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

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

<p class="MDPI17abstract"><strong>Objective: </strong>The objective of this study was to investigate the genetic diversity of Sragen Black Cattle based on D-loop sequences analysis.</p><p class="MDPI17abstract"><strong>Methods: </strong>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.<strong></strong></p><p class="MDPI17abstract"><strong>Results: </strong>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.<strong></strong></p><p class="MDPI17abstract"><strong>Conclusions: </strong>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.</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 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 Short Communication: Identification of Leptin gene in crossbred beef cattle

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.

Evaluation of Genetic Diversity in Castor (Ricinus communis L.) using RAPD Markes

2011 ◽  
Vol 343-344 ◽  
pp. 981-987
Author(s):  
Feng Juan Li ◽  
Chang Lu Wang ◽  
Dong He ◽  
Ya Qiong Liu ◽  
Mian Hua Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Genetic Distance ◽  
Oil Content ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Ricinus Communis ◽  
Major Group ◽  
Ricinus Communis L ◽  
Polymorphic Bands

RAPD markers are used to study the genetic diversity of the main planting on 37 castor varieties widely cultivated in china according to the oil content and other characteristic of different castor varieties. Genetic distance of 37 Chinese castor varieties is studied by RAPD markers analysis. RAPD analysis shows that a total of 122 bands are amplified from random primers of 20 S series, including 71 polymorphic bands with polymorphic rate of 58.20%. 37 castor beans are divided into four major groups in the phylogenetic tree. One castor germplasm is included in1, 2, 3 groups respectively, and two sub-groups are included in the 4 major group.

scholarly journals Keragaman Genetik Kukang Jawa (Nycticebus javanicus) Menggunakan Control Region (D-loop) DNA Mitokondria (mtDNA) (GENETIC DIVERSITY ON JAVAN SLOW LORIS (NYCTICEBUS JAVANICUS) USING OF CONTROL REGION (D-LOOP) mtDNA)

2019 ◽  
Vol 20 (3) ◽  
pp. 360
Author(s):  
Wirdateti Wirdateti ◽  
Hayati Aziza ◽  
Handayani Handayani
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Control Region ◽  
West Java ◽  
Slow Loris ◽  
Genetic Population ◽  
Central Java ◽  
Low Genetic Diversity ◽  
The Status ◽  
D Loop

Javan slow loris (Nycticebus javanicus)  one of the species of the genus Nycticebus is endemic in Java.  Their distribution region  is in West Java and Banten, and also reported to be found in Central Java and East Java, although very rarely.  Status of the species is Critically Endangered due to high levels of poaching, habitat loss and habitat fragmentation, so that the necessary conservation in order to increase the population. For conservation management it is necessary to know the status of genetic resources that play of  role in breeding, then this research is to explore the genetic population of the Javan slow loris  from some locations in West Java. The research objective was to assess the diversity of their current population of Java loris through the control region (D-loop) of mitochondrial DNA (mtDNA). A total of 23 individuals samples from Gunung Halimun Park, Tasikmalaya, Garut, Ciamis, Jember and confiscated at the Rehabilitation Center IAR Bogor were used in this stydy. Specific primers of D-loop are used for loris with a length of 296 bp sequence. The result showed there are only five different sites and formed six haplotypes, each haplotypes only 1-3 nucleotides different. Low genetic diversity is shown as much as 42.96% of individuals show the same sequence or genetic distance (d) = 0 that indicate was monomorf population from different population. The genetic distance of the entire population was 0.003 ± 0:01 (0.3%).

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.

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

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<em> b</em>, 464 bp, were amplified using the polymerase chain reaction technique (forward primer: L14735 and reverse primer: H15149). Thirty-four reference sequences of <em>Bos taurus</em>, <em>Bos indicus</em>, and <em>Bos javanicus</em> 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<em> b</em> 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 <em>Bos javanicus</em>. Overall, most of the Indonesian native and local cattle populations had a considerable genetic diversity and shared a common maternal origin with <em>Bos javanicus</em>.

scholarly journals Genetic structure of the Southern meat cattle breed based on microsatellite markers

2019 ◽  
Vol 21 (91) ◽  
pp. 21-28
Author(s):  
A. S. Kramarenko
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Microsatellite Markers ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Cattle Breed ◽  
Animal Husbandry ◽  
State Enterprise ◽  
Tissue Samples ◽  
Cattle Breeds

The Southern Meat cattle is a composite breed developed by crossing Cuban zebu (Bos indicus) with different cattle breeds (Bos taurus) – local the Red Steppe, Hereford, Charolais, Santa Gertrudis, Dairy Shorthorn. Genetic structure of the Southern meat cattle breed from the State Enterprise Experimental Farm “Askaniyske” NAAS Ukraine (Kherson region) were investigated based on the microsatellite DNA loci. Analysis included 192 animals. A panel of 12 bovine-specific microsatellite markers (TGLA227, BM2113, TGLA53, ETH10, SPS115, TGLA122, INRA23, TGLA126, BM1818, ETH3, ETH225 and BM1824), recommended of the ISAG for cattle genetic diversity studies, was selected for genetic characterization and revealing the extent of genetic diversity in the Southern Meat cattle breed. Genomic DNA was extracted from tissue samples using Nexttec column (Nexttec Biotechnology GmbH, Germany) following the manufacturer's instructions. All laboratory tests were conducted in the laboratory of Molecular Genetics, Animal Center of Biotechnology and Molecular Diagnostics, All-Russian Research Institute for Animal Husbandry named after academy member L.K. Ernst. We report the distribution and the frequency of a taurine and an indicine specific alleles in the Southern Meat cattle breed using literature data about the Zebu and different cattle breeds genetic structure based on microsatellite loci from our list. It can be assumed that the TGLA22777, BM2113141-143, ETH10209-211, TGLA122149, INRA23194-198, TGLA126123, ETH225156-158-160 alleles among the Southern Meat cattle breed examined individuals were inherited from a B. indicus ancestor. On the other hand, the TGLA53156, ETH10217-219, TGLA122143, INRA23202, TGLA126115, ETH225148-150, BM1824188-190 alleles in the Southern Meat cattle gene pool may be inherited from a B. taurus ancestor (i.e., taurine breeds diagnostic alleles).

scholarly journals Genetic Relationship Among Ten Promising Eggplant Varieties Using RAPD Markers

1970 ◽  
Vol 19 (2) ◽  
pp. 119-126 ◽  
Author(s):  
Md. Sanaullah Biswas ◽  
Md. Abdullah Yousuf Akhond ◽  
Md. Al-Amin ◽  
Mahmuda Khatun ◽  
Muhammed Rezwan Kabir
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Genetic Relationship ◽  
Plant Tissue ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Similarity Index ◽  
The Other ◽  
Upgma Dendrogram ◽  
Potential Tool

RAPD technique was used as a tool for assessing genetic diversity and varietal relationships among ten varieties of eggplant. Out of 21 primers screened four were selected. With these primers 76 clear and bright fragments were obtained of which 44 fragments considered polymorphic. The proportion of polymorphic loci and gene diversity values across all loci were 57.89% and 0.23, respectively. The UPGMA dendrogram based on genetic distance segregated the ten varieties of eggplant into two main clusters. Dohazari, Kazla, Nayantara and ISD-006 were grouped together in cluster I whereas Uttara, Islampuri, Khatkhatia, Singnath, BARI Begun-08 and Eggplant Line-083 into cluster II. Kazla and Nayantara variety pair was very close to each other with the highest intervarietal similarity index (92.54%) and lowest genetic distance (0.14). On the other hand, Khatkhatia and Nayantara pair was the lowest intervarietal similarity index (41.67%) with highest genetic distance (0.48). Therefore, identification of genetically distinct varieties using RAPD markers could be a potential tool for eggplant improvement. Key words: Eggplant, Polymorphism, Genetic relationship, RAPD D.O.I. 10.3329/ptcb.v19i2.5006 Plant Tissue Cult. & Biotech. 19(2): 119-126, 2009 (December)

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

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.

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