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

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.

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

Ciencia y Tecnología Agropecuaria ◽

10.21930/rcta.vol7_num2_art:66 ◽

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

El continente americano fue colonizado en el siglo XVI por los europeos quienes introdujeron por primera vez el ganado bovino de origen Bos taurus. La introducción de ganado Bos indicus 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 Bos taurus en el origen del ganado Cebú colombiano, se secuenció un fragmento del ADN mitocondrial de 374 pb (D-Loop) 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 Bos taurus. 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 Bos taurus europeo que con relación a las secuencias consenso Bos indicus, frente a las que se hallaron mayores divergencias. Adicionalmente, las divergencias de las razas criollas colombianas con respecto al consenso Bos taurus europeo variaron entre 0,005 y 0,014, resultado que sugiere la participación de matrilineajes Bos taurus en el origen del Cebú Brahman colombiano. Identification of mitochondrial DNA of Bos taurus origin in Colombian Zebu Brahman cattle 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.

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Genetic diversity of Sragen Black Cattle based on D-Loop gene sequencing analysis

Livestock and Animal Research ◽

10.20961/lar.v18i2.42934 ◽

2020 ◽

Vol 18 (2) ◽

pp. 124

Author(s):

Rahayu Kusumaningrum ◽

Sutopo Sutopo ◽

Edy Kurnianto

Keyword(s):

Genetic Diversity ◽

Phylogenetic Tree ◽

Genetic Distance ◽

Genetic Relationship ◽

Bos Taurus ◽

Bos Indicus ◽

Evolutionary Genetics ◽

Sequencing Analysis ◽

Dna Sequence Polymorphism ◽

D Loop

Objective: The objective of this study was to investigate the genetic diversity of Sragen Black Cattle based on D-loop sequences analysis.Methods: A total of 25 blood samples belonged to Sragen Black Cattle that had no genetic relationship within sample. The DNA genome was extracted based on the manufacturer’s standard protocol using gSYNC DNA Mini Kit (Geneaid Biotech Ltd.). D-loop gene was amplified using specific primer forward: 5’- TAGTGCTAATACCAACGGCC-3’ and reverse: 5’- AGGCATTTTGAGTGCCTTGC-3’ and then was sequenced. The sequencing result was aligned and analyzed by Molecular Evolutionary Genetics Analysis (MEGA) version 6.0 to reveal genetic distance and phylogenetic tree. Genetic diversity and haplotype were analysed by DNA Sequence Polymorphism (DnaSp) v6.12.03.Results: The results revealed that there were 11 haplotypes with Pi = 0.00675±0.00201 and Hd = 0.767±0.086. Sragen Black Cattle was divided by two cluster in phylogenetic tree with average of genetic distance was 0.0032.Conclusions: In conclusion, all of Sragen Black Cattle are on the same cluster and have closer genetic relationship to Bos indicus rather than Bos taurus with similarity level 85.76 % based on BLAST program.

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

Animal Breeding and Genetics ◽

10.31073/abg.53.33 ◽

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.

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Short Communication: Identification of Leptin gene in crossbred beef cattle

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d210129 ◽

2019 ◽

Vol 21 (1) ◽

Author(s):

Laksa Ersa Anugratama ◽

Tety Hartatik

Keyword(s):

Beef Cattle ◽

Phylogenetic Tree ◽

Genetic Distance ◽

Short Communication ◽

Bos Taurus ◽

Bos Indicus ◽

Bubalus Bubalis ◽

Exon 2 ◽

Central Java ◽

Bali Cattle

Abstract. Anugratama LE, Hartatik T. 2020. Short Communication: Identification of Leptin gene in crossbred beef cattle. Biodiversitas 21: 226-230. Leptin is a gene that affects animal weight. Leptin gene is known to control body weight, feed intake, energy expenditure, immune function, and reproduction. This study aims to identify the diversity of the Leptin gene in crossbred beef cattle, Sumba Ongole cattle, Brahman cross cattle, Bali cattle, buffalo, sheep, and goat by comparing with four GenBank data of cattle. Crossbred beef cattle obtained from Klaten, Central Java, Indonesia. Leptin nucleotide sequences were analyzed using BioEdit to identify Single Nucleotide Polymorphism (SNP). To create amino acid change in Leptin gene, the coding sequence of exon 2 was established using BioEdit ver. 7.0.5. Phylogenetic tree and genetic distance have been analyzed based on the Leptin gene using MEGA 10.1.1 program. The result shows that eight variations of SNP were found in exon 2. The phylogenetic tree represents that crossbreed beef cattle, Sumba Ongole cattle, Brahman cross cattle, Bali cattle, Bos taurus, Bos indicus, Bos frontalis, Bos grunniens, Bubalus bubalis are in the same cluster with various genetic distance. The results of this study are expected to provide genetic information that will be used for further research on the relationship between Leptin gene polymorphisms to animal weight.

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Cytogenetic and molecular analysis of the Pantaneiro cattle breed

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2006001100006 ◽

2006 ◽

Vol 41 (11) ◽

pp. 1609-1615 ◽

Cited By ~ 6

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.

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Population data for 101 Austrian Caucasian mitochondrial DNA d-loop sequences: Application of mtDNA sequence analysis to a forensic case

International Journal of Legal Medicine ◽

10.1007/s004140050132 ◽

1998 ◽

Vol 111 (3) ◽

pp. 124-132 ◽

Cited By ~ 115

Author(s):

W. Parson ◽

T. J. Parsons ◽

R. Scheithauer ◽

M. M. Holland

Keyword(s):

Mitochondrial Dna ◽

Sequence Analysis ◽

Population Data ◽

Mtdna Sequence ◽

D Loop ◽

Forensic Case

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Genetic Variation of Calpastation Gene of Indigenous Bali Cattle (Bos javanicus) in Indonesia

HAYATI Journal of Biosciences ◽

10.4308/hjb.26.1.44 ◽

2019 ◽

Vol 26 (1) ◽

pp. 44

Author(s):

Endang Tri Margawati ◽

Slamet Diah Volkandari ◽

Indriawati Indriawati ◽

Emma M. Svensson

Keyword(s):

Genetic Variation ◽

Bos Taurus ◽

Bos Indicus ◽

Meat Tenderness ◽

Gene Markers ◽

Bos Javanicus ◽

Restriction Fragment Polymorphism ◽

Pcr Rflp ◽

Bali Cattle ◽

Cast Gene

Calpastatin is one of gene markers affecting meat tenderness. The study aimed to evaluate genetic variation of calpastatin (CAST) gene of Bali cattle (Bos javanicus) in lndonesia. A total of 61 samples consisting of 21 Bali cattle, 22 Ongole cattle (Bos indicus), and 18 Friesian Holstein (FH) cattle (Bos taurus) were applied. The Ongole and FH cattle were involved for breed comparison. DNA was extracted from fresh blood using a High Salt method and measured their quality by a Spectrophotometer. A 523 bp of Calpastatin gene fragment was amplified by Polymerase Chain Reaction and Restriction Fragment Polymorphism (PCR-RFLP) technique with RsaI restriction enzyme for genotyping. Result showed that two variants alleles (C and G) and three genotypes (CC, GC, GG) were found in those Bali, Ongole and FH samples. Allele G was dominant allele with the highest G allele was in Bali cattle population (0.88). The higher percentage of allele C was found in Ongole and Friesian Holstein compared to that in Bali cattle. The Ongole breed tends to have a potential source of lean meat quality. This finding identified that genetic variation of CAST gene was exist in Bali cattle and adapted cattle of Ongole and FH in Indonesian.

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

Acta Agraria Debreceniensis ◽

10.34101/actaagrar/69/1783 ◽

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.

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Genetic Diversity of Mitochondrial DNA Cytochrome b in Indonesian Native and Local Cattle Populations

Jurnal Ilmu Ternak dan Veteriner ◽

10.14334/jitv.v25i2.2496 ◽

2020 ◽

Vol 25 (2) ◽

pp. 39

Author(s):

Peni Wahyu Prihandini ◽

A Primasari ◽

M Luthfi ◽

J Efendy ◽

D Pamungkas

Keyword(s):

Genetic Diversity ◽

Bos Taurus ◽

Phylogenetic Analyses ◽

Bos Indicus ◽

Haplotype Diversity ◽

Genetic Distances ◽

Conservation Strategies ◽

Bos Javanicus ◽

Reverse Primer ◽

Relationship Of

Information on the genetic diversity of native and local cattle in Indonesia is vital for the development of breeding and conservation strategies. This study was aimed to assess the genetic diversity and phylogenetic relationship of the Indonesian native (Bali) and local [(Donggala, Madura, Sragen, Galekan, Rambon, dan Peranakan Ongole Grade x Bali (POBA)] cattle populations. Genomic DNA was extracted from blood samples (n= 75). Partial sequences of mtDNA cyt b, 464 bp, were amplified using the polymerase chain reaction technique (forward primer: L14735 and reverse primer: H15149). Thirty-four reference sequences of Bos taurus, Bos indicus, and Bos javanicus were included in the phylogenetic analyses. A total of 55 polymorphic sites and 13 haplotypes were observed in the whole breeds. No variable sites of mtDNA cyt b were observed in Galekan (kept in BCRS) and Rambon cattle. Overall haplotype diversity and nucleotide diversity were 0.515 ± 0.070 and 0.0184 ± 0.0045, respectively. The highest (0.092) and the lowest (0.000) genetic distances were between Bali and Donggala cattle populations and among Galekan (kept in BCRS), Rambon, and POBA cattle populations, respectively. Both mtDNA network and phylogenetic analyses revealed two major maternal lineages (A and B) of the studied population. Most of the sampled individuals (69.33%, present in haplotype H8-H19) were linked to lineage B, which belonged to the same cluster with Bos javanicus. Overall, most of the Indonesian native and local cattle populations had a considerable genetic diversity and shared a common maternal origin with Bos javanicus.

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