scholarly journals Genetic diversity of H’mong short tail dog based on sequencing of the D-loop hypervariable -1 region (HV1)

2021 ◽  
Vol 19 (2) ◽  
pp. 245-257
Author(s):  
Pham Thanh Hai ◽  
Bui Xuan Phuong ◽  
Tran Huu Coi ◽  
Phung Thanh Tung ◽  
Ngo Quang Duc ◽  
...  

The H'mong short tail dog is breed indigenous dogs, distributed in mountainousareas of northern Vietnam. H'mong short tail dog possesses many valuable properties such as intelligence, agility, good health, good shape, human friendliness, ease of training and it can fully meet the needs of war Dogs intelligence, strength, good parenting, people friendly and more importantly, still keeping wild characteristics of hunting dogs. The total 45 samples (blood) collected from 45 individuals in two provinces of Northern Vietnam (Ha Giang and Lao Cai), were used to assess genetic diversity based on sequencing hypervariable – 1 region (HV1) in D-loop genes. In the current study showed that genetic diversity of H'mong short tail dog was high with nucleotide diversity (Pi = 0.00801), haplotype diversity (Hd = 0.96162) and average number of nucleotide differences (Kt = 5.18384). Furthermore, 25 different haplotypes were recorded and divided into four main groups: A, B, C, and E. Of which, seven new haplotypes in haplogroups A (An1 to An7) and 18 haplotypes have been published in the world. In addition, H'mong short tail dog was found rare haplogroups (B1, C2, E1 and E4). Notably, there is none individuals contain haplotype of haplogroups (D and F). H'mong short tail dog were identified 38 single nucleotide polymorphisms, including 32 nucleotide base substitution/base insertion and 6 nucleotide indel mutation. Almost mutation was transversion (31/32) and only one nucleotide transition mutations. Phylogenetic tree shown that H'mong short tail dog have close relationship with dogs origin from East Asia (China, Japan and Korea).

2021 ◽  
Vol 20 (1) ◽  
pp. 1-11
Author(s):  
S.O. DUROSARO ◽  
B.T. OSHINOWO ◽  
A.C. AKPOJO ◽  
L.T. OLUYOMBO ◽  
I.C. NWOSU ◽  
...  

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.


2012 ◽  
Vol 33 (1) ◽  
pp. 45-53 ◽  
Author(s):  
Cinthya Alejandra Ureña-Aranda ◽  
Alejandro Espinosa de los Monteros

Gopherus flavomarginatus (Testudinidae) is endemic to a series of discontinuous, isolated basins collectively known as the Bolson de Mapimí in the Chihuahuan Desert. Its numbers declined after catastrophic levels of exploitation during the mid-20th century. However currently, the Bolson Tortoise appears to be on a path to recovery owing to intensive, sustained conservation efforts. We sequenced an 842-bp-long fragment of the D-loop from 76 individuals distributed throughout the species’ range. The results revealed only two haplotypes. An AMOVA showed that 95% of the variance occurred among populations, whereas the remaining 5% was explained by genetic differences within populations. Tectonic processes together with ecological transformation during the Pleistocene and Holocene may be responsible for the reduction in this species’ genetic variation. A bottleneck during which a significant percentage of the haplotype diversity was lost would result in genetic homogeneity. Although there is demographic growth, the lack of genetic diversity is indicative of the potential crisis that the Bolson Tortoise is facing, and awareness must be brought to this situation.


2021 ◽  
Vol 17 (2) ◽  
pp. 105-114
Author(s):  
Anik Budhi Dharmayanthi ◽  
Achmad Muchsinin ◽  
Afriana Pulungan ◽  
Moch Syamsul Arifin Zein

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.


2021 ◽  
Vol 46 (2) ◽  
pp. 93-105
Author(s):  
S. Suhardi ◽  
P. Summpunn ◽  
S. Wuthisuthimethavee

Kalang (KBuf), Krayan (KrBuf), and Thale Noi buffaloes (TBuf) are swamp buffalo genetic resources in Indonesia and Thailand. The maternally inherited mitochondrial DNA (mtDNA), particularly D-loop region is an important material for phylogenetic inference and analyzing genetic diversity. Therefore, the objectives of the present study were to evaluate genetic diversity and to reconstruct the phylogenetic tree within buffalo breeds in Kalimantan, Indonesia, and Phatthalung, Thailand using mtDNA D-loop sequences. A total of one hundred forty buffaloes (70 males and 70 females) were observed including 40 buffaloes from North (NK), 40 from East (EK), and 40 from South Kalimantan (SK) provinces Indonesia and 20 from Phatthalung (PT) province, Thailand. DNA samples were isolated from buffalo tail hairs. DNA sequences were manually assembled using BioEdit program with consideration of gaps and ambiguous sequences. The phylogenetic tree of buffalo was generated by PHYLIP software. The observed variables included haplotype diversity, genetic distance, and genetic tree. The 956 bp of amplified mtDNA D-loop fragment presented a total of 24 haplotypes with several mutations that included transitions (293), transversions (60), deletions (15), and insertions (20). The neighbor-joining tree using the Kimura 2 parameter model demonstrated two local buffalo clusters among buffalo from Kalimantan and Thailand with four buffalo relationship patterns observed from buffaloes in Kalimantan Island (KBuf and KrBuf), Indonesia. The Results of the present study demonstrated that the buffaloes sequence analysis revealed relatively high diversity and is a good basis to perform selection and modern buffalo breeding development.


Author(s):  
Athumani Nguluma

The Small East African (SEA) goat (Capra hircus) breeds are widely distributed in different agro-ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goats populations, namely Fipa (n = 44), Songwe (n = 34), Tanga (n = 33), Pwani (n = 40), Newala (n = 49), Lindi (n = 46), Gogo (n = 73), Pare (n = 67), Maasai (n = 72), Sukuma (n = 67), and Ujiji (n = 67), based on the mitochondrial DNA (mtDNA) D-loop. High haplotype (Hd = 0.9619-0.9945) and nucleotide (π = 0.0120-0.0162) diversities were revealed from a total of 389 haplotypes. The majority of the haplotypes (h = 334) drawn from all the goat populations belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro-ecological regions of the country.


2020 ◽  
Vol 33 (1) ◽  
pp. 89-97
Author(s):  
Salah H. Faraj ◽  
Asaad Y. Ayied ◽  
Khalaf A. H. Al-Rishdy

The present study was undertaken to characterize the genetic diversity of the aromatase cytochrome P450 (CYP19) gene in 34 cows (15 local, 14 Holstein, and 5 Crosses) in Iraq. The objectives of the present study are to detect SNPs (mutations) in promoter p1.1 of the CYP19 gene in cattle bred in Iraq using sequencing techniques. We identified five single-nucleotide polymorphisms (SNP) loci of the CYP19 gene that were detected, namely G933T, G994C, A1044G, A1062T, and C1468A. The results showed the presence of 3, 4, and 2 polymorphic sites leading to the construction of 4, 5, and 3 different haplotypes for Holstein, local, and crosses respectively. Haplotype diversity were 0.791, 0.752, and 0.700 respectively. While nucleotide diversity was 0.0017, 0.0022, and 0.0013 respectively. Besides, we carried out a phylogenetic analysis of these sequences to address the evolutionary relationship between the animal species. These fragments were assigned in the GenBank database under the accession numbers: LC490756, LC490757, LC491437, LC491438, LC491439, LC491588, and LC491589.


Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1970
Author(s):  
Emel Özkan Ünal ◽  
Fulya Özdil ◽  
Selçuk Kaplan ◽  
Eser Kemal Gürcan ◽  
Serdar Genç ◽  
...  

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.


2021 ◽  
Vol 16 (10) ◽  
pp. 131-143
Author(s):  
Hai Pham Thanh ◽  
Phuong Bui Xuan ◽  
Coi Tran Huu ◽  
Duc Ngo Quang ◽  
Duy Vu Dinh

The H'mong docked tail is indigenous breed of dogs distributed in mountainous area of northern Vietnam. These dogs possess positive characteristics such as intelligence, agility, good health, good shape, human friendliness, ease of training and fully meet the criteria of a war dog. We had studied the diversity and origin of Vietnamese H’mong dogs based on the molecular data of the mitochondrial HV1 region. A total of seventy individual dogs were sampled from Lao Cai, Ha Giang and Hai Phong provinces of northern Vietnam and were sequenced. Among the targeted dogs, 29 haplotypes were recorded and divided into four main groups: A, B, C and E. In our study, nine new haplotypes were recorded and all of them belong to haplotype group A. Group A was the most common with 24 haplotypes (82.76%) followed by C, E and B with 2 (6.9%), 2 (6.9%) and 1 haplotypes (3.4%) respectively. The genetic variations in the H'mong dogs were high with nucleotide diversity (Pi = 0.03179), haplotype diversity (Hd = 0.95648) and average number of nucleotide differences (Kt = 5.18384) and the p-genetic distances range was from 0.2 to 2.9%. This study has provided a valuable platform for breeding and conservation and management of the species in Vietnam.


2021 ◽  
Author(s):  
Yingying Ye ◽  
Chengrui Yan ◽  
Ferruccio Maltagliati ◽  
Zeqin Fu ◽  
Baoying Guo ◽  
...  

Abstract Perna viridis is a mussel commonly distributed along the Asian Indo-Pacific coasts. It is one of the main cultured species of that region. Previous studies focused mostly on the native populations within single countries; with the present study we analyzed the genetic diversity of P. viridis in a large study area, spanning from Oman to southern China. Three molecular markers were used, namely portions of the nuclear ITS region, and the mitochondrial COI gene and D-Loop region. The nuclear marker showed moderate levels of genetic diversity (haplotype diversity h = 0.543 to 0.897) and nucleotide diversity π = 0.0022 to 0.0064); whereas mitochondrial markers exhibited higher levels of genetic variability (h = 0.858 to 0.964 and π = 0.0012 to 0.0079). The estimates of inter-sample genetic divergence (FST) and the analysis of molecular variance highlighted that the Thai population is genetically divergent from the others. Our results showed the genetic variation of P. viridis at the rim of South China Sea and obtained the genetic basic information of P. viridis.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10607
Author(s):  
David H. Mauki ◽  
Adeniyi C. Adeola ◽  
Said I. Ng’ang’a ◽  
Abdulfatai Tijjani ◽  
Ibikunle Mark Akanbi ◽  
...  

The African cattle provide unique genetic resources shaped up by both diverse tropical environmental conditions and human activities, the assessment of their genetic diversity will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the genetic diversity of cattle samples from Nigeria using both maternal and paternal DNA markers. Nigerian cattle can be assigned to 80 haplotypes based on the mitochondrial DNA (mtDNA) D-loop sequences and haplotype diversity was 0.985 + 0.005. The network showed two major matrilineal clustering: the dominant cluster constituting the Nigerian cattle together with other African cattle while the other clustered Eurasian cattle. Paternal analysis indicates only zebu haplogroup in Nigerian cattle with high genetic diversity 1.000 ± 0.016 compared to other cattle. There was no signal of maternal genetic structure in Nigerian cattle population, which may suggest an extensive genetic intermixing within the country. The absence of Bos indicus maternal signal in Nigerian cattle is attributable to vulnerability bottleneck of mtDNA lineages and concordance with the view of male zebu genetic introgression in African cattle. Our study shades light on the current genetic diversity in Nigerian cattle and population history in West Africa.


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