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 Exploring genetic diversity and phylogenic relationships of Chinese cattle using gene mtDNA 16S rRNA

2019 ◽  
Vol 62 (1) ◽  
pp. 325-333 ◽  
Author(s):  
Linjun Yan ◽  
Yifan She ◽  
Mauricio A. Elzo ◽  
Chunlei Zhang ◽  
Xingtang Fang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Haplotype Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Cattle Breeds ◽  
Chinese Cattle

Abstract. The objective of this research was to characterize the genetic diversity and phylogenetic diversity among 12 cattle breeds (10 Chinese breeds and two foreign taurine breeds as controls) utilizing gene mtDNA 16S rRNA. The complete sequences of the mtDNA 16S rRNA genes of the 251 animals were 1570 bp long. The mean percentages of the four nitrogen bases were 37.8 % for adenine (A), 23.7 % for thymine (T), 20.9 % for cytosine (C), and 17.6 % for guanine (G). The mtDNA 16S rRNA gene base percentages had a strong bias towards A + T. All detected nucleotide variations in gene mtDNA 16S rRNA were either transitions (62.3 %) or transversions (37.7 %); no indels (insertions and deletions) were found. A total of 40 haplotypes were constructed based on these mutations. A total of 36 haplotypes of these 40 haplotypes were present in 10 Chinese cattle breeds. The haplotype diversity of all Chinese cattle populations was 0.903±0.077, while the nucleotide diversity was 0.0071±0.0039. Kimura's two-parameter genetic distances between pairs of the studied 12 breeds ranged from 0.001 to 0.010. The phylogenetic analysis assigned the 10 Chinese breeds to two distinct lineages that likely differed in their percentage of Bos taurus and Bos indicus ancestry.

scholarly journals Hubungan Kekerabatan Sapi Aceh dengan Menggunakan Daerah Displacement-loop

2008 ◽  
Vol 8 (2) ◽  
pp. 9-14 ◽  
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.

scholarly journals Genetic Diversity and Population Divergence of a Rare, Endemic Grass (Elymus breviaristatus) in the Southeastern Qinghai-Tibetan Plateau

2019 ◽  
Vol 11 (20) ◽  
pp. 5863 ◽  
Author(s):  
Qingqing Yu ◽  
Qian Liu ◽  
Yi Xiong ◽  
Yanli Xiong ◽  
Zhixiao Dong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Tibetan Plateau ◽  
Isolation By Distance ◽  
Genetic Distances ◽  
Conservation Strategy ◽  
Conservation Strategies ◽  
Grass Species ◽  
Population Divergence ◽  
High Genetic Diversity ◽  
Widespread Species

Elymus breviaristatus is a grass species only distributed in the southeast of Qinghai-Tibetan Plateau (QTP), which has suffered from serious habitat fragmentation. Therefore, understanding patterns of genetic diversity within and among natural E. breviaristatus populations could provide insight for future conservation strategies. In this study, sequence-related amplified polymorphism markers were employed to investigate the genetic diversity and hierarchical structure of seven E. breviaristatus populations from QTP, China. Multiple measures of genetic diversity indicated that there is low to moderate genetic variation within E. breviaristatus populations, consistent with its presumed mating system. In spite of its rarity, E. breviaristatus presented high genetic diversity that was equivalent to or even higher than that of widespread species. Bayesian clustering approaches, along with clustering analysis and principal coordinate analysis partitioned the studied populations of E. breviaristatus into five genetic clusters. Differentiation coefficients (Fst, GST, etc.) and AMOVA analysis revealed considerable genetic divergence among different populations. BARRIER analyses indicated that there were two potential barriers to gene flow among the E. breviaristatus populations. Despite these patterns of differentiation, genetic distances between populations were independent of geographic distances (r = 0.2197, p = 0.2534), indicating little isolation by distance. Moreover, despite detecting a common outlier by two methods, bioclimatic factors (altitude, annual mean temperature, and annual mean precipitation) were not related to diversity parameters, indicating little evidence for isolation caused by the environment. These patterns of diversity within and between populations are used to propose a conservation strategy for E. breviaristatus.

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 and Variability in Endangered Pantesco and Two Other Sicilian Donkey Breeds Assessed by Microsatellite Markers

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Salvatore Bordonaro ◽  
Anna Maria Guastella ◽  
Andrea Criscione ◽  
Antonio Zuccaro ◽  
Donata Marletta
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Genetic Information ◽  
Gene Diversity ◽  
Genetic Distances ◽  
Conservation Strategies ◽  
Population Structure Analysis ◽  
The Mean ◽  
Differentiation Index

The genetic variability of Pantesco and other two Sicilian autochthonous donkey breeds (Ragusano and Grigio Siciliano) was assessed using a set of 14 microsatellites. The main goals were to describe the current differentiation among the breeds and to provide genetic information useful to safeguard the Pantesco breed as well as to manage Ragusano and Grigio Siciliano. In the whole sample, that included 108 donkeys representative of the three populations, a total of 85 alleles were detected. The mean number of alleles was lower in Pantesco (3.7), than in Grigio Siciliano and Ragusano (4.4 and 5.9, resp.). The three breeds showed a quite low level of gene diversity (He) ranging from 0.471 in Pantesco to 0.589 in Grigio. The overall genetic differentiation index (Fst) was quite high; more than 10% of the diversity was found among breeds. Reynolds’ () genetic distances, correspondence, and population structure analysis reproduced the same picture, revealing that, (a) Pantesco breed is the most differentiated in the context of the Sicilian indigenous breeds, (b) within Ragusano breed, two well-defined subgroups were observed. This information is worth of further investigation in order to provide suitable data for conservation strategies.

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

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.

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 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.

scholarly journals High Genetic Diversity and Low Differentiation in Michelia shiluensis, an Endangered Magnolia Species in South China

Forests ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 469 ◽  
Author(s):  
Yanwen Deng ◽  
Tingting Liu ◽  
Yuqing Xie ◽  
Yaqing Wei ◽  
Zicai Xie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Human Disturbance ◽  
Haplotype Diversity ◽  
Conservation Strategy ◽  
Ex Situ ◽  
Conservation Strategies ◽  
High Genetic Diversity ◽  
Cpdna Markers

Research Highlights: This study is the first to examine the genetic diversity of Michelia shiluensis (Magnoliaceae). High genetic diversity and low differentiation were detected in this species. Based on these results, we discuss feasible protection measures to provide a basis for the conservation and utilization of M. shiluensis. Background and Objectives: Michelia shiluensis is distributed in Hainan and Guangdong province, China. Due to human disturbance, the population has decreased sharply, and there is thus an urgent need to evaluate genetic variation within this species in order to identify an optimal conservation strategy. Materials and Methods: In this study, we used eight nuclear single sequence repeat (nSSR) markers and two chloroplast DNA (cpDNA) markers to assess the genetic diversity, population structure, and dynamics of 78 samples collected from six populations. Results: The results showed that the average observed heterozygosity (Ho), expected heterozygosity (He), and percentage of polymorphic loci (PPL) from nSSR markers in each population of M. shiluensis were 0.686, 0.718, and 97.92%, respectively. For cpDNA markers, the overall haplotype diversity (Hd) was 0.674, and the nucleotide diversity was 0.220. Analysis of markers showed that the genetic variation between populations was much lower based on nSSR than on cpDNA (10.18% and 77.56%, respectively, based on an analysis of molecular variance (AMOVA)). Analysis of the population structure based on the two markers shows that one of the populations (DL) is very different from the other five. Conclusions: High genetic diversity and low population differentiation of M. shiluensis might be the result of rich ancestral genetic variation. The current decline in population may therefore be due to human disturbance rather than to inbreeding or genetic drift. Management and conservation strategies should focus on maintaining the genetic diversity in situ, and on the cultivation of seedlings ex-situ for transplanting back to their original habitat.

scholarly journals Genetic diversity and selection signatures in maize landraces compared across 50 years of in situ and ex situ conservation

Heredity ◽  
2021 ◽  
Author(s):  
Francis Denisse McLean-Rodríguez ◽  
Denise Elston Costich ◽  
Tania Carolina Camacho-Villa ◽  
Mario Enrico Pè ◽  
Matteo Dell’Acqua
Keyword(s):  
Genetic Diversity ◽  
Selection Criteria ◽  
Sampling Site ◽  
In Situ Conservation ◽  
Genetic Distances ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Genome Wide ◽  
Agrobiodiversity Conservation

AbstractGenomics-based, longitudinal comparisons between ex situ and in situ agrobiodiversity conservation strategies can contribute to a better understanding of their underlying effects. However, landrace designations, ambiguous common names, and gaps in sampling information complicate the identification of matching ex situ and in situ seed lots. Here we report a 50-year longitudinal comparison of the genetic diversity of a set of 13 accessions from the state of Morelos, Mexico, conserved ex situ since 1967 and retrieved in situ from the same donor families in 2017. We interviewed farmer families who donated in situ landraces to understand their germplasm selection criteria. Samples were genotyped by sequencing, producing 74,739 SNPs. Comparing the two sample groups, we show that ex situ and in situ genome-wide diversity was similar. In situ samples had 3.1% fewer SNPs and lower pairwise genetic distances (Fst 0.008–0.113) than ex situ samples (Fst 0.031–0.128), but displayed the same heterozygosity. Despite genome-wide similarities across samples, we could identify several loci under selection when comparing in situ and ex situ seed lots, suggesting ongoing evolution in farmer fields. Eight loci in chromosomes 3, 5, 6, and 10 showed evidence of selection in situ that could be related with farmers’ selection criteria surveyed with focus groups and interviews at the sampling site in 2017, including wider kernels and larger ear size. Our results have implications for ex situ collection resampling strategies and the in situ conservation of threatened landraces.

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