scholarly journals Mitochondrial DNA D-loop sequence variability reveals high haplotype diversity and multiple maternal origins in twelve indigenous goat populations from Tanzania.

2021 ◽  
Author(s):  
Athumani Nguluma
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Haplotype Diversity ◽  
Capra Hircus ◽  
Maternal Origin ◽  
High Genetic Diversity ◽  
Ecological Zones ◽  
Goat Population ◽  
D Loop ◽  
Indigenous Goats

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.

Short Communication: Mitochondrial DNA D-loop sequence diversity and origin of Chinese pony breeds (Equus caballus)

2013 ◽  
Vol 93 (3) ◽  
pp. 313-319 ◽  
Author(s):  
Sheng-lin Yang ◽  
Ai-Ping Li ◽  
Long-xing Xu ◽  
Haibing Yang
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Short Communication ◽  
Phylogenetic Analyses ◽  
Haplotype Diversity ◽  
Equus Caballus ◽  
Sequence Diversity ◽  
Maternal Origin ◽  
Loop Sequence ◽  
D Loop

Yang, S.-l., Li, A.-P., Xu, L.-x. and Yang, H. 2013. Short Communication: Mitochondrial DNA D-loop sequence diversity and origin of Chinese pony breeds ( Equus caballus ). Can. J. Anim. Sci. 93: 313–319. Previous studies based on mitochondrial DNA (mtDNA) data have shown that Chinese horses have high genetic diversity. However, little is known about the genetic diversity of mtDNA D-loop sequences and maternal origin of five Chinese pony breeds. In the present study, genetic diversity of 343-bp D-loop sequences for136 individuals representing five Chinese pony breeds was analyzed. To address the question of the single and multiple maternal origin of Chinese pony populations, 13 partial mtDNA D-loop reference sequences from GenBank representing eight ancient and modern horse breeds (Connemara, Garrano, Sorraia, Pottok, Losino, Cheju, Tuva and a Swedish horse) were added to conduct the phylogenetic analyses. A total of 59 haplotypes and 50 polymorphic loci were detected, the haplotype diversity (h) ranged from 0.894 to 0.947 and nucleotide diversity (π) ranged from 0.0184 to 0.0229, suggesting relatively abundant genetic diversity in the Debao, Yunnan and the Guizhou breeds. The phylogenetic tree and median-joining network show multiple maternal origins of the five Chinese pony breeds.

scholarly journals The genetic profiles and maternal origin of local sheep breeds on Java Island (Indonesia) based on complete mitochondrial DNA D-loop sequences

2020 ◽  
Vol 13 (12) ◽  
pp. 2625-2634
Author(s):  
Alek Ibrahim ◽  
I Gede Suparta Budisatria ◽  
Rini Widayanti ◽  
Wayan Tunas Artama
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Relationships ◽  
Haplotype Diversity ◽  
Maternal Origin ◽  
Loop Analysis ◽  
High Genetic Diversity ◽  
Sheep Breeds ◽  
Loop Region ◽  
D Loop ◽  
Genetic Profiles

Background and Aim: Java Island is one of the islands in Indonesia which has local sheep breeds with specific characteristics and native development geography in certain regions. This study aimed to determine the genetic profiles and maternal origin of six local sheep breeds on Java Island. Materials and Methods: This study was conducted by identifying the profiles of complete mitochondrial DNA (mtDNA) displacement loop (D-loop) region sequences on a total of 22 individual in six local sheep breeds on Java Island, including Javanese thin-tailed (JTT), Javanese Fat-Tailed (JFT), Batur (BTR), Wonosobo (WSB), Garut (GRT), and Priangan (PRG) sheep. The D-loop region was amplified using specific primers, and the polymerase chain reaction (PCR) was performed. The PCR products were purified and sequenced. Results: The mtDNA D-loop analysis identified 21 haplotypes in the analyzed 22 animals with 123 polymorphic sites (V) consisting of 60 singleton variable sites (S) and 63 parsimony informative sites (P). Within all breeds tested, the haplotype diversity, the average number of pairwise differences (K), and nucleotide diversity (Pi) were 0.99567, 25.36364, and 0.02153, respectively. The genetic distance (D) within groups and between groups was 0.001-0.006 and 0.004-0.036, respectively. The phylogeny resulted in the presence of two haplogroups (Hap), which are 5 Hap A and 16 Hap B. All JTT, JFT, BTR, and WSB breeds were in the same cluster in Hap B, whereas GRT and PRG breeds were in clusters in both Hap A and Hap B. Conclusion: The high genetic diversity in six local sheep breeds on Java Island suggests that they originated from different genetic sources. JTT sheep have closer genetic relationships to JFT, BTR, and WSB sheep, and they are close to European sheep, whereas GRT sheep have closer genetic relationships to PRG sheep. Both are closer to Asian sheep than to European sheep.

scholarly journals Mitochondrial DNA-based diversity study of Hungarian brown hares (Lepus europaeus Pallas 1778)

2016 ◽  
pp. 23-29
Author(s):  
Noémi Soós ◽  
Szilvia Kusza
Keyword(s):  
Mitochondrial Dna ◽  
Large Scale ◽  
Haplotype Diversity ◽  
Lepus Europaeus ◽  
Brown Hare ◽  
High Genetic Diversity ◽  
Ongoing Research ◽  
European Continent ◽  
Hair Samples ◽  
D Loop

The brown hare being an important game species which is widespread across the European continent has been in focus of many population genetic studies. However only a few comprising researches can be found on the diversity of Central-European populations. The aim of our large scale long term ongoing study is to fill this gap of information on the species by describing the genetic history and structure of the brown hare populations of the area using both mitochondrial DNA markers and genomic skin and hair colour regulating genes. This article gives forth a part of our results concerning the mitochondrial DNA diversity of Hungarian brown hares based on amplification of a 512 bp long D-loop sequence. N=39 tissue or hair samples have been collected from 15 sampling sites on the Hungarian Great Plain. We have described a high level of haplotype diversity (Hd=0.879±0.044) based on a 410 bp alignment of our sequences. We have found 17 haplotypes within our sample set with the nucleotid diversity of π=0.01167±0.0022. Our ongoing research shows high genetic diversity for the brown hare in the studied region and a second alignment with 156 sequences downloaded from GenBank indicates a geographic pattern of haplotypes among the studied populations though these results need confirmation by our further analyses.

scholarly journals Microsatellite and mitochondrial DNA analyses unveil the genetic structure of native sheep breeds from three major agro-ecological regions of India

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Rekha Sharma ◽  
Sonika Ahlawat ◽  
Himani Sharma ◽  
Priyanka Sharma ◽  
Poonam Panchal ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Relationships ◽  
Haplotype Diversity ◽  
Genetic Erosion ◽  
Population Expansion ◽  
Scientific Management ◽  
Ecological Zones ◽  
Sheep Breeds ◽  
Indigenous Sheep

AbstractSheep farming has been fundamental to many civilizations in the world and is practiced in India since antiquity. Several thousand years of adaptation to local environmental conditions and selective breeding have evolved 44 sheep breeds in India. They are paramount in terms of economic, scientific, and cultural heritage. Genetic characterization information is imperative for sustainable utilization and conservation of ovine heritage. In this study, the genetic diversity, differentiation, and structure of 11 indigenous sheep breeds from three different agro-ecological zones of India were explored with genomic microsatellite loci and mitochondrial DNA (D loop). The estimated diversity parameters indicated that populations retained high levels of genetic diversity (Na = 8.27 ± 0.17; Ho = 0.65 ± 0.01), which provides an optimistic viewpoint for their survival. However, significant inbreeding was also observed in the nine populations. Moderate genetic differentiation existed among the groups (FST = 0.129 ± 0.012), and most likely clusters existing in the dataset are seven. Phylogenetic clustering was in line with the geographical locations of sheep populations. Mitochondrial sequences revealed high haplotype diversity with the existence of maternal haplogroups A, B, and C, and signals of population expansion. Decreased genetic diversity and unique maternal lineage (C) in endangered Tibetan and Bonpala sheep breed, warrant their immediate scientific management. Overall, the quantitative data reported here on the extant variability, and genetic relationships among the Indian sheep breeds, provide critically important inputs that will be valuable for the decision-making process on their management, both for the conservation of endangered breeds, and formulation of breeding programs to check genetic erosion.

GENETIC DIVERSITY OF BROILER CHICKEN BRANDS RAISED IN ARID AND SEMI-ARID ZONES OF NORTHERN NIGERIA USING MITOCHONDRIAL DNA

2021 ◽  
Vol 5 (2) ◽  
pp. 456-461
Author(s):  
A. Y. Abdullahi ◽  
M. Nasir ◽  
A. G. Khalee ◽  
R. M. Ashiru ◽  
H. M. Zango ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Rural Areas ◽  
Dna Analysis ◽  
Haplotype Diversity ◽  
Climatic Conditions ◽  
Arid Zones ◽  
High Genetic Diversity ◽  
Hot Dry Season ◽  
Semi Arid

A sector of broiler production is growing very fast to meet the high demand of meat in Nigeria. However, high mortality rates among the broilers especially during the hot dry season in arid and semi-arid zones is worrisome. There is a need for molecular genetics study that could aid in management, conservation and sustainable exploitation of this species. To evaluate the genetic diversity of broilers raised in these regions, a total of forty-six broilers were randomly sampled from eight different brands (Agrited, Amo, Chi, Fol-hope, Obasanjo, Olam, Yammfy and Zatech) for mitochondrial DNA analysis. Four haplotypes were detected among all the samples used that belong to the four strains. The sequences of mitochondrial regions revealed high haplotype diversity (0.78600) and low nucleotide diversity (0.00286).  Lower genetic diversity observed may increase the chances of rapid disease infection and distribution during any disease outbreak. Introduction of new strains of broilers with high genetic diversity is highly recommended. Future study should be conducted on the performance of these strains during the extremely hot temperature period in arid and semi-arid zones of Nigeria. This is to provide reliable information for the sake of local broiler farmer’s benefit who invests largely on this sector. The study will also help the geneticists from these brands to develop a strain that could survive and perform excellently under severe climatic conditions of the rural areas of arid and semi-arid zones of Nigeria

scholarly journals Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10607
Author(s):  
David H. Mauki ◽  
Adeniyi C. Adeola ◽  
Said I. Ng’ang’a ◽  
Abdulfatai Tijjani ◽  
Ibikunle Mark Akanbi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Bos Indicus ◽  
Haplotype Diversity ◽  
Population History ◽  
Genetic Introgression ◽  
High Genetic Diversity ◽  
African Cattle ◽  
D Loop ◽  
Mtdna Lineages

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.

scholarly journals PSVII-23 Phylogenetic analysis of mitochondrial DNA D-loop region for excavated horse bones at the Asian archaeological sites

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 311-312
Author(s):  
Jihye Cha ◽  
Haesu Ko ◽  
Bong-Hwan Choi ◽  
Gulwon Jang ◽  
Dajeong Lim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Haplotype Diversity ◽  
Reference Sequence ◽  
Archaeological Sites ◽  
Migration Route ◽  
Human Society ◽  
Loop Region ◽  
Domestic Horses ◽  
D Loop

Abstract Horses have played a significant role in the development of human society. As an important domestic animal, horses have been used for transport, labor, food and recreation. It is widely accepted that the horse was probably first domesticated on the Eurasian steppes from Ukraine to Turkestan between the fifth and fourth millennium BC, and the earliest domesticated horses subsequently spread out from their original range. However, we currently have little genetic evidence to demonstrate whether Korean domestic horse breeds originated in Korea or if it came into the area via an ancient migration route. In the present study, to obtain more knowledge of the origin and genetic diversity of Korean domestic horses, we analyzed seventeen 247-bp mitochondrial DNA (mtDNA) D-loop sequences of ancient horse bones excavated from seven archaeological sites located in the southern Korean Peninsula and Mongolia, aged between the fifth century B.C and nineteenth century A.D. The seventeen ancient horses revealed 9 variable positions when compared with the reference sequence (GenBank X79547). All the substitutions were transitions, and defined a total of 11 unique haplotypes with the haplotype diversity value of 0.9118±0.056. Among the 11 haplotypes, 3 haplotypes were detected more than once and were thus shared by individuals from the same or close archaeological sites. The largest haplotype consisted of 5 individuals, with another two haplotypes containing 2 individuals respectively, and eight haplotypes were singletons. The data indicate an abundant genetic diversity of the Korean ancient horses, and also suggest that the origin of Korean domestic horses is complex, and several maternal lines were introduced into the gene pool of Korean horses after their initial domestication.

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.

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