Genomic characterization of three Vietnamese indigenous chicken varieties using mitochondrial D-loop sequences

2019 ◽  
Vol 99 (4) ◽  
pp. 833-839
Author(s):  
Son Quang Do ◽  
Lan Thi Phuong Nguyen ◽  
Thinh Hoang Nguyen ◽  
Trung Quoc Nguyen
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Diversity Indices ◽  
Fixation Index ◽  
Indigenous Chicken ◽  
Loop Region ◽  
Red Junglefowl ◽  
D Loop ◽  
Genomic Characterization

In this study, partial mitochondrial DNA (mtDNA) D-loop sequences of three Vietnamese indigenous chicken varieties, including Mong Tien Phong, To, and Sau Ngon, were analyzed to access genetic diversity and the maternal lineages of origin. A 525 bp fragment of the mtDNA D-loop region was sequenced from a total of 61 chickens of the three varieties. A neighbor-joining phylogenetic tree was assembled from the haplotypes obtained and reference sequences of mtDNA D-loop sequences of Red Junglefowl and domestic chickens from National Center for Biotechnology Information database. Genetic diversity indices and analysis of molecular variance were performed. Evaluation of genetic relationships between the three varieties was carried out with pairwise fixation index (FST). In total, 16 haplotypes were identified in the chickens studied. These haplotypes were classified in three haplogroups (A, B, and E) with the majority grouped in haplogroup B and haplogroup E. All three chicken varieties studied were distributed into 2–3 haplogroups and all three haplogroups found in this study are also represented by Red Junglefowl. In conclusion, all three Vietnamese indigenous chicken varieties have likely originated from multiple maternal lineages and potentially descended from the Red Junglefowl.

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.

scholarly journals Molecular Characterization of Sudanese and Southern Sudanese Chicken Breeds Using mtDNA D-Loop

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Charles E. Wani ◽  
Ibrahim A. Yousif ◽  
Muntasir E. Ibrahim ◽  
Hassan H. Musa
Keyword(s):  
Genetic Variation ◽  
Genetic Difference ◽  
Genetic Relationships ◽  
Indigenous Chicken ◽  
Commercial Strain ◽  
Pcr Product ◽  
D Loop ◽  
Chicken Breeds ◽  
Networks Analysis

The objective of this study was to assess the genetic relationships and diversity and to estimate the amount of gene flow among the five chicken populations from Sudan and South Sudan and commercial strain of egg line White Leghorn chickens. The chicken populations were genotyped using mtDNA D-loop as a molecular marker. PCR product of the mtDNA D-loop segment was 600 bp and 14 haplotypes were identified. The neighbor-joining phylogenetic tree indicated that the indigenous Sudanese chickens can be grouped into two clades, IV and IIIa only. Median joining networks analysis showed that haplotype LBB49 has the highest frequency. The hierarchal analysis of molecular variance (AMOVA) showed that genetic variation within the population was 88.6% and the differentiation among the population was 11.4%. When the populations was redefined into two geographical zones, rich and poor Savanna, the results were fractioned into three genetic variations: between individuals within population 95.5%, between populations within the group 0.75%, and genetic variation between groups 3.75%. The pair wise Fst showed high genetic difference between Betwil populations and the rest with Fst ranging from 0.1492 to 0.2447. We found that there is large number of gene exchanges within the Sudanese indigenous chicken (Nm=4.622).

scholarly journals Genomic Characterization of a Set of Iberian Peninsula Bovine Local Breeds at Risk of Extinction: Morenas Gallegas

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1956
Author(s):  
María Asunción García-Atance ◽  
Carlos Carleos ◽  
Susana Dunner ◽  
Paulina G. Eusebi ◽  
Castor José Rivero ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Nucleotide Polymorphisms ◽  
Inbreeding Coefficients ◽  
Genomic Tools ◽  
Conservation Plan ◽  
Genomic Characterization ◽  
Conservation Plans ◽  
Genetic Signatures

A set of five local bovine breeds in danger of extinction named Cachena, Caldelá, Limiá, Frieiresa, and Vianesa and included in the group of Morenas Gallegas are located in the Autonomous Community of Galicia at the Northwest of Spain. Local authorities launched a conservation plan at the end of the 21th century in order to preserve this important genetic reservoir. However, Morenas Gallegas bovine breeds never have been analyzed with genomic tools and this information may be crucial to develop conservation plans. The aim of the study was to analyze their genetic diversity and genetic relationships with a set of local and cosmopolitan European bovine breeds using single nucleotide polymorphisms. Our results show own genetic signatures for the Morenas Gallegas breeds which form a separate cluster when compared to the Spanish breeds analyzed, with the exception of the Cachena breed. The genetic diversity levels of the Morenas Gallegas were intermediate or high, and low inbreeding coefficients can be found except for the Frieiresa breed (11%). Vianesa breed evidenced two lineages depending on the Frieiresa component influence. The Morenas Gallegas bovine breeds group represent an important Spanish bovine genetic reservoir and despite their classification within a single generic group, the five breeds show their own genetic uniqueness.

scholarly journals 220 Mitochondrial DNA polymorphism as a measure of genetic diversity in African tilapia fish

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 47-48
Author(s):  
Ekei Ikpeme ◽  
Ekerette Ekerette ◽  
Michael Ozoje
Keyword(s):  
Genetic Diversity ◽  
Genetic Analysis ◽  
Cytochrome B ◽  
Fixation Index ◽  
Cyt B ◽  
Important Species ◽  
Loop Region ◽  
South West ◽  
D Loop ◽  
Two Populations

Abstract This study focused on the assessment of genetic diversity in African tilapia fish (Oreochromis niloticus) obtained from two populations (Domita in South-South and Odeda in South-West, Nigeria) using the displacement loop (D-loop) and cytochrome B region of the mitochondrial deoxyribonucleic acid (mtDNA). A total of 28 samples (15 from South-South and 13 from South-West) were used for the genetic analysis. DNA was extracted from the tissue of all the samples using Quik-gDNATM miniPrep kit. The D-loop region was sequenced for all samples from the two populations, while cytochrome b (cyt b) region of mtDNA was only sequenced for samples from South-South population Multiple sequence alignment was carried out using molecular evolutionary genetic analysis (MEGA) software before subsequent genetic analyses. There were 176, 162 and 144 polymorphic sites for D-loop of South-South, South-West and cyt b of South-South populations, respectively. Haplotype diversities (Hd) were 1.00 ± 0.024 and 1.00 ± 0.030 while nucleotide diversities were 0.168 ± 0.086 and 0.161 ± 0.084 for D-loop of South-South and South-West populations, respectively. For the cyt b, haplotype and nucleotide diversities were 0.91 ± 0.003 and 0.051 ± 0.016. The genetic distance inferred between D-loop regions of South-South and South-West populations was 0.243. Phylogenetic analysis grouped the samples into two clusters based on population. Analysis of molecular variance (AMOVA) revealed 37.32% variation within population and 62.68% variation among population with a significant fixation index of 0.627 (P < 0.05). The findings of this study revealed high level of genetic diversity among the tilapia populations and may serve as pivot information for the genetic improvement of this important species.

scholarly journals Characterization of genetic diversity of an invasive Lessepsian Migrant, Nemipterus randalli Russell, 1986 from its native and non-native regions using mitochondrial DNA marker

2020 ◽  
Author(s):  
MURUGESAN SRIHARI ◽  
SUSANTHI SILPA ◽  
ANNAM PAVAN-KUMAR ◽  
YARON TIKOCHINSKI ◽  
DANIEL GOLANI ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Mediterranean Sea ◽  
Haplotype Diversity ◽  
Loop Region ◽  
Geographical Population ◽  
D Loop ◽  
The Mediterranean ◽  
Network Tree

This study assessed and compared the genetic diversity of Nemipterus randalli across its native and non-native regions analysing the mitochondrial DNA D-loop region. Including all the geographical population samples, 68 haplotypes were observed with an average haplotype diversity value of 0.92±0.04. Relatively, a smaller number of haplotypes was observed in the invasive range of the Mediterranean Sea. All other native geographical samples showed high haplotype and nucleotide diversity values. A significant high genetic differentiation value was observed between the native population samples of India and the invasive samples of the Mediterranean Sea. In the median-joining network tree, N. randalli from the Mediterranean Sea and the Red Sea formed a single haplogroup while other samples from India are clustered into two haplogroups.

scholarly journals Genetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese

2021 ◽  
Vol 9 (8) ◽  
pp. 1612
Author(s):  
Werner Ruppitsch ◽  
Andjela Nisic ◽  
Patrick Hyden ◽  
Adriana Cabal ◽  
Jasmin Sucher ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Safety Evaluation ◽  
Gene Clusters ◽  
Northern Region ◽  
Genomic Diversity ◽  
High Genetic Diversity ◽  
Pathogenic Factors ◽  
Flavor Development ◽  
Genomic Characterization

In many dairy products, Leuconostoc spp. is a natural part of non-starter lactic acid bacteria (NSLAB) accounting for flavor development. However, data on the genomic diversity of Leuconostoc spp. isolates obtained from cheese are still scarce. The focus of this study was the genomic characterization of Leuconostoc spp. obtained from different traditional Montenegrin brine cheeses with the aim to explore their diversity and provide genetic information as a basis for the selection of strains for future cheese production. In 2019, sixteen Leuconostoc spp. isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro. All isolates were identified as Ln. mesenteroides. Classical multilocus sequence tying (MLST) and core genome (cg) MLST revealed a high diversity of the Montenegrin Ln. mesenteroides cheese isolates. All isolates carried genes of the bacteriocin biosynthetic gene clusters, eight out of 16 strains carried the citCDEFG operon, 14 carried butA, and all 16 isolates carried alsS and ilv, genes involved in forming important aromas and flavor compounds. Safety evaluation indicated that isolates carried no pathogenic factors and no virulence factors. In conclusion, Ln. mesenteroides isolates from Montenegrin traditional cheeses displayed a high genetic diversity and were unrelated to strains deposited in GenBank.

scholarly journals Genetic Diversity of Maternal Lineage in the Endangered Kiso Horse Based on Polymorphism of the Mitochondrial DNA D-Loop Region

2014 ◽  
Vol 76 (11) ◽  
pp. 1451-1456 ◽  
Author(s):  
Masaki TAKASU ◽  
Namiko ISHIHARA ◽  
Teruaki TOZAKI ◽  
Hironaga KAKOI ◽  
Masami MAEDA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Maternal Lineage ◽  
Loop Region ◽  
D Loop

Genetic diversity in mitochondrial DNA D-loop region of indigenous pig breeds of India

2022 ◽  
Vol 101 (1) ◽  
Author(s):  
Rongala Laxmivandana ◽  
Yoya Vashi ◽  
Dipjyoti Kalita ◽  
Santanu Banik ◽  
Nihar Ranjan Sahoo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Pig Breeds ◽  
Loop Region ◽  
D Loop
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