Genetic variability in the canker pathogen fungus, Gremmeniella abietina. 2. Fine-scale investigation of the population genetic structure

1997 ◽  
Vol 75 (9) ◽  
pp. 1460-1469 ◽  
Author(s):  
Xiao-Ru Wang ◽  
Alfred E. Szmidt ◽  
Richard A. Ennos ◽  
Per Hansson
Keyword(s):  
Genetic Variability ◽  
Population Genetic ◽  
Pinus Contorta ◽  
Random Amplified Polymorphic Dna ◽  
Sampling Site ◽  
Population Subdivision ◽  
Northern Sweden ◽  
Canker Pathogen ◽  
Total Genetic Diversity ◽  
Small Clusters

Genetic variation at 32 polymorphic random amplified polymorphic DNA loci was analysed in the ascomycete canker pathogen fungus Gremmeniella abietina (Lagerb.) Morelet collected from one plantation of Pinus contorta Dougl. ex Loud, in northern Sweden. The genetic variability maintained in the G. abietina population was high. Many different multilocus genotypes were found on each tree and in each sampling site within the plantation. The clonal fraction of the population was small, and identical genotypes were found either on the same tree or branch or on trees in the same sampling site. The finding of very few widely distributed clones suggests that the effective dispersal of asexual spores is limited to a few metres and resulted in small clusters of clones in local sites. Analysis of molecular variance revealed that 45.3% of the total variation was attributable to differences among isolates within trees, 22.5% to trees within sites and 32.3% to sampling sites differences. Allele frequencies at most of the loci varied significantly among the sampling sites and average total genetic diversity over the 32 loci was 0.27 indicating high population subdivision. The factors that could have contributed to the observed population structure were discussed. Key words: Gremmeniella abietina, genotype and clone distribution, population subdivision, RAPD.

scholarly journals KARAKTERISASI GENETIKA RUMPUT LAUT Kappaphycus alvarezii YANG DIBUDIDAYAKAN DI SULAWESI SELATAN

2016 ◽  
Vol 1 (1) ◽  
pp. 1
Author(s):  
Andi Parenrengi ◽  
Sulaeman Sulaeman ◽  
Emma Suryati ◽  
Andi Tenriulo
Keyword(s):  
Polymerase Chain Reaction ◽  
Genetic Variability ◽  
Population Genetic ◽  
Random Amplified Polymorphic Dna ◽  
Kappaphycus Alvarezii ◽  
Similarity Index ◽  
Chain Reaction ◽  
Dna Fragment ◽  
Polymerase Chain ◽  
Population Genetic Analyses

Karakterisasi genetika rumput laut Kappaphycus alvarezii telah dilakukan dengan menggunakan teknik Random Amplified Polymorphic DNA (RAPD) dengan tujuan untuk mengetahui variasi genetika rumput laut K. alvarezii dari beberapa lokasi budi daya di Sulawesi Selatan yakni Polmas, Pinrang, Takalar, dan Bantaeng. Sampel dipreservasi dengan menggunakan larutan TNES-Urea sebelum ekstraksi DNA. Ekstraksi genom DNA dilakukan dengan menggunakan metode konvensional fenol-khloroform. Amplifikasi DNA dilakukan dengan teknik Polymerase Chain Reaction (PCR). Untuk dokumentasi riset, hasil PCR dielektroforesis pada agarosa gel dengan menggunakan buffer TBE. Data dianalisis menggunakan program Tools for Population Genetic Analyses (TFPGA). Hasil penelitian menunjukkan bahwa kelima “primers” (P-40, P-50, DALRP, Ca01, dan Ca-02) yang digunakan dapat menghasilkan beberapa fragmen spesifik yang mengindikasikan fragmen spesifik spesies dan lokasi budi daya K. alvarezii. Keragaan genetika intra dan inter lokasi rumput laut menunjukkan variasi yang relatif kecil yang ditandai dengan rendahnya perbedaan jumlah/ukuran fragmen DNA, polimorfisme, indeks similaritas, dan jarak genetikanya. Total fragmen yang didapatkan dari lima primer adalah 47—55 pada ukuran fragmen 175—2.600 bp, sedangkan polimorfisme dan indeks similaritas masing-masing adalah 3,6%—31,0% dan 0,79%—0,99%. Jarak genetika antar beberapa lokasi K. alvarezii berkisar antara 0,1758—0,5689 di mana kekerabatan yang terdekat didapatkan antara Takalar dan Bantaeng.Genetic characterization of seaweed Kappaphycus alvarezii was observed using Random Amplified Polymorphic DNA (RAPD) technique to reveal the genetic variability of seaweed from different locations in South Sulawesi. The sample of farmed seaweed K. alvarezii was collected from Polmas, Pinrang, Takalar, and Bantaeng. Genomic DNA was extracted by using the conventional method of phenol-chloroform. Sample was preserved by TNES-Urea buffer prior to DNA extraction. DNA was amplified by Polymerase Chain Reaction (PCR) method. DNA Fragment was documented by gel electrophoresis using TBE buffer. The data was analyzed by computer program called Tools for Population Genetic Analyses (TFPGA). The results showed that the five primers (P-40, P-50, DALRP, Ca-01, and Ca-02) used, revealed specific fragment for species and location of K. alvarezii . The low genetic variability both intra and inter locations of farmed seaweed was indicated by variation in total and size of DNA fragment, polymorphism and similarity index. The total of fragment generated by the five primers was 47—55 in size range of 175-2,600 bp, while proportion of polymorphism and similarity index were 3.6%—31.0% and 0.79%—0.99%, respectively. Genetic distance between farmed seaweed was 0.1758—0.5689 where the closest genetic distance was found between Takalar and Bantaeng.

Random amplified polymorphic DNA diversity of marginal and central populations in Pinus contorta subsp. latifolia

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 13-22 ◽  
Author(s):  
Aron J Fazekas ◽  
Francis C Yeh
Keyword(s):  
Pinus Contorta ◽  
Random Amplified Polymorphic Dna ◽  
Single Locus ◽  
Population Subdivision ◽  
Founder Effects ◽  
Marginal Populations ◽  
Clear Trend ◽  
Wahlund Effect ◽  
Multilocus Associations ◽  
F Statistics

Fifteen populations of lodgepole pine (Pinus contorta subsp. latifolia) were surveyed for diversity across 52 random amplified polymorphic DNAs (RAPDs). The objective was to compare single-locus and multilocus structures in four marginal, three intermediate, and eight central populations. Single-locus estimates indicated average observed and expected heterozygosity to be 0.19 and 0.17, respectively. When these estimates were split into population categories, a clear trend of increasing diversity was detected in the direction of marginal to central populations. F-statistics indicated an excess of heterozygotes, with FIS ranging from -0.08 for marginal populations to -0.15 for central populations and averaging -0.12 over 15 populations. The estimates of FST decreased towards the margins of the species range, indicating increased population differentiation. Forty-nine of 52 RAPDs tested neutral in the Ewens-Watterson analysis. Multilocus analysis showed significant two-locus and high-order gametic disequilibria in all 15 populations. The most prominent components of the two-locus analysis were the variance of disequilibrium (VD, 46.2%) and the multilocus Wahlund effect (31.9%). This high value for VD indicated that founder effects could explain much of the observed multilocus associations. When analyzed by population categories, the VD showed a decreasing trend indicating that variation due to founder effects was more prominent in marginal populations. The two-locus Wahlund effect (WC) that is characteristic of strong population subdivision was highest in the central populations. This indicated significant levels of gene flow between populations with different allelic combinations.Key words: multilocus genetic structure, central and marginal populations, RAPD, Pinus contorta subsp. latifolia.

Detection of genetic diversity in tea (Camellia sinensis) using RAPD markers

Genome ◽  
1995 ◽  
Vol 38 (2) ◽  
pp. 201-210 ◽  
Author(s):  
F. N. Wachira ◽  
R. Waugh ◽  
W. Powell ◽  
C. A. Hackett
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Southeast Asia ◽  
Camellia Sinensis ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Systematic Assessment ◽  
Tree Crop ◽  
Taxonomic Relationships

Camellia sinensis is a beverage tree crop native to Southeast Asia and introductions have been made into several nonindigenous countries. No systematic assessment of genetic variability in tea has been done anywhere. In this study, random amplified polymorphic DNA (RAPD) analysis was used to estimate genetic diversity and taxonomic relationships in 38 clones belonging to the three tea varieties, assamica, sinensis, and assamica ssp. lasiocalyx. Extensive genetic variability was detected between species, which was partitioned into between and within population components. Seventy percent of the variation was detected within populations. Analyses based on band sharing separated the three populations in a manner consistent with both the present taxonomy of tea and with the known pedigrees of some clones. RAPD analysis also discriminated all of the 38 commercial clones, even those which cannot be distinguished on the basis of morphological and phenotypic traits.Key words: genetic diversity, RAPDs, Camellia sinensis.

scholarly journals Random amplified polymorphic DNA (RAPD) finger prints evidencing high genetic variability among marine angiosperms of India

2016 ◽  
Vol 97 (6) ◽  
pp. 1307-1315 ◽  
Author(s):  
Elangovan Dilipan ◽  
Jutta Papenbrock ◽  
Thirunavakkarasu Thangaradjou
Keyword(s):  
Genetic Variability ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Seagrass Species ◽  
Complex Species ◽  
Marine Angiosperms ◽  
Different Populations ◽  
High Degree ◽  
Identification Tool

In India 14 seagrass species can be found with monospecific genera (Enhalus, ThalassiaandSyringodium),Cymodoceawith two species andHalophilaandHalodulerepresented by more than two taxonomically complex species. Considering this, the present study was made to understand the level and pattern of genetic variability among these species collected from Tamilnadu coast, India. Random amplified polymorphic DNA (RAPD) analysis was used to evaluate the level of polymorphism existing between the species. Out of the 12 primers tested, 10 primers amplified 415 DNA fragments with an average of 41.5 fragments per primer. Of the total 415 amplified fragments only 123 (29.7%) were monomorphic and the remaining 292 (70.3%) were polymorphic for Indian seagrass species. Among the 10 primers used four are identified as the key primers capable of distinguishing all the Indian seagrasses with a high degree of polymorphism and bringing representative polymorphic alleles in all the tested seagrasses. From the present investigation, this study shows that the RAPD marker technique can be used not only as a tool to analyse genetic diversity but also to resolve the taxonomic uncertainties existing in the Indian seagrasses. The efficiency of these primers in bringing out the genetic polymorphism or homogeneity among different populations of theHalophilaandHalodulecomplex still has to be tested before recommending these primers as an identification tool for Indian seagrasses.

Effects of Selection at Linked Sites on Patterns of Genetic Variability

2021 ◽  
Vol 52 (1) ◽  
pp. 177-197
Author(s):  
Brian Charlesworth ◽  
Jeffrey D. Jensen
Keyword(s):  
Genetic Variability ◽  
Population Genetic ◽  
Selective Sweeps ◽  
Recombination Rates ◽  
Frequency Distributions ◽  
A Genome ◽  
Demographic Processes ◽  
Dna Sequence Variants ◽  
Genomic Regions ◽  
Functional Components

Patterns of variation and evolution at a given site in a genome can be strongly influenced by the effects of selection at genetically linked sites. In particular, the recombination rates of genomic regions correlate with their amount of within-population genetic variability, the degree to which the frequency distributions of DNA sequence variants differ from their neutral expectations, and the levels of adaptation of their functional components. We review the major population genetic processes that are thought to lead to these patterns, focusing on their effects on patterns of variability: selective sweeps, background selection, associative overdominance, and Hill–Robertson interference among deleterious mutations. We emphasize the difficulties in distinguishing among the footprints of these processes and disentangling them from the effects of purely demographic factors such as population size changes. We also discuss how interactions between selective and demographic processes can significantly affect patterns of variability within genomes.

scholarly journals The use of random amplified polymorphic DNA to evaluate the genetic variability of Ponkan mandarin (Citrus reticulata Blanco) accessions

2000 ◽  
Vol 23 (1) ◽  
pp. 169-172 ◽  
Author(s):  
Helvécio Della Coletta Filho ◽  
Marcos Antonio Machado ◽  
M. Luiza P.N. Targon ◽  
Jorgino Pompeu Jr.
Keyword(s):  
Genetic Variability ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Point Mutations ◽  
The Other ◽  
Citrus Reticulata ◽  
Random Primers ◽  
Citrus Reticulata Blanco ◽  
Ponkan Mandarin

RAPD analysis of 19 Ponkan mandarin accessions was performed using 25 random primers. Of 112 amplification products selected, only 32 were polymorphic across five accessions. The absence of genetic variability among the other 14 accessions suggested that they were either clonal propagations with different local names, or that they had undetectable genetic variability, such as point mutations which cannot be detected by RAPD.

Genetic variability in the natural populations of Lasioderma serricorne (F.) (Coleoptera: Anobiidae), detected by RAPD markers and by esterase isozymes

2015 ◽  
Vol 106 (1) ◽  
pp. 47-53 ◽  
Author(s):  
T. Coelho-Bortolo ◽  
C.A. Mangolin ◽  
A.S. Lapenta
Keyword(s):  
Genetic Variability ◽  
Random Amplified Polymorphic Dna ◽  
Natural Populations ◽  
Electrophoretic Analysis ◽  
Effective Control ◽  
Lasioderma Serricorne ◽  
Control Programs ◽  
Dried Fruit ◽  
High Level ◽  
High Degree

AbstractLasioderma serricorne (F.) is a small cosmopolitan beetle regarded as a destructive pest of several stored products such as grains, flour, spices, dried fruit and tobacco. Chemical insecticides are one of the measures used against the pest. However, intensive insecticide use has resulted in the appearance of resistant insect populations. Therefore, for the elaboration of more effective control programs, it is necessary to know the biological aspects of L. serricorne. Among these aspects, the genetic variability knowledge is very important and may help in the development of new control methods. The objective of this study was to evaluate the genetic variability of 11 natural populations of L. serricorne collected respectively in three and four towns in the states of Paraná and São Paulo, Brazil, using 20 primers random amplified polymorphic DNA (RAPD) and polymorphisms of esterases. These primers produced 352 polymorphic bands. Electrophoretic analysis of esterases allowed the identification of four polymorphic loci (Est-2, Est-4, Est-5 and Est-6) and 18 alleles. Results show that populations are genetically differentiated and there is a high level of genetic variability within populations. The high degree of genetic differentiation is not directly correlated to geographical distance. Thus, our data indicate that movement of infested commodities may contribute to the dissemination of L. serricorne, facilitating gene flow.

scholarly journals A spectral theory for Wright’s inbreeding coefficients and related quantities

PLoS Genetics ◽  
2021 ◽  
Vol 17 (7) ◽  
pp. e1009665
Author(s):  
Olivier François ◽  
Clément Gain
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Population Genetic ◽  
Principal Component ◽  
Large Data ◽  
Population Subdivision ◽  
Adaptive Genetic Variation ◽  
Genomic Locus ◽  
Inbreeding Coefficients ◽  
Definition Of

Wright’s inbreeding coefficient, FST, is a fundamental measure in population genetics. Assuming a predefined population subdivision, this statistic is classically used to evaluate population structure at a given genomic locus. With large numbers of loci, unsupervised approaches such as principal component analysis (PCA) have, however, become prominent in recent analyses of population structure. In this study, we describe the relationships between Wright’s inbreeding coefficients and PCA for a model of K discrete populations. Our theory provides an equivalent definition of FST based on the decomposition of the genotype matrix into between and within-population matrices. The average value of Wright’s FST over all loci included in the genotype matrix can be obtained from the PCA of the between-population matrix. Assuming that a separation condition is fulfilled and for reasonably large data sets, this value of FST approximates the proportion of genetic variation explained by the first (K − 1) principal components accurately. The new definition of FST is useful for computing inbreeding coefficients from surrogate genotypes, for example, obtained after correction of experimental artifacts or after removing adaptive genetic variation associated with environmental variables. The relationships between inbreeding coefficients and the spectrum of the genotype matrix not only allow interpretations of PCA results in terms of population genetic concepts but extend those concepts to population genetic analyses accounting for temporal, geographical and environmental contexts.

Study of genetic variability of umbilical cord blood using RAPD assay

2021 ◽  
Vol 20 (4) ◽  
pp. 848-854
Author(s):  
Md Faruque Miah ◽  
Md Shad Ebna Rahaman ◽  
Sanjana Fatema Chowdhury ◽  
Mohammad Golam Rob Mahmud
Keyword(s):  
Genetic Variability ◽  
Genetic Distance ◽  
Cord Blood ◽  
Umbilical Cord ◽  
Umbilical Cord Blood ◽  
Gene Diversity ◽  
Human Subjects ◽  
Random Amplified Polymorphic Dna ◽  
Medical Science ◽  
Wiener Index

Background: The genetic variability of Umbilical Cord Blood (UCB) is most important for newborn screening, therapeutic possibility of haematological disorders as well as for the establishment of cord blood banking and stem cell research. Method: Genetic variability of umbilical cord blood (UCB) of 22 human subjects was evaluated first time by applying Random Amplified Polymorphic DNA (RAPD) assay using six decamar primers (B-14, OPB-05, OPB-08, OPB-12, OPB-19 and UBC-122). Result: A total number of bands were recorded 312 from 116 polymorphic loci and single monomorphic locus. All the markers showed highest polymorphism (100%) except the primer OPB 08 (92.31%) among tested individuals. The genetic distance was observed with highest 1.0 and lowest 0.72 respectively whereas mean genetic distance was recorded 0.90. Considering Shannon-Wiener index average diversity was recorded 0.139365. The mean Nei genetic similarity was found 0.17 which was found opposition to genetic distances. A phylogenetic relationship among the individual subjects was also observed between the linkage distances of 11 to 27 with 8 clades, 3 subclusters and a cluster. In addition, average allele frequency p and q was observed 0.08156 and 0.948751 respectively whereas highest intra locus gene diversity and average gene diversity were found 3.323817 and 0.144572 respectively. Conclusion: Considering different parameters, higher genetic variability was found among the experimental subjects, probably due to the mixture DNA of parents and newborn. Bangladesh Journal of Medical Science Vol.20(4) 2021 p.848-854

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