondrial COI and COII haplotypes

2020 ◽  
Author(s):  
Juncong Yan ◽  
Chandan Pal ◽  
Diane Anderson ◽  
Gábor Vétek ◽  
Péter Farkas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Genetic Difference ◽  
Management Strategies ◽  
Haplotype Diversity ◽  
Halyomorpha Halys ◽  
Brown Marmorated Stink Bug ◽  
Stink Bug ◽  
China And Japan

Abstract Background: In the past decade, the brown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera: Pentatomidae) has caused extensive damage to global agriculture. As a high-risk pest for many countries, including New Zealand, it is important to explore its genetic diversity to enhance our knowledge on and devise management strategies for BMSB populations. In this study, two mitochondrial genes, Cytochrome c oxidase I (COI) and Cytochrome c oxidase II (COII) were used to explore the genetic diversity among 463 BMSB individuals collected from 12 countries.Result: In total, 51 COI and 29 COII haplotypes of BMSB were found, which formed 59 combined haplotypes (5 reported and 54 novel). Of these, H1h1 was the predominant haplotype. The haplotype diversity (Hd) and nucleotide diversity (π) were high while the neutrality (Fu's Fs) values were negative for the BMSB populations in the native countries, China, and Japan. For the BMSB populations from the invaded countries, the Fu's Fs values were negative for populations from Chile, Georgia, Hungary, Italy, Romania, Turkey, and USA, indicating that those populations are under demographic expansion. In comparison, the Fu's Fs values were positive for the populations from Austria, Serbia, and Slovenia, revealing a potential population bottleneck. Analysis of molecular variance (AMOVA) suggested that significant genetic difference exist between groups of populations: China, Japan, and the invasive populations.Conclusion: This study revealed that the haplotype diversity of the BMSB populations was high in those two studied countries where BMSB is native to (China and Japan) but low in those countries which have been invaded by the species. The analysis indicated that multiple invasions of BMSB occurred and a new stable genetic cluster has established in Europe and the USA. The study also revealed that three ancestral lines and most of the novel haplotypes were evolved from them. Moreover, we observed two genetic clusters in the invasive populations that are formed during different invasion events. Our study provided a comprehensive overview on the global haplotypes distribution thus expanding the existing knowledge on BMSB genetic diversity that potentially could play an important role in formulating feasible pest management strategies, especially biocontrol.

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