scholarly journals Regional and Temporal Population Structure of Pseudoperonospora cubensis in Michigan and Ontario

2016 ◽  
Vol 106 (4) ◽  
pp. 372-379 ◽  
Author(s):  
R. P. Naegele ◽  
L. M. Quesada-Ocampo ◽  
J. D. Kurjan ◽  
C. Saude ◽  
M. K. Hausbeck
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Growing Season ◽  
Pseudoperonospora Cubensis ◽  
Genetic Cluster ◽  
Simple Sequence Repeat Markers ◽  
Northern Regions ◽  
Genetic Clusters ◽  
Oomycete Pathogen ◽  
Simple Sequence

Cucurbit downy mildew (CDM), caused by the oomycete pathogen Pseudoperonospora cubensis, is a devastating disease that affects cucurbit species worldwide. This obligate, wind-dispersed pathogen does not overwinter in Michigan or other northern regions and new isolates can enter the state throughout the growing season. To evaluate the regional and temporal population structure of P. cubensis, sporangia from CDM lesions were collected from cucurbit foliage grown in Michigan and Ontario field locations in 2011. Population structure and genetic diversity were assessed in 257 isolates using nine simple sequence repeat markers. Genetic diversity was high for isolates from Michigan and Canada (0.6627 and 0.6131, respectively). Five genetic clusters were detected and changes in population structure varied by site and sampling date within a growing season. The Michigan and Canada populations were significantly differentiated, and a unique genetic cluster was detected in Michigan.

Genetic diversity and population structure of Vigna exilis and Vigna grandiflora (Phaseoleae, Fabaceae) from Thailand based on microsatellite variation

Botany ◽  
2013 ◽  
Vol 91 (10) ◽  
pp. 653-661 ◽  
Author(s):  
Anochar Kaewwongwal ◽  
Arunee Jetsadu ◽  
Prakit Somta ◽  
Sompong Chankaew ◽  
Peerasak Srinives
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Allelic Richness ◽  
Gene Diversity ◽  
In Situ Conservation ◽  
Natural Populations ◽  
Microsatellite Variation ◽  
Genetic Clusters ◽  
Simple Sequence

The objective of this research was to determine the genetic diversity and population structure of natural populations of two rare wild species of Asian Vigna (Phaseoleae, Fabaceae), Vigna exilis Tateishi & Maxted and Vigna grandiflora (Prain) Tateishi & Maxted, from Thailand. Employing 21 simple sequence repeat markers, 107 and 85 individuals from seven and five natural populations of V. exilis and V. grandiflora, respectively, were analyzed. In total, the markers detected 196 alleles for V. exilis and 219 alleles for V. grandiflora. Vigna exilis populations showed lower average values in number of alleles, allelic richness, observed heterozygosity, gene diversity, and outcrossing rate than V. grandiflora populations, namely 58.00% versus 114.60%, 51.96% versus 74.80%, 0.02% versus 0.18%, 0.40% versus 0.66%, and 3.24% versus 17.41%, respectively. Pairwise FST among populations demonstrated that V. exilis was much more differentiated than V. grandiflora. Analysis of molecular variance revealed that 41.83% and 15.06% of total variation resided among the populations of V. exilis and V. grandiflora, respectively. Seven and two genetic clusters were detected for V. grandiflora and V. exilis by STRUCTURE analysis. Our findings suggest that different strategies are required for in situ conservation of the two species. All V. exilis populations, or as many as possible, should be conserved to protect genetic resources of this species, while a few V. grandiflora populations can capture the majority of its genetic variation.

scholarly journals Assessment of genetic diversity in Thai upland rice varieties using SSR markers

2020 ◽  
pp. 597-604
Author(s):  
Somrudee Nilthong ◽  
Ekachai Chukeatirote ◽  
Rungrote Nilthong
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Simple Sequence Repeat ◽  
Genetic Resource ◽  
Upland Rice ◽  
Oryza Sativa L ◽  
Polymorphic Information Content ◽  
Rice Varieties ◽  
Simple Sequence Repeat Markers ◽  
Simple Sequence

Upland rice (Oryza sativa L.) is precious genetic resource containing some valuable alleles not common in modern germplasm. In this study, genetic diversity and population structure of 98 upland rice varieties from northern part of Thailand were examined using nine simple sequence repeat markers. Number of alleles detected by the above primers was 50 with a minimum and maximum frequency of 2 to 10 alleles per locus, respectively. The polymorphic information content (PIC) values ranged from 0.375 to 0.714 with an average of 0.605 for the primers RM164 and RM1, respectively. Dendrogram cluster analysis of the SSR data distinctly classified all genotypes into three major groups (I, II and III), which corresponded to their places of collection. Population structure divided these genotypes into two distinct subpopulations. Subpopulation 1 consisted of upland rice varieties that collected from Chiang Rai province while the majority of subpopulation 2 were collected from Phayao and Phitsanulok provinces. Analysis of molecular variance revealed 68% variance among two subpopulations and 32% variance within subpopulations, suggesting a high genetic differentiation between the two subpopulations. The huge genetic variability of upland rice in northern part of Thailand can be used to complement the gene pool of modern genotypes in rice breeding program.

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