Phylogenetic Study of Madura Cattle Based on Mitochondrial Cyt b and D-loop Sequences

Madura Cattle is one breed of local cattle from Indonesia. Madura cattle are estimated to originate from a crossbreeding between Bos indicus and Bos javanicus. Another presumption is that Madura cattle are the result of a crossbreeding between B. indicus males and mixed B. javanicus or Bos taurus. Tracing the history of Madura cross and another cattle phylogenetic based on maternal lineage can be done by analyzing the variation of the mitochondrial genome (mtDNA). The purpose of this study was to determine the clarity of the origin of Madura cattle based on maternal lineage using mtDNA markers Cyt b and D-loop. This research is expected to provide genetic information and the origin of Madura cattle, so that it can be used to help improve the breeding and conservation program for Madura cattle. The results of the phylogeny tree reconstruction, using the Cyt b and D-loop genes showed that Madura cattle originated from Sampang region (Polagan, Golbung, and Komis) were grouped into two types of maternal origin. Madura cattle clade I are grouped with B. indicus and B. taurus, while Madura cattle clade II are grouped with B. javanicus. A crossbreeding between B. javanicus and B. indicus is estimated to have been carried out since the entry of Hindu culture brought by the India peoples to Indonesia around 1800 years ago. The crossing between B. javanicus and B. indicus was then more intensively carried out at the time of the government's promoting the development of Ongol cattles (B. indicus) in the days of the Dutch East Indies. The length segment of Cyt b that can be amplified is 230 bp and the D-loop segment of varying length, 577 bp for the Madura 41 and 29 samples, and 624 bp for sample 32.

Download Full-text

Hubungan Kekerabatan Sapi Aceh dengan Menggunakan Daerah Displacement-loop

Jurnal Agripet ◽

10.17969/agripet.v8i2.609 ◽

2008 ◽

Vol 8 (2) ◽

pp. 9-14 ◽

Cited By ~ 4

Author(s):

Mohd. Agus Nashri Abdullah

Keyword(s):

Whole Blood ◽

Bos Indicus ◽

Loop Analysis ◽

Blood Samples ◽

Bos Javanicus ◽

Pcr Product ◽

Two Samples ◽

D Loop ◽

Whole Blood Samples ◽

Relationship Of

Relationship of aceh cattle using displacement-loop regionABSTRACT. The aims of this study were to describe relationship of D-loop of mtDNA Aceh cattle which is useful database for conducting conservation programme. The whole blood samples were collected (8 samples for D-loop analysis) from four locations which were Aceh Besar, Pidie, North Aceh regencies and Banda Aceh city. Out group whole blood samples were collected from two samples from Bali cattles (Bali Island), Madura cattle (Madura Island), Pesisir cattle (West Sumatera) respectively and one sample from PO cattle (West Java). Amplification of D-loop sequences of mtDNA with BIDLF and BIDLR primary have PCR product 980 bp. The Data were analyzed using Squint 1.02 and MEGA 4.0 programme. Result of analysis indicate that Aceh cattle have nearer relationship with zebu and there is items inset of genetik Bali cattle (Bos javanicus) at the end sequences start ke-354 situs up to 483, so that the origin Aceh cattle was from Bos indicus which have hybridization with Bos javanicus.

Download Full-text

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.

Download Full-text

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.

Download Full-text

An insight into the evolutionary history of Indonesian cattle assessed by whole genome data analysis

PLoS ONE ◽

10.1371/journal.pone.0241038 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0241038

Author(s):

Pita Sudrajad ◽

Subiharta Subiharta ◽

Yudi Adinata ◽

Af’idatul Lathifah ◽

Jun Heon Lee ◽

...

Keyword(s):

Demographic History ◽

Bos Indicus ◽

Molecular Evidence ◽

Effective Population ◽

Genome Data ◽

Bos Javanicus ◽

History Of ◽

Genome Data Analysis ◽

Almost All ◽

Insight Into

The domestication of Indonesian cattle was investigated through a study of their genetic diversity, up to the genome level. Little documentation exists regarding the history of domestication of Indonesian cattle and questions remain despite a growing body of molecular evidence. In this study, we genotyped seven Indonesian cattle breeds using an Illumina BovineSNP50 Bead Chip to provide insight into their domestication and demographic history in a worldwide population context. Our analyses indicated the presence of hybrid cattle, with Bos javanicus and Bos indicus ancestries being most prevalent, as well as purebred cattle. We revealed that all the breeds were interconnected through several migration events. However, their demographic status varied widely. Although almost all the Indonesian cattle had an effective population size higher than the minimum level required to ensure breed fitness, efforts are still needed to maintain their genetic variability and purity.

Download Full-text

Phylogenetic tree analysis for Bali Cattle based on partial sequence 16S rRNA Mitochondrial DNA

E3S Web of Conferences ◽

10.1051/e3sconf/202233500014 ◽

2022 ◽

Vol 335 ◽

pp. 00014

Author(s):

R. Misrianti ◽

S.H. Wijaya ◽

C. Sumantri ◽

J. Jakaria

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

Phylogenetic Tree ◽

Bos Taurus ◽

Bos Indicus ◽

Partial Sequence ◽

Bos Grunniens ◽

Bos Javanicus ◽

Mitochondria Dna ◽

Bali Cattle

Mitochondria DNA (mtDNA) as a source of genetic information based on the maternal genome, can provide important information for phylogenetic analysis and evolutionary biology. The objective of this study was to analyze the phylogenetic tree of Bali cattle with seven gene bank references (Bos indicus, Bos taurus, Bos frontalis, and Bos grunniens) based on partial sequence 16S rRNA mitochondria DNA. The Bayesian phylogenetic tree was constructed using BEAST 2.4. and visualization in Figtree 1.4.4 (tree.bio.ed.ac.uk/software/figtree/). The best model of evolution was carried out using jModelTest 2.1.7. The most optimal was the evolutionary models GTR + I + G with p-inv (I) 0,1990 and gamma shape 0.1960. The main result indicated that the Bali cattle were grouped into Bos javanicus. Phylogenetic analysis also successfully classifying Bos javanicus, Bos indicus, Bos taurus, Bos frontalis and Bos grunniens. These results will complete information about Bali cattle and useful for the preservation and conservation strategies of Indonesian animal genetic resources.

Download Full-text

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.

Download Full-text

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.

Download Full-text

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

Journal of the Indonesian Tropical Animal Agriculture ◽

10.14710/jitaa.44.4.335-345 ◽

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.

Download Full-text

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.

Download Full-text

The origin of pesisir cattle based on D-loop mitochondrial DNA

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d200919 ◽

2019 ◽

Vol 20 (9) ◽

Author(s):

Anzalia Eka Putri ◽

ACHMAD FARAJALLAH ◽

DYAH PERWITASARI

Keyword(s):

Mitochondrial Dna ◽

Phylogenetic Trees ◽

Mitochondrial Gene ◽

Small Body ◽

Bos Indicus ◽

Neighbor Joining ◽

Bos Javanicus ◽

Loop Region ◽

D Loop ◽

Cattle Blood

Abstract. Putri AE, Farajallah A, Perwitasari D. 2019. The origin of pesisir cattle based on D-loop mitochondrial DNA. Biodiversitas 20: 2569-2575. Pesisir cattle is one of Indonesia's local cattle descended from Bos indicus which has small body characteristics. It was assumed due to crossbreeding between pesisir cattle and other cattle. Therefore this study aims to study the origin of pesisir cattle based on the D-loop mtDNA region and to find out the phylogenetic relationships between pesisir cattle and other cattle. Cattle blood samples were taken in two locations, Krui Way and Tanah Rekah. Amplification of the mitochondrial gene using the primary pair of collections of Dr. Achmad Farajallah, namely AF22 (forward) 5'-GCGTACGCAATCTTACGATCA-3' and AF23 (reverse) 5'-ATGCAGTTAAGTCCAGCTAC-3'. Reconstruction of phylogenetic trees was analyzed using the Neighbor-Joining Method based on Kimura 2 Parameters. The results of the mtDNA analysis in the D-loop region showed that there were two broods in pesisir cattle, namely Bos indicus and Bos javanicus. The closeness between these species is due to the close geographical distance between Bos indicus originating from Way Krui, Lampung and Bos javanicus from Java.

Download Full-text