scholarly journals Genetic structure and diversity among three Greek sheep breeds using Random Amplified Polymorphic DNA-PCR

2017 ◽  
Vol 62 (4) ◽  
pp. 301 ◽  
Author(s):  
I. MASTRANESTASIS (Ι. ΜΑΣΤΡΑΝΕΣΤΑΣΗΣ) ◽  
Ch. LIGDA (Χρ. ΛΙΓΔΑ) ◽  
K. THEODOROU (Κ. ΘΕΟΔΩΡΟΥ) ◽  
L. V. EKATERINIADOU (Λ.Β. ΑΙΚΑΤΕΡΙΝΙΑΔΟΥ)
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Phylogenetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Distances ◽  
Genetic Identity ◽  
Rapd Pcr ◽  
Pcr Method ◽  
Genetic Structure And Diversity

Genetic structure and diversity of 120 animals from three Greek local breeds were investigated by Random Amplified Polymorphic DNA (RAPD) - PCR method. Sheep samples originated from the Lesvos, Chios and Karagouniko breeds were treated with 11 random primers to estimate their genetic diversity and phylogenetic relationships. Our analysis comprised two levels of the breeds' genetic structure: i) the genetic differentiation among the three breeds and ii) the genetic differentiation among the flocks within each breed. This combined approach gave two main findings: i) the study of genetic distances and identity revealed that the Karagouniko sheep breed is genetically distinct from Chios (GD=0.1979) and Lesvos (GD=0.1691) breeds, while ii) the Chios and Lesvos breeds are genetically similar (GI=0.9631); half of the flocks of Lesvos have a relatively closer relationship with those of Chios than with the other Lesvos flocks. This is the first study that reports the close genetic relationship between the Chios and Lesvos breeds and gives strong evidence to hypotheses about their related origin. Furthermore, the study of polymorphic loci revealed particular indicators located in Karagouniko breed, as definitional datum of genetic identity or as a fingerprint of breed. Therefore, RAPD-DNA methods can be an efficient tool for the determination of phylogenetic relationships and genetic identity among the bloodstock breed of sheep.

scholarly journals Diversity and genetic structure of Ornithogalum L. (Hyacinthaceae) populations as revealed by RAPD-PCR markers

Genetika ◽  
2015 ◽  
Vol 47 (1) ◽  
pp. 275-288
Author(s):  
Andrijana Andric ◽  
Natasa Kocis-Tubic ◽  
Milica Rat ◽  
Dragana Obreht-Vidakovic
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Distances ◽  
Shannon Index ◽  
Similarity Coefficients ◽  
Additional Tool ◽  
Population Genetic Differentiation ◽  
Rapd Pcr

Random amplified polymorphic DNA (RAPD) PCR method was used to assess the level of diversity and genetic structure in Ornithogalum L. populations from Serbia and Hungary with the main goal of improving the knowledge of this genus in the given region. The material was collected from 19 populations and identified as two morphologically similar and phylogenetically close taxa: O. umbellatum L. 1753 and O. divergens Boreau 1887. All ten RAPD primers used for the analysis gave PCR products, with length between 3000bp and 300bp. There were 101 amplified fragments in total; number of polymorphic bands per primer varied between seven and 13. Percentage of polymorphic loci was 96% in total and 12% in average in each population. Genetic variation statistics for all loci also showed that genetic diversity for all populations was 0.29 and Shannon index 0.45, while mean values for these parameters calculated for each population were 0.04 and 0.06, respectively. Analysis of molecular variance demonstrated high population genetic differentiation; however Mantel test showed no significant correlation between geographic distances of populations and genetic distances expressed through population pairwise FST. UPGMA dendrogram based on Jaccard genetic similarity coefficients showed subclustering and principal coordinate analysis based on Nei and Li coefficients of genetic distances indicated grouping. Analysis of populations genetic structure was in accordance with these results and clearly separated populations of O. umbellatum from O. divergens. RAPDs proved to be a reliable and rapid method suitable for distinguishing genetic differentiation in Ornithogalum, thus could be applied as a useful additional tool in resolving taxonomic problems.

scholarly journals Determination of Genetic Diversity of Four Guppy Strains Using the Random Amplified Polymorphic DNA-PCR

2021 ◽  
pp. 1-8
Author(s):  
Riva Hafidah ◽  
Ayi Yustiati ◽  
Yuniar Mulyani ◽  
Ibnu Bangkit Bioshina Suryadi
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Descriptive Analysis ◽  
Similarity Index ◽  
Quantitative Descriptive Analysis ◽  
Rapd Pcr ◽  
Result Show ◽  
Pcr Method ◽  
Quantitative Descriptive

This research aims to determine genetic diversity of four strains guppy, respectively are japan blue double sword (JBD), japan blue tiger double sword (JBTD), blue moscow (BM), and panda guppy (PG) with RAPD-PCR method. The obtained genetic diversity data is used as guide reference for hybridization between four strains. The research was conducted in September 2020 to April 2021 with explorative methods and in qualitative and quantitative descriptive analysis. The research was carried out in biotechnology Laboratory, Fishery and Marine Sciences Faculty and Central Laboratory,Padjadjaran University, Indonesia.Strains of JBD, JBTD, BM obtained fromCilengkrangSubdistrict, Bandung and PG strain obtained from Parung market, Bogor. Primary OPA-03 (AGTCAGCCAC) is used for standard parameters to interpret genetic diversity among four strains of guppy. Based on results, amplification with OPA-03 primary visualize 25 bands that include five polymorphic bands and 20 monomorphic bands. The phylogenetic tree result show that there are two relationship groups. The first group are JBD, JBTD, and BM with similarity index in the range of 80-89%The first group consist two sub groups of relationship. The first sub group are JBD and JBTD with similarity index of 89%. The second sub group is BM with similarity index of 80%. The second group isPG with similarity index of 65.5%.

scholarly journals Characterization of Mexican Isolates of Colletotrichum lindemuthianum by Using Differential Cultivars and Molecular Markers

1998 ◽  
Vol 88 (4) ◽  
pp. 292-299 ◽  
Author(s):  
Mario González ◽  
Raul Rodríguez ◽  
Maria Elena Zavala ◽  
Juan L. Jacobo ◽  
Fernando Hernández ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Location ◽  
Genetic Distances ◽  
Colletotrichum Lindemuthianum ◽  
Aflp Data ◽  
Bootstrap Analysis ◽  
Differential Cultivars ◽  
Bean Anthracnose

Differential cultivars and molecular markers were used to analyze 59 isolates of the bean anthracnose pathogen, Colletotrichum lindemuthianum, from different regions of Mexico. Ten distinct races were determined, three of which had not been reported previously in Mexico. Isolates were found to infect only a narrow range of the differential cultivars used and were restricted to cultivars of Middle American origin. A comparison of random amplified polymorphic DNA and amplified fragment length polymorphism (AFLP) analyses was carried out on a subset of the fungal isolates. Determination of genetic distances based on AFLP data and production of a dendrogram demonstrated two levels of association: i) isolates classified into two major groups according to the type of cultivar or system of cultivation from which they originated, and ii) isolates could be classified into smaller subgroups generally associated with the geographic location from which they were obtained. Bootstrap analysis and determination of confidence intervals showed these geographic groupings to be extremely robust.

scholarly journals Spectrum of genetic diversity and networks of clonal organisms

2007 ◽  
Vol 4 (17) ◽  
pp. 1093-1102 ◽  
Author(s):  
Alejandro F Rozenfeld ◽  
Sophie Arnaud-Haond ◽  
Emilio Hernández-García ◽  
Víctor M Eguíluz ◽  
Manuel A Matías ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Genetic Structure ◽  
Small World ◽  
Clonal Plants ◽  
Posidonia Oceanica ◽  
Genetic Distances ◽  
Wide Range ◽  
Clonal Organisms ◽  
Genetic Structure And Diversity

Clonal reproduction characterizes a wide range of species including clonal plants in terrestrial and aquatic ecosystems, and clonal microbes such as bacteria and parasitic protozoa, with a key role in human health and ecosystem processes. Clonal organisms present a particular challenge in population genetics because, in addition to the possible existence of replicates of the same genotype in a given sample, some of the hypotheses and concepts underlying classical population genetics models are irreconcilable with clonality. The genetic structure and diversity of clonal populations were examined using a combination of new tools to analyse microsatellite data in the marine angiosperm Posidonia oceanica . These tools were based on examination of the frequency distribution of the genetic distance among ramets, termed the spectrum of genetic diversity (GDS), and of networks built on the basis of pairwise genetic distances among genets. Clonal growth and outcrossing are apparently dominant processes, whereas selfing and somatic mutations appear to be marginal, and the contribution of immigration seems to play a small role in adding genetic diversity to populations. The properties and topology of networks based on genetic distances showed a ‘small-world’ topology, characterized by a high degree of connectivity among nodes, and a substantial amount of substructure, revealing organization in subfamilies of closely related individuals. The combination of GDS and network tools proposed here helped in dissecting the influence of various evolutionary processes in shaping the intra-population genetic structure of the clonal organism investigated; these therefore represent promising analytical tools in population genetics.

scholarly journals Genetic variability of Pantaneiro horse using RAPD-PCR markers

2007 ◽  
Vol 36 (4) ◽  
pp. 799-806 ◽  
Author(s):  
Andréa Alves do Egito ◽  
Beatriz Helena Fuck ◽  
Concepta McManus ◽  
Samuel Rezende Paiva ◽  
Maria do Socorro Maués Albuquerque ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Distances ◽  
Jaccard Coefficient ◽  
Mato Grosso ◽  
Rapd Pcr ◽  
Close Relationship ◽  
Polymerase Chain ◽  
Genic Diversity ◽  
Mato Grosso Do Sul

Blood samples were collected from Pantaneiro Horses in five regions of Mato Grosso do Sul and Mato Grosso States. Arabian, Mangalarga Marchador and Thoroughbred were also included to estimate genetic distances and the existing variability among and within these breeds by RAPD-PCR (Random Amplified Polymorphic DNA - Polymerase Chain Reaction) molecular markers. From 146 primers, 13 were chosen for amplification and 44 polymorphic bands were generated. The analysis of molecular variance (AMOVA) indicated that the greatest portion of detected variability was due to differences between individuals within populations (75.47%). Analysis of the genetic variability between pairs of populations presented higher estimates for the five Pantaneiro populations with the Arabian breed, while lowest estimates were presented by pairs formed among the Pantaneiro populations with the Mangalarga Marchador. Highest genic diversity was shown by the Pantaneiro (0.3396), which also showed highest genetic distance with the Arabian and lowest with Mangalarga Marchador breed. UPGMA dendrogram showed distinct differences between naturalized (Pantaneiro and Mangalarga Marchador) and exotic (Arabian and Thoroughbred) breeds. In the dendrogram generated by UPGMA method, the similarity matrix generated by the Jaccard coefficient showed distinction between the naturalised breeds, Pantaneiro and Mangalarga Marchador, and the exotic breeds, Árab and English Thoroughbred. Results suggest that the Pantaneiro presents a higher genetic variability than the other studied breeds and has a close relationship with the Mangalarga Marchador.

scholarly journals Isozyme and RAPD studies in Prosopis glandulosa and P. Velutina (Leguminosae, Mimosoideae)

2000 ◽  
Vol 23 (3) ◽  
pp. 639-648 ◽  
Author(s):  
Cecilia Bessega ◽  
Beatriz O. Saidman ◽  
Juan C. Vilardi
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Variability ◽  
Genetic Differentiation ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Mantel Test ◽  
Prosopis Glandulosa ◽  
Geographical Distance ◽  
Taxonomic Studies

Allozyme and random amplified polymorphic DNA (RAPD) techniques have been compared for their usefulness for genetic and taxonomic studies in Prosopis glandulosa and P. velutina populations. Isozymes and RAPDs yielded similarly high estimates of genetic variability. Genetic structure and differentiation were analyzed through non-hierarchical Wright's F DT. For all populations considered, both markers produced low gene flow (Nm < 1) estimates. When only P. glandulosa populations were analyzed, isozyme data yielded higher gene flow estimates (Nm > 1), in agreement with that expected for conspecific populations. However, in RAPD data the expected reduction in F DT and the increase in Nm were not observed. Correlation between F DT and geographical distance matrices (Mantel test) for all populations was significant (P = 0.02) when based on isozymes, but not so (P = 0.33) when based on RAPDs. No significant associations among genetic and geographical or climatic variables were observed. Two isoenzyme systems (GOT and PRX) enabled us to distinguish between P. glandulosa and P. velutina, but no diagnostic band for recognition of populations or species studied here were detected by RAPD. However, RAPD markers showed higher values for genetic differentiation among conspecific populations of P. glandulosa and a lower coefficient of variation than those obtained from isozymes.

scholarly journals Genetic Structure of Cronartium ribicola Populations in Eastern Canada

1999 ◽  
Vol 89 (10) ◽  
pp. 915-919 ◽  
Author(s):  
K. Et-touil ◽  
L. Bernier ◽  
J. Beaulieu ◽  
J. A. Bérubé ◽  
A. Hopkin ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Distribution Systems ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Random Amplified Polymorphic Dna ◽  
Cronartium Ribicola ◽  
Eastern Canada ◽  
Long Distance ◽  
Evolutionary Forces

The genetic structure of populations of Cronartium ribicola was studied by sampling nine populations from five provinces in eastern Canada and generating DNA profiles using nine random amplified polymorphic DNA markers. Most of the total gene diversity (Ht = 0.386) was present within populations (Hw = 0.370), resulting in a low level of genetic differentiation among populations in northeastern North America (Fst = 0.062). A hierarchical analysis of genetic structure using an analysis of molecular variance (AMOVA) revealed no statistically significant genetic differentiation among provinces or among regions. Yet, genetic differentiation among populations within regions or provinces was small (AMOVA φst = 0.078) but statistically significant (P < 0.001) and was several orders of magnitude larger than differentiation among provinces. This is consistent with a scenario of subpopulations within a metapopulation, in which random drift following migration and new colonization are major evolutionary forces. A phenetic analysis using genetic distances revealed no apparent correlation between genetic distance and the province of origin of the populations. The hypothesis of isolation-by-distance in the eastern populations of C. ribicola was rejected by computing Mantel correlation coefficients between genetic and geographic distance matrices (P > 0.05). These results show that eastern Canadian provinces are part of the same white pine blister rust epidemiological unit. Nursery distribution systems are controlled provincially, with virtually no seedling movement among provinces; therefore, infected nursery material may not play an important role in the dissemination of this disease. Long-distance spore dispersal across provincial boundaries appears to be an epidemiologically important factor for this pathogen.

scholarly journals Genetic Differentiation Studies among Natural Populations of Tilapia zillii

2015 ◽  
Vol 7 (4) ◽  
pp. 423-429
Author(s):  
Tofunmi E. OLADIMEJI ◽  
Michael O. AWODIRAN ◽  
Olaniyi O. KOMOLAFE
Keyword(s):  
Genetic Differentiation ◽  
Random Amplified Polymorphic Dna ◽  
Natural Populations ◽  
Principal Component ◽  
Genetic Distances ◽  
Morphological Studies ◽  
Tilapia Zillii ◽  
Meristic Counts ◽  
Ctab Method ◽  
Group Relationships

The population structure of Tilapia zillii (Gervais 1848) from three reservoirs in Nigeria, Osun State (Opa, Osu and Igun) was determined by employing morphological and molecular (Random Amplified Polymorphic DNA) methods. For morphological studies, 25 morphometric measurements and six meristic counts were recorded on 40 individuals within each population. Principal Component Analysis (PCA) was performed on the morphometric and meristic data using the PAST software. For RAPD studies, genomic DNA was extracted from caudal fin tissue using CTAB method and five primers were used to initiate PCR amplifications. All the clusters produced by the Principal components analysis (PCA) of the morphometric and meristic parameters overlapped indicating a low level of genetic differentiation between the three populations of T. zillii studied. The UPGMA cluster diagram from RAPD analysis identified two major genotypic groups with inter and intra group relationships. All individuals in the first cluster were from the Osu reservoir, while individuals from Opa and Igun reservoirs constituted the second cluster. Nei’s unbiased measure of genetic distances was 0.8532, 0.7321 and 0.7111 for Osu, Igun and Opa populations respectively. This revealed that Opa and Igun populations were genetically closer, while Osu populations is distant from them. The results suggest that the RAPD technique could be used to differentiate populations of T. zillii. However, additional methods such as microsatellite and sequence analysis can be used to maximize the efficiency of genetic differentiation studies.

scholarly journals Molecular Identification and Polymorphism Determination of Cutaneous and Visceral Leishmaniasis Agents Isolated from Human and Animal Hosts in Iran

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Homa Hajjaran ◽  
Mehdi Mohebali ◽  
Setareh Mamishi ◽  
Farzaneh Vasigheh ◽  
Mohammad Ali Oshaghi ◽  
...  
Keyword(s):  
Visceral Leishmaniasis ◽  
Random Amplified Polymorphic Dna ◽  
Rflp Analysis ◽  
Domestic Dogs ◽  
Animal Reservoir ◽  
Rapd Pcr ◽  
Animal Hosts ◽  
Reservoir Hosts ◽  
Culture Positive

Amplification of internal transcript spacer 1 of ribosomal RNA (ITS1-RNA) gene followed by RFLP analysis and sequencing was used to identify the causing agents of cutaneous and visceral leishmaniasis (CL and VL) in humans and animal reservoir hosts from various geographical areas in Iran. We also used random amplified polymorphic DNA (RAPD-PCR) to obtain polymorphisms among isolates ofLeishmaniaspp. Totally, 362 suspected human and animal cases including 173 CL, 49 VL, 60 rodents, and 80 domestic dogs were examined forLeishmaniainfection. From 112 culture-positive samples prepared from CL cases, 75 (67%) were infected withL. majorand 37 (33%) withL. tropica. Of the 60 rodents examined, 25 (41.6%) harbored theLeishmaniainfection; 21 were infected withL. majorand 4 withL. turanica. From 49 suspected VL, 29 were positive by direct agglutination test (DAT), whereas microscopy detected parasite in bone marrow of 25 and culture in 28 of the patients. Two VL patients were infected withL. tropicaand 26 withL. infantum. Of the 80 domestic dogs, 56 showed anti-Leishmaniaantibodies with DAT. Of these, 55 were positive by both microscopy and culture. Molecular identity, obtained only for 47 samples, revealedL. infantumin 43 andL. tropicain 4 dogs. The polymorphisms amongL. tropicaandL. majorisolates were 3.6% and 7.3%; the rate among human and canine VL isolates was 2.8% and 9.8%, respectively. Our results showed that at least four differentLeishmaniaspecies with various polymorphisms circulate among humans and animal hosts in Iran.

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