scholarly journals Maternal ancestry analyses of red tilapia strains based on D-loop sequences of seven tilapia populations

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7007
Author(s):  
Bingjie Jiang ◽  
Jianjun Fu ◽  
Zaijie Dong ◽  
Min Fang ◽  
Wenbin Zhu ◽  
...  
Keyword(s):  
Genetic Relationship ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Important Food ◽  
Red Tilapia ◽  
The Gift ◽  
D Loop ◽  
Food Fish ◽  
Genetic Structures ◽  
Relationship Of

Background Many tilapia species or varieties have been widely introduced and have become an economically important food fish in China. Information on the genetic backgrounds of these populations is deficient and requires more research, especially for red tilapia strains. Methods In the present study, displacement loop (D-loop) sequences were used to evaluate the genetic relationship and diversity of seven tilapia populations that are widely cultured in China; this was done specifically to speculate on the maternal ancestry of red tilapia strains. Three red tilapia varieties of Oreochromis ssp., Taiwan (TW), Israel (IL), and Malaysia (MY) strains and other populations, including O. aureus (AR), O. niloticus (NL), O. mossambicus (MS), and the GIFT strain of O. niloticus, were collected and analyzed in this study. Results A total of 146 polymorphic sites and 32 haplotypes of D-loop sequences were detected among 332 fish and four major haplotypes were shared among the populations. The TW and NL populations had a greater number of haplotypes (20 and 8, respectively). The haplotype diversity (Hd) and nucleotide diversity (π) of each population ranged from 0.234 to 0.826, and 0 to 0.060, respectively. The significant positive Tajima’s D value of neutral test were detected in the NL, IL, and MY populations (P < 0.05), which indicated these populations might have not experienced historical expansion. According to the pairwise F-statistics, highly significant genetic differentiations were detected among populations (P < 0.01), with the exception of the IL and MY populations (P > 0.05). The nearest K2P genetic distance (D = 0.014) was detected between the MS and TW populations, whereas, the farthest (D = 0.101) was found between the GIFT and AR populations. The results from the molecular variance analysis (AMOVA) showed that there was an extremely significant genetic variation observed among the populations (P < 0.01), which contained 63.57% of the total variation. In view of the genetic relationship of red tilapia strains with other populations, TW and IL were detected with more similar genetic structures related to MS, and MY was more genetically similar to GIFT (or NL), which could provide more genetic evidence for the red tilapia strains maternal ancestry.

scholarly journals Diversitas Genetika dan Identifikasi Jenis Kelamin Burung Pelikan (Pelecanus conspicillatus Temminck, 1824) di Penangkaran Taman Margasatwa Ragunan Jakarta

2021 ◽  
Vol 17 (2) ◽  
pp. 105-114
Author(s):  
Anik Budhi Dharmayanthi ◽  
Achmad Muchsinin ◽  
Afriana Pulungan ◽  
Moch Syamsul Arifin Zein
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Bird Populations ◽  
Low Genetic Diversity ◽  
In Captivity ◽  
D Loop ◽  
Haplotype 1

Pelicans (Pelecanus conspicillatus) is one of the wild species that have a widely distribution. This bird has been successfully bred in Ragunan Zoo, Jakarta. The indicator of inbreeding in the captive population is shown by the decrease of nucleotide diversity and number of haplotypes. The result of genetic diversity analysis using D-loop fragment sequences showed low genetic diversity with nucleotide diversity (p) = 0.00064 ± 0.00010 and haplotype diversity (Hd) = 0.532 ± 0.061 in Pelecanus conspicillatus populations in the Ragunan Zoo. However, negative Fu's Fs value (-3,246) indicates population expansion. We found that there were seven haplotypes in bird populations in the captivity: haplotype 1, 2 and 3 consist of 43 individuals (65.15%), five individuals (7.57%), and 14 individuals (21.21%), respectively. For each haplotype 4, 5, 6 and 7 is only represented by one individual of Pelecanus conspicillatus (1.51%). The sex ratio of males to females is 1: 8.86 with four males identified as haplotype 1, and one male on haplotypes 3, 5 and 7, respectively. Genetic diversity data of the population is an important way for designing long-term plans and goals in efforts to maintain genetic diversity of the Pelecanus conspicillatus population in captivity.

scholarly journals Maternal Phylogenetic Relationships and Genetic Variation among Rare, Phenotypically Similar Donkey Breeds

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1109
Author(s):  
Andrea Mazzatenta ◽  
Massimo Vignoli ◽  
Maurizio Caputo ◽  
Giorgio Vignola ◽  
Roberto Tamburro ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Total Population ◽  
Maternal Inheritance ◽  
Genetic Material ◽  
Breeding Programs ◽  
Phylogenetic Relations ◽  
Bioinformatics Software ◽  
D Loop ◽  
Components Analysis ◽  
Relationship Of

The mitochondrial DNA (mtDNA) D-loop of endangered and critically endangered breeds has been studied to identify maternal lineages, characterize genetic inheritance, reconstruct phylogenetic relations among breeds, and develop biodiversity conservation and breeding programs. The aim of the study was to determine the variability remaining and the phylogenetic relationship of Martina Franca (MF, with total population of 160 females and 36 males), Ragusano (RG, 344 females and 30 males), Pantesco (PT, 47 females and 15 males), and Catalonian (CT) donkeys by collecting genetic data from maternal lineages. Genetic material was collected from saliva, and a 350 bp fragment of D-loop mtDNA was amplified and sequenced. Sequences were aligned and evaluated using standard bioinformatics software. A total of 56 haplotypes including 33 polymorphic sites were found in 77 samples (27 MF, 22 RG, 8 PT, 19 CT, 1 crossbred). The breed nucleotide diversity value (π) for all the breeds was 0.128 (MF: 0.162, RG: 0.132, PT: 0.025, CT: 0.038). Principal components analysis grouped most of the haplogroups into two different clusters, I (including all haplotypes from PT and CT, together with haplotypes from MF and RG) and II (including haplotypes from MF and RG only). In conclusion, we found that the primeval haplotypes, haplogroup variability, and a large number of maternal lineages were preserved in MF and RG; thus, these breeds play putative pivotal roles in the phyletic relationships of donkey breeds. Maternal inheritance is indispensable genetic information required to evaluate inheritance, variability, and breeding programs.

scholarly journals Maternal Origins and Haplotype Diversity of Seven Russian Goat Populations Based on the D-loop Sequence Variability

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1603
Author(s):  
Tatiana Deniskova ◽  
Nekruz Bakoev ◽  
Arsen Dotsev ◽  
Marina Selionova ◽  
Natalia Zinovieva
Keyword(s):  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Maternal Origin ◽  
Migration Routes ◽  
Altai Mountain ◽  
Loop Sequence ◽  
Genetic Pattern ◽  
D Loop ◽  
Diverse Groups ◽  
Official Recognition

The territory of modern Russia lies on the crossroads of East and West and covers various geographical environments where diverse groups of local goats originated. In this work, we present the first study on the maternal origin of Russian local goats, including Altai Mountain (n = 9), Dagestan Downy (n = 18), Dagestan Local (n = 12), Dagestan Milk (n = 15), Karachaev (n = 21), Orenburg (n = 10), and Soviet Mohair (n = 7) breeds, based on 715 bp D-loop mitochondrial DNA (mtDNA) sequences. Saanen goats (n = 5) were used for comparison. Our findings reveal a high haplotype (HD = 0.843–1.000) and nucleotide diversity (π = 0.0112–0.0261). A total of 59 haplotypes were determined in the Russian goat breeds, in which all differed from the haplotypes of the Saanen goats. The haplotypes identified in Altai Mountain, Orenburg, Soviet Mohair, and Saanen goats were breed specific. Most haplotypes (56 of 59) were clustered together with samples belonging to haplogroup A, which was in accordance with the global genetic pattern of maternal origin seen in most goats worldwide. The haplotypes that were grouped together with rare haplogroups D and G were found in the Altai Mountain breed and haplogroup C was detected in the Soviet Mohair breed. Thus, our findings revealed that local goats might have been brought to Russia via various migration routes. In addition, haplotype sharing was found in aboriginal goat populations from overlapping regions, which might be useful information for their official recognition status.

Genetic analysis of populations of brown trout (Salmo trutta L.) from the Romanian Carpathians

2019 ◽  
Vol 32 ◽  
pp. 23
Author(s):  
Gina-Oana Popa ◽  
Andreea Dudu ◽  
Doru Bănăduc ◽  
Angela Curtean-Bănăduc ◽  
Alexandru Burcea ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Brown Trout ◽  
Salmo Trutta ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Population Genetic Analysis ◽  
High Haplotype Diversity ◽  
Brown Trout Salmo Trutta ◽  
D Loop ◽  
Romanian Carpathians

The Carpathian Mountains are one of the most complex orogenetic areas of Europe, with unique fauna, including the brown trout (Salmo trutta). In this study we performed population genetic analysis of 12 different S. trutta populations using two types of molecular markers: nine microsatellites and mitochondrial D-loop sequences. The following working hypothesis was considered: the Romanian Carpathians and their surrounding lowlands can be key relief units based on which the S. trutta genetic diversity, spread, distribution, connectivity, relative isolation and genetic divergence can be at least partially explained. The phylogenetic analysis revealed that the majority of sequences were grouped in the Danubian clade. The high haplotype diversity of the 12 analyzed brown trout populations can be explained by the high nucleotide diversity. The microsatellite analysis revealed an inbreeding event for all the loci and for the populations analyzed. The Romanian Carpathians' shape and geographic orientation play a zoogeographical key role driving force in respect to the S. trutta populations.

scholarly journals Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1970
Author(s):  
Emel Özkan Ünal ◽  
Fulya Özdil ◽  
Selçuk Kaplan ◽  
Eser Kemal Gürcan ◽  
Serdar Genç ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Loop Region ◽  
Geographical Regions ◽  
D Loop ◽  
Significant Comparison ◽  
Loop Regions ◽  
Frequent Haplotype

In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD) and nucleotide diversity (πD), for the Turkish donkey populations ranged from 0.533 ± 0.180 (Tekirdağ–Malkara, MAL) to 0.933 ± 0.122 (Aydin, AYD), and from 0.01196 ± 0.0026 (Antalya, ANT) to 0.02101 ± 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries’ donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions.

scholarly journals Genetic diversity of Cyprinion macrostomus (Heckel, 1843) populations in the Euphrates and Tigris rivers based on partial cytochrome b sequences of mitochondrial DNA

2018 ◽  
Vol 65 (4) ◽  
Author(s):  
Arif Parmaksız
Keyword(s):  
Sequence Analysis ◽  
Genetic Structure ◽  
Cytochrome B ◽  
Nucleotide Diversity ◽  
Important Food ◽  
Tigris River ◽  
The Family ◽  
Total Dna ◽  
Food Fish ◽  
Neutrality Tests

Cyprinion macrostomus (Heckel, 1843), thriving in both Euphrates and Tigris river systems, is an economically important food fish species of the family Cyprinidae. It is important to know genetic structure of fis populations in terms of identification of genetic structure of stocks for facilitating sustainable fishing and conservation strategies.The present study, evaluated genetic structure of C. macrostomus populations in Euphrates and Tigris rivers using mtDNA cytochrome b sequence analysis. A total number of 44 C. macrostomus specimens were collected from Euphrates and Tigris rivers and total DNA was isolated from muscle tissue. Approximately 600 bp of mtDNA cyt b site was amplified by PCR and 8 polymorphic and 8 haplotypes were identified after sequence analysis. Mean haplotype and nucleotide diversity were calculated as 0.738 and 0.00253 respectively. Both populations had similar values in terms of haplotype as well as nucleotide diversity and neutrality tests were also found to be statistically insignificant.

scholarly journals A PRELIMINARY COMPARISON OF MITOCHONDRIAL D-LOOP REGION OF FUNAAB ALPHA AND NIGERIAN INDIGENOUS CHICKENS

2021 ◽  
Vol 20 (1) ◽  
pp. 1-11
Author(s):  
S.O. DUROSARO ◽  
B.T. OSHINOWO ◽  
A.C. AKPOJO ◽  
L.T. OLUYOMBO ◽  
I.C. NWOSU ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Genetic Erosion ◽  
Nucleotide Polymorphisms ◽  
Indigenous Chickens ◽  
Loop Region ◽  
D Loop ◽  
Selective Forces ◽  
Loss Of Diversity

Nigerian indigenous chickens possess immunity from endemic diseases and have a better survival rate than commercial hybrid strains under local production conditions. FUNAAB Alpha chicken was developed by improving Nigerian indigenous chickens through crossbreeding and selection. This study compared the mitochondrial d-loop of FUNAAB Alpha and Nigerian indigenous chickens to check likely genetic erosion and loss of diversity in development of FUNAAB Alpha breed. Blood samples were collected from Nigerian indigenous (n=23) and FUNAAB Alpha (n=20) chickens sampled from farms and houses in Ogun state, Nigeria. The Hypervariable 1 (HV1) of the mitochondrial d-loop region was amplified and sequenced. Single nucleotide polymorphisms present in HV1 of chickens were identified using Clustal W. Genetic diversity of the region was determined using DnaSp v5 while selective forces acting on the chickens were predicted using HyPhy software implemented inside MEGA 6 software. Phylogenetic relationship among FUNAAB Alpha, Nigerian indigenous and other chicken breeds was determined using MEGA 6 software. Five polymorphisms were identified in FUNAAB Alpha chickens while twelve were identified in Nigerian indigenous chickens. All the polymorphisms identified in FUNAAB Alpha chickens were also observed in Nigerian indigenous chickens while seven polymorphisms were unique to Nigerian indigenous chickens. Higher diversity indices were observed in Nigerian indigenous chickens (number of haplotype: 4; haplotype diversity: 0.743±0.012; nucleotide diversity: 0.014±0.0013 and average number of nucleotide differences: 4.332) compared with FUNAAB Alpha chickens (number of haplotype: 2; haplotype diversity: 0.485±0.001; nucleotide diversity: 0.008±0.0001 and average number of nucleotide differences: 2.424). Positive selective forces were acting on FUNAAB Alpha chickens while negative selective forces were acting on Nigerian indigenous chickens. Phylogenetic analysis revealed that FUNAAB Alpha chickens clustered with Nigerian indigenous and South American chickens. It can be concluded that there was likely genetic erosion and loss of diversity in development of FUNAAB Alpha breed. Breeding programmes aimed at improvement of genetic diversity and reduction of genetic erosion should be applied in subsequent improvement of FUNAAB Alpha chickens.

scholarly journals Short Communication: Lack of differentiation within the bigeye tuna population of Indonesia

2017 ◽  
Vol 18 (4) ◽  
pp. 1406-1413
Author(s):  
NI PUTU DIAN PERTIWI ◽  
BUDI NUGRAHA ◽  
RIRIK KARTIKA SULISTYANINGSIH ◽  
IRWAN JATMIKO ◽  
ANDRIANUS SEMBIRING ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Short Communication ◽  
Haplotype Diversity ◽  
Genetic Data ◽  
Bigeye Tuna ◽  
High Haplotype Diversity ◽  
Loop Control ◽  
Thunnus Obesus ◽  
Sampling Locations ◽  
D Loop

Pertiwi NPD, Nugraha B, Kartika R, Sulistyaningsih RK, Jatmiko I, Sembiring A, Mahardini A, Cahyani NKD, Anggoro AW, Madduppa HH, Ambariyanto A, Barber PH, Mahardika GN. 2017. Short Communication: Lack of differentiation within the bigeye tuna population of Indonesia. Biodiversitas 18: 1406-1413. All highly migratory tuna and tuna-like species have vast feeding grounds and spawning grounds. Indonesia’s tuna catch is the largest in the world. However, genetic diversity in the population structure within particular tuna species in Indonesia is very limited. Here we provide genetic data for bigeye tuna (Thunnus obesus) covering fishing grounds and local fish markets throughout Indonesia. A fragment of mitochondrial DNA in the D-loop control region was amplified from samples collected across Indonesia in the biennium 2012-2013. The results showed high haplotype diversity and low nucleotide diversity in our samples. Little differentiation occured between the eleven diverse sampling locations, nor was any separation detected between general regions of Indonesia, nor between samples from fishing grounds and samples from fish markets.

Genetic Relationship of Ramie Germplasm Revealed by RSAP, SRAP, and SSR Markers

2013 ◽  
Vol 38 (5) ◽  
pp. 840-847 ◽  
Author(s):  
Zi-Zheng ZOU ◽  
Jian-Hua CHEN ◽  
Ming-Bao LUAN ◽  
Jin-Xia GUO ◽  
Chao WANG ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Genetic Relationship ◽  
Relationship Of
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