scholarly journals Regional Population Diversity of Pyricularia grisea in Arkansas and the Influence of Host Selection

Plant Disease ◽  
2000 ◽  
Vol 84 (8) ◽  
pp. 877-884 ◽  
Author(s):  
J. Q. Xia ◽  
J. C. Correll ◽  
F. N. Lee ◽  
W. J. Ross ◽  
D. D. Rhoads
Keyword(s):  
Genetic Diversity ◽  
Dna Fingerprinting ◽  
Rice Blast ◽  
Nuclear Dna ◽  
The United States ◽  
Population Diversity ◽  
Dna Fingerprint ◽  
Pyricularia Grisea ◽  
Virulence Phenotype ◽  
Regional Population

MGR586 DNA fingerprinting has been widely used to characterize population diversity of the rice blast pathogen, Pyricularia grisea. However, the frequency and distribution of particular haplotypes (individuals) within MGR-delimited lineages has not been examined in the United States. MGR586 DNA fingerprinting, mitochondrial DNA (mtDNA) restriction fragment length polymorphism (RFLPs), and virulence phenotyping were used to examine genetic diversity of P. grisea in Arkansas. A total of 470 monoconidial isolates were recovered from eight rice cultivars in 18 commercial fields in nine counties in Arkansas. All isolates were examined for nuclear DNA RFLPs with the MGR586 DNA fingerprint probe, and both the MGR lineage (isolates with >80% similarity) and the haplotype frequencies were determined. Four distinct MGR586 DNA fingerprint lineages (designated A, B, C, and D) were identified among the 470 field isolates. All four lineages were found in 9 of the 18 locations. Three lineages were found in four locations, two lineages in three locations, and only a single lineage was found at two locations. In all, 10, 19, 16, and 13 haplotypes (isolates which had MGR586 DNA fingerprints which differed by 1 to 20%) were identified within lineages A, B, C, and D, respectively, among the 470 isolates examined. Within each lineage, a single haplotype (clone) predominated, representing 51 to 71% of the isolates collected for each of the four lineages. Overall, 60% of the 470 isolates belonged to one of only four haplotypes (A1, B1, C1, and D1) and these four predominant haplotypes were recovered from between 7 and 14 of the 18 locations sampled, indicating a widespread distribution of these four clones. These data indicate an exceptionally low level of genetic diversity in the regional rice blast pathogen population in Arkansas relative to several other populations of P. grisea examined from tropical environments. In addition, no mtDNA RFLPs were detected among representative haplotypes within each of the lineages, indicating a single mtDNA haplotype was present in the population. Examination of virulence indicated that two races predominated in the regional collection. All 30 isolates in lineages A and C tested had an IB-49 virulence phenotype. Out of 30 isolates in lineages B and D, 29 had an IC-17 virulence phenotype. One isolate in lineage B, isolated from a highly susceptible cultivar (L201), had an IG-1 virulence phenotype. The frequencies of the four lineages varied among the locations sampled and may have been due, in part, to the cultivar from which isolates were recovered. A single lineage was recovered from two cultivars, Mars and Millie. Although only a single field of each of these cultivars was sampled, the data indicate that certain cultivars grown in Arkansas may serve as a “bottleneck”, selecting out specific lineages in the regional population. To test this hypothesis, an additional 283 isolates were recovered from replicated plots of cvs. M204 and Mars located within commercial rice fields at two locations during two seasons. All four MGR586 lineages were recovered from each location. However, there was a strong bias for lineage B on cv. M204 (79% of all isolates) and a strong bias for lineage A on cv. Mars (95% of all isolates), indicating some cultivars were effective in excluding certain lineages.

scholarly journals Genetic Diversity Among Ophiosphaerella agrostis Strains Causing Dead Spot in Creeping Bentgrass

Plant Disease ◽  
2006 ◽  
Vol 90 (2) ◽  
pp. 146-154 ◽  
Author(s):  
John E. Kaminski ◽  
Peter H. Dernoeden ◽  
Sue Mischke ◽  
Nichole R. O'Neill
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Creeping Bentgrass ◽  
The United States ◽  
Dna Fingerprint ◽  
Fingerprint Analysis ◽  
Putting Greens ◽  
Geographic Origins ◽  
Colony Color ◽  
Asexual State

Dead spot (Ophiosphaerella agrostis) is a relatively new disease of young creeping bentgrass and hybrid bermudagrass putting greens in the United States. Little is known about the biology or genetic diversity of the pathogen. O. agrostis is unusual in that it produces prodigious numbers of pseudothecia in the field throughout the summer months and has no known asexual state. A total of 77 O. agrostis isolates were collected from 21 different bentgrass putting greens and one hybrid bermudagrass green in 11 states. DNA fingerprint analysis revealed that 78 out of 97 markers were polymorphic (80.4%), providing 57 unique profiles. Genetic variation of O. agrostis was diverse, and isolates separated into three distinct clades with ≥69% similarity. Analysis of molecular variance indicated that the geographic origins of the isolates and the ability to produce pseudothecia were the best indicators for genetic similarity among O. agrostis isolates. Colony color varied among the isolates, but generally was similar for isolates residing within two clades (B and C). Colony color of isolates within clade A appeared to be a mixture of the colony colors exhibited by clades B and C. Isolates examined within each clade generally had varying levels of pseudothecia production and varying colony colors when grown on PDA. Although O. agrostis is a homothallic species, it is unclear if outcrossing among strains occurs.

scholarly journals ISSR primer screening for analysis of genetic diversity among Scutellaria tuvensis (Lamiaceae) populations

2021 ◽  
Vol 38 ◽  
pp. 00082
Author(s):  
Dinara S. Muraseva ◽  
Alexandra A. Guseva
Keyword(s):  
Genetic Diversity ◽  
Nuclear Dna ◽  
Natural Populations ◽  
Issr Markers ◽  
Population Diversity ◽  
Point Scale ◽  
High Quality ◽  
Issr Primer ◽  
Issr Analysis ◽  
Selection Of

Using the Diamond DNA kit, high quality nuclear DNA was isolated from dry leaves of the endemic species Scutellaria tuvensis. The selection of primers for ISSR analysis of genetic polymorphism of natural populations is described. During the experiment, 22 primers were tested, their effectiveness was assessed on a point scale. When assessing the primers, the number of reproducible amplified DNA fragments, the clarity and brightness of the obtained fragments, and only distinctive bands were taken into account. As a result, 10 ISSR markers were selected that are the most informative for assessing the population diversity of the species.

scholarly journals Characterization of Pyricularia grisea in the United States Using Independent Genetic and Molecular Markers

2000 ◽  
Vol 90 (12) ◽  
pp. 1396-1404 ◽  
Author(s):  
J. C. Correll ◽  
T. L. Harp ◽  
J. C. Guerber ◽  
R. S. Zeigler ◽  
B. Liu ◽  
...  
Keyword(s):  
United States ◽  
Mating Type ◽  
Population Data ◽  
The United States ◽  
Vegetative Compatibility ◽  
Dna Fingerprint ◽  
Pyricularia Grisea ◽  
Vegetative Compatibility Groups ◽  
Large Numbers ◽  
Nit Mutants

A total of 540 isolates of Pyricularia grisea from rice in the United States were examined for vegetative compatibility, MGR586 DNA fingerprint diversity, and mating type based on hybridization with the mat1-1 and mat1-2 sexual mating type alleles. The collections contained both archived and contemporary field isolates representative of the known MGR586 lineages and races that occur throughout the United States. Complementary nitrate nonutilizing (nit) or sulfate nonutilizing (sul) mutants were used to assess vegetative compatibility in P. grisea. There was a complete correspondence between vegetative compatibility groups (VCGs), MGR586 lineage, and mating type among 527 contemporary isolates (collected between 1991 and 1997) from Arkansas, Louisiana, Missouri, Mississippi, and Texas; all isolates in MGR586 lineages A, B, C, and D belonged to VCGs US-01, US-02, US-03, and US-04, respectively. In addition, all isolates tested in VCGs US-01 and US-04 had the mat1-1 mating type allele whereas those in VCGs US-02 and US-03 had the mat1-2 allele. The strict association of independent markers during this sample period was consistent with a strictly asexual mode of reproduction. However, examination of archived isolates collected in the 1970s and 1980s and contemporary isolates revealed an incongruent relationship between the independent markers. MGR586 C and E isolates were vegetatively compatible which indicated that multiple robust MGR586 delineated lineages could be nested within certain VCGs. Although isolates in lineages C and E were vegetatively compatible, they were of opposite mating type. Several hypotheses, including recombination, could account for the incongruence between the various markers. Among the eight MGR586 lineages (A through H) that occur in the United States, all isolates in lineages A, D, E, G, and H had the mat1-1 allele, whereas isolates in lineages B, C, and F had the mat1-2 allele. Nit mutants can be recovered relatively easy from P. grisea and should allow large numbers of individuals within a population to be assessed for vegetative compatibility. VCGs may prove to be an effective multilocus marker in P. grisea. Thus, VCGs should be a useful means for characterizing genetic structure in populations of the rice blast fungus worldwide, provide a useful genetic framework to assist in interpreting molecular population data, and may provide insight into potential sexual or asexual recombination events.

scholarly journals GENETIC DIVERSITY OF RICE BLAST FUNGUS POPULATIONS (Pyricularia grisea) USING MOLECULAR MARKERS

2016 ◽  
Vol 7 (3) ◽  
pp. 57-65 ◽  
Author(s):  
S. El-Wahsh ◽  
Y. El-Refaee ◽  
A. Emeran ◽  
S. Mashaal ◽  
R. Arafa
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rice Blast ◽  
Rice Blast Fungus ◽  
Pyricularia Grisea ◽  
Blast Fungus

scholarly journals Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Fehintola V. Ajogbasile ◽  
Adeyemi T. Kayode ◽  
Paul E. Oluniyi ◽  
Kazeem O. Akano ◽  
Jessica N. Uwanibe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Control Strategies ◽  
Population Diversity ◽  
Parasite Population ◽  
Nested Polymerase Chain Reaction ◽  
Public Health Burden ◽  
Genetic Diversity And Structure

Abstract Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

scholarly journals Molecular Analysis of a Plum pox virus W Isolate in Plum Germplasm Hand Carried into the USA from the Ukraine Shows a Close Relationship to a Latvian Isolate

Plant Disease ◽  
2013 ◽  
Vol 97 (1) ◽  
pp. 44-52 ◽  
Author(s):  
Vessela Mavrodieva ◽  
Delano James ◽  
Karen Williams ◽  
Sarika Negi ◽  
Aniko Varga ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
The United States ◽  
Common Source ◽  
Plum Pox Virus ◽  
High Genetic Diversity ◽  
Close Relationship ◽  
The Usa ◽  
Sequence Identities ◽  
Germplasm Accessions

Four of 19 Prunus germplasm accessions hand carried from the Ukraine into the United States without authorization were found to be infected with Plum pox virus (PPV). Of the three isolates characterized, isolates UKR 44189 and UKR 44191 were confirmed to be isolates of PPV strain W, and UKR 44188 was confirmed to be an isolate of PPV strain D. UKR 44189 and UKR 44191 are very closely related to the PPV strain W isolate LV-145bt (HQ670748) from Latvia. Nucleotide and amino acid sequence identities between these three isolates were greater than 99%. This indicates that the isolates are very closely related and likely originated from a common source. The high genetic diversity among PPV-W strain isolates allowed the identification of potential recombination events between PPV isolates. It appears also that GF 305 peach and Prunus tomentosa are not hosts for the PPV isolate UKR 44189.

scholarly journals Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2005

Plant Disease ◽  
2007 ◽  
Vol 91 (8) ◽  
pp. 979-984 ◽  
Author(s):  
J. A. Kolmer ◽  
D. L. Long ◽  
M. E. Hughes
Keyword(s):  
United States ◽  
Leaf Rust ◽  
Great Plains ◽  
Durable Resistance ◽  
Puccinia Triticina ◽  
Leaf Rust Resistance ◽  
The United States ◽  
Ohio River ◽  
Virulence Phenotype ◽  
Common Phenotype

Collections of Puccinia triticina were obtained from rust-infected wheat leaves by cooperators throughout the United States and from surveys of wheat fields and nurseries in the Great Plains, Ohio River Valley, southeast, California, and Washington State, in order to determine the virulence of the wheat leaf rust population in 2005. Single uredinial isolates (797 in total) were derived from the collections and tested for virulence phenotype on lines of Thatcher wheat that are near-isogenic for leaf rust resistance genes Lr1, Lr2a, Lr2c, Lr3a, Lr9, Lr16, Lr24, Lr26, Lr3ka, Lr11, Lr17a, Lr30, LrB, Lr10, Lr14a, Lr18, Lr21, Lr28, and winter wheat lines with genes Lr41 and Lr42. In the United States in 2005, 72 virulence phenotypes of P. triticina were found. Virulence phenotype TDBGH, selected by virulence to resistance gene Lr24, was the most common phenotype in the United States, and was found throughout the Great Plains region. Virulence phenotype MCDSB with virulence to Lr17a and Lr26 was the second most common phenotype and was found widely in the wheat growing regions of the United States. Virulence phenotype MFPSC, which has virulence to Lr17a, Lr24, and Lr26, was the third most common phenotype, and was found in the Ohio Valley region, the Great Plains, and California. The highly diverse population of P. triticina in the United States will continue to present a challenge for the development of wheat cultivars with effective durable resistance to leaf rust.

Genetic Diversity of Wild Oat (Avena fatua)Populations from China and the United States

Weed Science ◽  
2007 ◽  
Vol 55 (2) ◽  
pp. 95-101 ◽  
Author(s):  
Runzhi Li ◽  
Shiwen Wang ◽  
Liusheng Duan ◽  
Zhaohu Li ◽  
Michael J. Christoffers ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
The United States ◽  
Mantel Test ◽  
Wild Oat ◽  
Chinese Populations ◽  
Nei's Distance ◽  
The Impact

Weed genetic diversity is important for understanding the ability of weeds to adapt to different environments and the impact of herbicide selection on weed populations. Genetic diversity within and among six wild oat populations in China varying in herbicide selection pressure and one population in North Dakota were surveyed using 64 polymorphic alleles resulting from 25 microsatellite loci. Mean Nei's gene diversity (h) for six wild oat populations from China was between 0.17 and 0.21, and total diversity (HT) was 0.23. A greater proportion of this diversity, however, was within (Hs= 0.19) rather than among (Gst= 0.15) populations. For the wild oat population from the United States,h= 0.24 andHT= 0.24 were comparable to the values for the six populations from China. Cluster analysis divided the seven populations into two groups, where one group was the United States population and the other group included the six Chinese populations. The genetic relationships among six populations from China were weakly correlated with their geographic distribution (r= 0.22) using the Mantel test. Minimal difference in gene diversity and small genetic distance (Nei's distance 0.07 or less) among six populations from China are consistent with wide dispersal of wild oat in the 1980s. Our results indicate that the wild oat populations in China are genetically diverse at a level similar to North America, and the genetic diversity of wild oat in the broad spatial scale is not substantially changed by environment, agronomic practices, or herbicide usage.

scholarly journals Limited Genetic Diversity in North American Isolates of Phytophthora erythroseptica Pathogenic to Potato Based on RAPD Analysis

Plant Disease ◽  
2005 ◽  
Vol 89 (4) ◽  
pp. 380-384 ◽  
Author(s):  
Rick D. Peters ◽  
Rod J. Clark ◽  
Albert D. Coffin ◽  
Antony V. Sturz ◽  
David H. Lambert ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
New Brunswick ◽  
Prince Edward Island ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
The United States ◽  
Vitro Assay ◽  
Phytophthora Erythroseptica

Pink rot of potato (Solanum tuberosum), caused by Phytophthora erythroseptica, is found wherever potatoes are grown, and in the last decade, it has reemerged as an economically important disease in Canada and the United States. A selection of isolates of P. erythroseptica from major potato-growing regions in North America, namely Prince Edward Island and New Brunswick, Canada, and Maine and Idaho, U.S.A., was assessed for genetic diversity with randomly chosen decanucleotide primers which were used to amplify regions of DNA to reveal polymorphisms among templates (random amplified polymorphic DNA [RAPD]). The isolates varied in their geographic origin as well as in their sensitivity to mefenoxam, as determined by an in vitro assay. In three separate RAPD screens (I, II, and III) with 23 isolates of P. erythroseptica chosen from a larger collection, 1,410, 369, and 316 robust, scorable bands were amplified, respectively. However, among the bands amplified in screens I, II, and III, only 3, 1, and 3 bands, respectively, were polymorphic. When three primers yielding polymorphisms were used to screen 106 isolates from Prince Edward Island and New Brunswick, or a representative collection of 32 isolates from Prince Edward Island, New Brunswick, Maine, and Idaho, no major variation was discovered. RAPD markers were not correlated with geographic origin or mefenoxam sensitivity of the isolates. From an evolutionary standpoint, the absence of genetic diversity among the isolates of P. erythroseptica we examined may be attributable to the relatively recent introduction of a small founding population of the pathogen in North America.

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