scholarly journals GENEBANK ANALYSIS: SINGLE NUCLEOTIDE POLYMORPHISMS OF ANIMALS MITOCHONDRIAL GENOME UKRAINIAN GRAY AND UKRAINIAN WHITEHEAD CATTLE BREEDS

2017 ◽  
Vol 53 ◽  
pp. 241-248
Author(s):  
Yu. V. Podoba ◽  
V. O. Pinchuk ◽  
V. P. Boroday
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Dna Sequences ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Ex Situ ◽  
Single Nucleotide ◽  
Cattle Breeds ◽  
D Loop ◽  
Mtdna Haplogroup

Examination of variation in mitochondrial DNA (mtDNA) control region sequences has been pivotal in the elucidation of bovine phylogeography. Initial studies have demonstrated a deep bifurcation in bovine mtDNA phylogeny, which indicates a predomestic divergence between the two major taxa of cattle, humped zebu (Bos indicus) and humpless taurine (Bos taurus). Subsequent genetic investigations have yielded further inference regarding origins within the B. taurus lineage. B. taurus mtDNA sequences fall into one of five ancestral star-like haplotypic clusters, which are geographically distributed. Just one of these clusters, T3, predominates in Western Europe. Symmetrically, diversity within Africa is composed almost exclusively of members of a separate haplotypic cluster, T1, which is rarely detected elsewhere. The almost mutually exclusive geographic distribution of these two haplotypic clusters allows geographical exceptions to be securely identified as secondary introductions. We investigated a comparative analysis of mitochondrial genome sequences for different breeds of cattle (Bos taurus, Bos indicus) with global genetic bank. Mitochondrial DNA sequences from bovine animals (Bos taurus) breeds Ukrainian Whitehead and Ukrainian Gray freely available on the global genetic bank (http://www.ncbi.nlm.nih.gov/Genebank/). Local alignment of sequences for mitochondrial genome of different cattle breeds was performed using the program MEGA 4.0. For the detection of nucleotide replacements used mitochondrial DNA sequence of Bos taurus Hereford breed (Anderson S. at al., 1982) as a reference (accession number V00645). Here we report the analysis results of testing for 9 genotypes Ukrainian Gray mitochondrial DNA sequences showed that one animal (GQ129208) has haplotype Bos indicus, other belongs to haplogroup T1 with European origin mtDNA. Analysis of single nucleotide replacement in one of the hypervariable regions mtDNA (position number 16019-16339) shows, that among 10 submitted genotypes of Ukrainian Whitehead the 3 of them (FJ014303, FJ014298, FJ014294) relating to T1a mtDNA haplogroup of African origin, which characterized by replacement of T to C at position 16255. Also have been two animals (FJ014301, FJ014295) with single nucleotide replacements with relatives to Bos indicus mtDNA haplogroup. We performed alignment with reference sequences (Bos_taurus_v00654.1) and comparative nucleotide sequences analysis of another hypervariable D-loop (position number 1-240) mtDNA with 5 Ukrainian Whitehead genotypes and 5 Ukrainian Gray genotypes represented in genetics bank. Among the Ukrainian Whitehead genotypes (FJ014298, FJ014297, FJ014296, FJ014295, FJ014294) all were polymorphic that characterizes large differentiation these animals for maternal and describe deep heterogeneous parent population of studied group. We determined one animal with genotype FJ014295 was significantly different by the number of segregation sites. The analyzed sequences (FJ014290, FJ014289, FJ014288, FJ014287, FJ014286) of 5 Ukrainian Gray genotypes showed no polymorphism in hypervariable D-loop (position number 1-240) mtDNA. The mtDNA analysis of different species of animals allowed to distribute their mtDNA belonging to European, African and Asian haplogroups. The technique, which allows to differentiate the animals represented by their belonging to the respective haplogroups. The process that gave rise to different genotypes in one lineage is clearly of fundamental importance in understanding intraspecific mitochondrial polymorphism and evolution in mammals. Сomprehensive study genetic material provide more opportunities to optimize costs in-situ conservation of different cattle breeds, to optimize methods and techniques which used in ex-situ conservation programmes of National gene bank of animal genetic resources.

scholarly journals Identificación de ADN mitocondrial Bos taurus en poblaciones de ganado Cebú Brahman colombiano

2007 ◽  
Vol 7 (2) ◽  
pp. 21
Author(s):  
Gloria Patricia Barrera ◽  
Rodrigo Alfredo Martínez ◽  
Manuel Fernando Ariza
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Divergence ◽  
Bos Taurus ◽  
Consensus Sequence ◽  
Bos Indicus ◽  
Zebu Cattle ◽  
American Continent ◽  
Brahman Cattle ◽  
D Loop ◽  
Dna Fragment

<p>El continente americano fue colonizado en el siglo XVI por los europeos quienes introdujeron por primera vez el ganado bovino de origen <em>Bos taurus</em>. La introducción de ganado <em>Bos indicus </em>ocurrió muchos años después, con las primeras importaciones desde la India, las cuales incluyeron principalmente machos. Con el fin de estudiar la participación de hembras <em>Bos taurus </em>en el origen del ganado Cebú colombiano, se secuenció un fragmento del ADN mitocondrial de 374 pb (<em>D-Loop</em>) en seis animales de la raza Cebú Brahman colombiano y 20 individuos representativos de las cinco razas criollas colombianas: seis de Blanco Orejinegro (BON), cinco de Costeño con  Cuernos (CCC), tres de Romosinuano (ROMO), cuatro de Casanareño (CAS) y dos de San Martinero (SM). Adicionalmente, para el mismo fragmento se secuenciaron dos individuos de la raza española Pirenaica, como referente <em>Bos taurus</em>. La comparación de las secuencias reveló que los animales de la raza Cebú Brahman colombiano analizados presentaron ADN mitocondrial de origen taurino con mayor cercanía respecto de las razas criollas de origen <em>Bos taurus </em>europeo que con relación a las secuencias consenso <em>Bos indicus</em>, frente a las que se hallaron mayores divergencias. Adicionalmente, las divergencias de las razas criollas colombianas con respecto al consenso <em>Bos taurus </em>europeo variaron entre 0,005 y 0,014, resultado que sugiere la participación de matrilineajes <em>Bos taurus </em>en el origen del Cebú Brahman colombiano.</p><p> </p><p><strong>Identification of mitochondrial DNA of Bos taurus origin in Colombian Zebu Brahman cattle </strong></p><p>The American continent was colonised in the XVI century by the Europeans who introduced the Bos taurus cattle. The introduction of Bos indicus cattle was done a few years later with cattle from India, mainly males. In order to study the participation of Bos Taurus females in the origin of the Colombian Zebu cattle, a 374 bp mitochondrial DNA fragment was sequenced (D-Loop) in six animals belonging to Colombian Zebu Brahman breed and 20 individuals representative of he five Colombian native breeds: 6 of Blanco Orejinegro (BON), five of Costeño Con Cuernos (CCC), three of Romosinuano (ROMO), four of Casanareño (CAS) and two of San Martinero (SM). As a reference to Bos taurus, two individuals of the Spanish Pirenaica breed were also sequenced for the same fragment. Comparison between sequences revealed that the Zebu Brahman cattle has mitochondrial DNA of Bos Taurus origin and closer to the native breeds of Spanish origin. Although described as Bos indicus, it showed the lowest genetic divergence when compared with the consensus sequence of European Bos taurus. The genetic divergences of the Colombian native breeds compared with the European Bos Taurus ranged between 0.005 and 0.014. This suggests the participation of Bos taurus matrilineages in the origin of the Colombian Zebu Brahman cattle.</p>

scholarly journals Diversity of D-loop mitochondrial DNA (mtDNA) sequence in Bali and Sumba Ongole cattle breeds

2019 ◽  
Vol 44 (4) ◽  
pp. 335
Author(s):  
J. Jakaria ◽  
T. Musyaddad ◽  
S. Rahayu ◽  
M. Muladno ◽  
C. Sumantri
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Distance ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Haplotype Diversity ◽  
Complete Sequence ◽  
Distance Method ◽  
Mtdna Sequence ◽  
D Loop ◽  
Bali Cattle

This study aimed to investigate the diversity of the complete sequence of D-loop mitochondrial DNA (mtDNA) in Bali and Sumba Ongole (SO) cattlebreeds. A total of 24 blood samples were collected from Bali cattle (19 heads) and SO cattle (5 heads), and were extracted and then analyzed to obtain the sequence of D-loop mt DNA.Multiple alignments of the whole sequence of D-loop mtDNA were determined using clustal W. Genetic distance was calculated using a p-distance method, while the genetic tree was constructed using neighbor-joining (NJ) based on MEGA 6. Haplotype number, haplotype diversity (Hd) and nucleotide diversity (Pi) were analyzed using DnaSP version 6. As a result, the sequence of D-loop mtDNA in Bali cattle (921-1119 bp) and SO cattle (913 bp) was reported to have 8 and 4 haplotypes. Hd and Pi of Bali cattle reached 0.625±0.139 and 0.0266±0.0145, respectively, which wwere different from that of SO cattle, namely 0.900±0.1610 and 0.0064±0.0015, respectively. Specifically, we found 22 bp-repetitive nucleotide in Bali cattle, existing 3-9 times with a length of 66-198 bp present in D-loop mtDNA. This unique feature did not exist in SO cattle. Genetic distance and genetic tree determined according to sequence in hypervariability (HV-1) region of D-loop mtDNA (166 bp) resulted in satisfied separation, successfully classifying Bos javanicus, Bos indicus, and Bos taurus cluster.

scholarly journals Suitability of existing commercial single nucleotide polymorphism chips for genomic studies in Bos indicus cattle breeds and their Bos taurus crosses

2018 ◽  
Vol 135 (6) ◽  
pp. 432-441 ◽  
Author(s):  
Nilesh Nayee ◽  
Goutam Sahana ◽  
Swapnil Gajjar ◽  
Ananthasayanam Sudhakar ◽  
Kamlesh Trivedi ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Cattle Breeds ◽  
Genomic Studies

scholarly journals Genetic Diversity of Nepalese Indigenous Cattle Breeds Based on D-Loop Mitochondrial DNA

2021 ◽  
Vol 19 (2) ◽  
pp. 103-108
Author(s):  
Neena Amatya Gorkhali ◽  
Chhiring Sherpa ◽  
Aashish Dhakal ◽  
Sanjay Dhungana ◽  
Saroj Sapkota ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Sample Population ◽  
Cattle Population ◽  
Indigenous Cattle ◽  
Ancestral Origin ◽  
Cattle Breeds ◽  
North East ◽  
D Loop

Nepalese cattle are known for their genetic potentiality concerning inhabitant in extreme climatic conditions, surviving in the scarce food supply, and resistant to several diseases. We aimed to assess Nepal’s ancestral origin and genetic diversity of indigenous cattle breeds based on hyper-variable D loop mtDNA sequences. Three cattle breeds (Siri, Achammi, & Lulu) comprising the total sample population (n= 75) were employed in the study where the mt DNA information of two breeds (Achammi & Lulu) were retrieved from the published source. Hyper-variable D loop (910bp) of Siri cattle was PCR amplified and sequenced. This study claims that the possible ancestral origin of Bos taurus and Bos indicus mtDNA lineage in the Nepalese cattle population is majorly influenced by China and India, respectively. This study suggests that Nepalese cattle can be divided into two major groups: Bos taurus and Bos indicus, where most of the cattle population was of Bos indicus origin. The sampled population can be classified into three significant haplogroups: T3 (25%), I1 (48%), and I2 (27%) revealing a higher genetic diversity among the Nepalese cattle population. Only T3 taurine haplogroup was found in the sampled population. It was consistent with the fact that the absence of T1 haplogroup in North-East Asian cattle. In terms of Bos indicus, the I1 haplogroup was dominant over I2. Higher genetic diversity can be appropriate reasoning for Nepalese cattle’s survival in a harsh environment and low food conditions.

scholarly journals Mitochondrial DNA Methylation and Human Diseases

2021 ◽  
Vol 22 (9) ◽  
pp. 4594
Author(s):  
Andrea Stoccoro ◽  
Fabio Coppedè
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Nuclear Dna ◽  
Epigenetic Modification ◽  
Nuclear Genome ◽  
Epigenetic Modifications ◽  
Human Diseases ◽  
Loop Region ◽  
D Loop

Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.

scholarly journals Cytogenetic and molecular analysis of the Pantaneiro cattle breed

2006 ◽  
Vol 41 (11) ◽  
pp. 1609-1615 ◽  
Author(s):  
Érica Cunha Issa ◽  
Wilham Jorge ◽  
José Robson Bezerra Sereno
Keyword(s):  
Mitochondrial Dna ◽  
Y Chromosome ◽  
Molecular Analysis ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Cattle Breed ◽  
Zebu Cattle ◽  
European Origin ◽  
Paternal Line

The objective of this work was to characterize Pantaneiro cattle genetically through its paternal ancestry by the morphology of the Y chromosome, whether submetacentric or acrocentric, as well as to identify the maternal ancestry through mitochondrial DNA. The karyotype and mitochondrial DNA of 12 bulls of Pantaneiro breed were analyzed. The Y chromosome was analyzed in lymphocyte metaphases and the mitochondrial DNA by diagnosing its haplotype (Bos taurus and Bos indicus). Among Pantaneiro animals analyzed three had a taurine (submetacentric) Y and nine had a zebuine (acrocentric) Y chromosome, suggesting breed contamination by Zebu cattle, once Pantaneiro is considered to be of European origin. The mitochondrial DNA was exclusively of taurine origin, indicating that the participation of zebuines in the formation of the breed occurred entirely through the paternal line.

Allele frequencies of gene polymorphisms related to economic traits in Bos taurus and Bos indicus cattle breeds

2011 ◽  
Vol 82 (6) ◽  
pp. 717-721 ◽  
Author(s):  
Makoto KANEDA ◽  
Bang Zhong LIN ◽  
Shinji SASAZAKI ◽  
Kenji OYAMA ◽  
Hideyuki MANNEN
Keyword(s):  
Gene Polymorphisms ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Allele Frequencies ◽  
Economic Traits ◽  
Cattle Breeds

Sequence amplification and gene rearrangement in parasitic nematode mitochondrial DNA.

Genetics ◽  
1988 ◽  
Vol 120 (3) ◽  
pp. 707-712
Author(s):  
B C Hyman ◽  
J L Beck ◽  
K C Weiss
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Dna Sequences ◽  
Gene Rearrangement ◽  
Tandem Repeats ◽  
Parasitic Nematode ◽  
Mitochondrial Gene ◽  
Sequence Organization ◽  
Large Size ◽  
Mitochondrial Gene Order

Abstract The nematode Romanomermis culicivorax, an obligate mosquito parasite, possesses a 26 kilobase (kb) mitochondrial genome. The unusually large size is due to transcriptionally active DNA sequences present as 3.0 kb direct tandem repeats and as inverted portions of the repeating unit located elsewhere in the mitochondrial DNA (mtDNA). The genome rearrangements involved in establishing this unusual sequence organization may have dramatically altered conventional mitochondrial gene order. Genes for subunits of the cytochrome c oxidase complex (COI and COII) are normally closely linked in animal mtDNAs, but are separated by approximately 8 kb in this mitochondrial genome.

scholarly journals The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
N. Z. Gebrehiwot ◽  
E. M. Strucken ◽  
H. Aliloo ◽  
K. Marshall ◽  
J. P. Gibson
Keyword(s):  
Genetic Diversity ◽  
Bos Taurus ◽  
Large Population ◽  
Bos Indicus ◽  
Principal Component ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
African Cattle ◽  
Snp Data

Abstract Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

Genetic Structure of the Western and Eastern African Sahel/Savannah Belt and the Role of Nomadic Pastoralists as Inferred from the Variation of D-Loop Mitochondrial DNA Sequences

Human Biology ◽  
2017 ◽  
Vol 89 (4) ◽  
pp. 281 ◽  
Author(s):  
Martina Čížková ◽  
Pavel Munclinger ◽  
Mame Yoro Diallo ◽  
Iva Kulichová ◽  
Mohammed G. Mokhtar ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Structure ◽  
Dna Sequences ◽  
Nomadic Pastoralists ◽  
D Loop ◽  
African Sahel
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