scholarly journals Genetic Variability of Natural Populations of Grapevine leafroll-associated virus 2 in Pacific Northwest Vineyards

2010 ◽  
Vol 100 (7) ◽  
pp. 698-707 ◽  
Author(s):  
Sridhar Jarugula ◽  
Olufemi J. Alabi ◽  
Robert R. Martin ◽  
Rayapati A. Naidu
Keyword(s):  
Genetic Variability ◽  
Pacific Northwest ◽  
Current Knowledge ◽  
Natural Populations ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
Enzyme Linked Immunosorbent Assay ◽  
Polymorphism Analysis ◽  
Nonsynonymous Site ◽  
Genomic Regions

Genetic variability of field populations of Grapevine leafroll-associated virus 2 (GLRaV-2) in Pacific Northwest (PNW) vineyards was characterized by sequencing the entire coat protein (CP) and a portion of the heat-shock protein-70 homolog (HSP70h) genes. Phylogenetic analysis of CP and HSP70h nucleotide sequences obtained in this study and corresponding sequences from GenBank revealed segregation of GLRaV-2 isolates into six lineages with virus isolates from PNW distributed in ‘PN’, ‘H4’, and ‘RG’ lineages. An estimation of the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site indicated that different selection pressures may be acting on the two genomic regions encoding proteins with distinct functions. Multiple alignments of CP amino acid sequences showed lineage-specific differences. Enzyme-linked immunosorbent assay results indicated that GLRaV-2-specific antibodies from a commercial source are unable to reliably detect GLRaV-2 isolates in the RG lineage, thereby limiting antibody-based diagnosis of all GLRaV-2 isolates currently found in PNW vineyards. A protocol based on reverse-transcription polymerase chain reaction and restriction fragment length polymorphism analysis was developed for differentiating GLRaV-2 isolates belonging to the three lineages present in the region. The taxonomic status of GLRaV-2 is discussed in light of the current knowledge of global genetic diversity of the virus.

scholarly journals Genetic variability in natural populations of Zeyheria montana mart. from the Brazilian Cerrado

2007 ◽  
Vol 64 (4) ◽  
pp. 409-415 ◽  
Author(s):  
Bianca Waléria Bertoni ◽  
Spartaco Astolfi Filho ◽  
Ernani Ronie Martins ◽  
Carlos Ferreira Damião Filho ◽  
Suzelei de Castro França ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Natural Populations ◽  
Mantel Test ◽  
Scientific Data ◽  
Group Method ◽  
Polymorphism Analysis ◽  
Popular Medicine ◽  
Pair Group ◽  
Optimized Protocol ◽  
Geographical Distances

Zeyheria montana, an endemic species of the Bignoniaceae family from the Brazilian Cerrado's known for its anti-cancer properties, is widely used as imuno stimulant in the popular medicine and its therapeutic activity must be validated by scientific data. The objective of this work was to evaluate the genetic variability of eight plant populations collected within the state of São Paulo, Brazil, via Random Amplification of Polymorphic DNA (RAPD) used as molecular markers. After an optimized protocol for the amplification reaction, nine selected primers generated 105 reproducible bands, indicating up to 60% polymorphism. Analysis of molecular variance (AMOVA) revealed higher genetic variation within populations (84.03%) than among populations (15.97%). The variation values estimated by phiST (0.160) indicated moderate to high inter population structuration. Levels of similarity inter plants with genetic and geographical distances, estimated by the unweighted pair-group method analysis (UPGMA) clustering and non-metric multidimensional scaling (NMDS) ordination methods and by the Mantel test (-0.2345 p = 0.118) denoted that the structure found follows the island model, which assumes that a single population of infinite size may have initiated the existing populations of Zeyheria montana, with no spatial position correlation. Based on the obtained data, a germplasm bank from individuals representing the species variability was established. Furthermore the information here reported can be of importance to develop strategies for the conservation of Z. montana.

scholarly journals Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

2018 ◽  
Author(s):  
Gabriel E. Rech ◽  
Maria Bogaerts-Marquez ◽  
Maite G. Barrón ◽  
Miriam Merenciano ◽  
José Luis Villanueva-Cañas ◽  
...  
Keyword(s):  
Transposable Element ◽  
Adaptive Evolution ◽  
Current Knowledge ◽  
Natural Populations ◽  
Nucleotide Polymorphisms ◽  
Induced Mutations ◽  
Phenotypic Effect ◽  
Single Nucleotide ◽  
Adaptive Mutations ◽  
Genomic Regions

AbstractMapping genotype to phenotype is challenging because of the difficulties in identifying both the traits under selection and the specific genetic variants underlying these traits. Most of the current knowledge of the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions in 91 samples from 60 worldwide natural populations of Drosophila melanogaster. We identified a set of 300 TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. Indeed, we, and others, found evidence of selective sweeps and/or population differentiation for 65 of them. The analysis of the genes located nearby these 65 candidate adaptive insertions suggested that the functional response to selection is related with the GO categories of response to stimulus, behavior, and development. We further showed that a subset of the candidate adaptive TEs affect expression of nearby genes, and five of them have already been linked to an ecologically relevant phenotypic effect. Our results provide a more complete understanding of the genetic variation and the fitness-related traits relevant for adaptive evolution. Similar studies should help uncover the importance of TE-induced adaptive mutations in other species as well.

scholarly journals Differentiation and genetic variability in natural populations of Anopheles (N.) triannulatus (Neiva& Pinto, 1922) of Brazilian Amazonia

2004 ◽  
Vol 64 (2) ◽  
pp. 327-336 ◽  
Author(s):  
J. M. M. Santos ◽  
J. F. Maia ◽  
W. P. Tadei
Keyword(s):  
Genetic Variability ◽  
Natural Populations ◽  
Isozyme Analysis ◽  
Brazilian Amazonia ◽  
F Statistics

Populations of Anopheles triannulatus from Macapá (AP), Aripuanã (MT), Ji-Paraná (RO), and Manaus-Janauari Lake (AM) were studied using 16 enzymatic loci. The results of the isozyme analysis showed that the population of Macapá presented higher polymorphism (56.3%). The lowest variability was observed in the population of Manaus (p = 25.0; Ho = 0.077 ± 0.046). The results of Wright's F statistics showed unbalance due to excess of homozygotes (Fis > Fst), denoting a certain intrapopulational differentiation. Although the populations are genetically very close (D = 0.003 - 0.052), the dendrogram separates the populations in two groups: Macapá separated from that of Manaus, Ji-Paraná, and Aripuanã. This result may suggest a reduction in the genic flow, which possibly had some influence in the substructuration of the populations.

scholarly journals Identification, Characterization, and Molecular Detection of Alfalfa mosaic virus in Potato

2006 ◽  
Vol 96 (11) ◽  
pp. 1237-1242 ◽  
Author(s):  
H. Xu ◽  
J. Nie
Keyword(s):  
Mosaic Virus ◽  
Gene Sequence ◽  
Alfalfa Mosaic Virus ◽  
Enzyme Linked Immunosorbent Assay ◽  
Polymorphism Analysis ◽  
Rt Pcr ◽  
Potato Leaf ◽  
Simple Method ◽  
Cp Gene ◽  
Nucleotide Sequence Alignment

Alfalfa mosaic virus (AMV) was detected in potato fields in several provinces in Canada and characterized by bioassay, enzyme-linked immunosorbent assay, and reverse-transcription polymerase chain reaction (RT-PCR). The identity of eight Canadian potato AMV isolates was confirmed by sequence analysis of their coat protein (CP) gene. Sequence and phylogenetic analysis indicated that these eight AMV potato isolates fell into one strain group, whereas a slight difference between Ca175 and the other Canadian AMV isolates was revealed. The Canadian AMV isolates, except Ca175, clustered together among other strains based on alignment of the CP gene sequence. To detect the virus, a pair of primers, AMV-F and AMV-R, specific to the AMV CP gene, was designed based on the nucleotide sequence alignment of known AMV strains. Evaluations showed that RT-PCR using this primer set was specific and sensitive for detecting AMV in potato leaf and tuber samples. AMV RNAs were easily detected in composite samples of 400 to 800 potato leaves or 200 to 400 tubers. Restriction analysis of PCR amplicons with SacI was a simple method for the confirmation of PCR tests. Thus, RT-PCR followed by restriction fragment length polymorphism analysis may be a useful approach for screening potato samples on a large scale for the presence of AMV.

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 Genetic variability of brycon orbignyanus (valenciennes, 1850) (characiformes: characidae) in cultivated and natural populations of the upper paraná river, and implications for the conservation of the species

2011 ◽  
Vol 54 (4) ◽  
pp. 839-848 ◽  
Author(s):  
Renata de Souza Panarari-Antunes ◽  
Alberto José Prioli ◽  
Sônia Maria Alves Pinto Prioli ◽  
Alexsandro Sobreira Galdino ◽  
Horácio Ferreira Julio Junior ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Natural Populations ◽  
Paraná River ◽  
Parana River ◽  
Upper Paraná River

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 Genetic structure and gene flow of Eugenia dysenterica natural populations

2005 ◽  
Vol 40 (10) ◽  
pp. 975-980 ◽  
Author(s):  
Maria Imaculada Zucchi ◽  
José Baldin Pinheiro ◽  
Lázaro José Chaves ◽  
Alexandre Siqueira Guedes Coelho ◽  
Mansuêmia Alves Couto ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Variability ◽  
Pearson Correlation ◽  
Natural Populations ◽  
Similarity Index ◽  
Genetic Distances ◽  
Strong Positive Correlation ◽  
Randomly Amplified Polymorphic Dna ◽  
Jaccard Similarity ◽  
Eugenia Dysenterica

This study was carried out to assess the genetic variability of ten "cagaita" tree (Eugenia dysenterica) populations in Southeastern Goiás. Fifty-four randomly amplified polymorphic DNA (RAPD) loci were used to characterize the population genetic variability, using the analysis of molecular variance (AMOVA). A phiST value of 0.2703 was obtained, showing that 27.03% and 72.97% of the genetic variability is present among and within populations, respectively. The Pearson correlation coefficient (r) among the genetic distances matrix (1 - Jaccard similarity index) and the geographic distances were estimated, and a strong positive correlation was detected. Results suggest that these populations are differentiating through a stochastic process, with restricted and geographic distribution dependent gene flow.

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