scholarly journals Population Structure of the Blueberry Pathogen Monilinia vaccinii-corymbosi in the United States

2015 ◽  
Vol 105 (4) ◽  
pp. 533-541 ◽  
Author(s):  
Kathleen M. Burchhardt ◽  
Marc A. Cubeta
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
New York ◽  
Population Structure ◽  
Population Biology ◽  
Random Mating ◽  
The United States ◽  
Restricted Gene Flow ◽  
Southeast United States ◽  
Genetic Diversity And Structure

The fungus Monilinia vaccinii-corymbosi causes disease of blueberry (Vaccinium section Cyanococcus) shoots, flowers, and fruit. The objective of our research was to examine the population biology and genetics of M. vaccinii-corymbosi in the United States. A total of 480 samples of M. vaccinii-corymbosi were collected from 18 blueberry fields in 10 states; one field in Georgia, Massachusetts, Maine, Michigan, Mississippi, New Jersey, New York, Oregon, and Washington and nine fields in North Carolina. Analysis with 10 microsatellite markers revealed 247 unique multilocus haplotypes (MLHs), with 244 MLHs detected within 11 fields in the Northeast, Northwest, Midwest, and Southeast and three MLHs detected within seven fields in the Southeast United States. Genetic similarity and low genetic diversity of M. vaccinii-corymbosi isolates from the seven fields in the Southeast United States suggested the presence of an expansive, self-fertile population. Tests for linkage disequilibrium within 10 fields that contained ≥12 MLHs supported random mating in six fields and possible inbreeding and/or self-fertilization in four fields. Analysis of molecular variance, discriminate analysis of principal components, and Bayesian cluster analysis provided evidence for population structure and restricted gene flow among fields. This research represents the first comprehensive investigation of the genetic diversity and structure of field populations of M. vaccinii-corymbosi.

scholarly journals Population structure of Drosophila suzukii and signals of multiple invasions into the continental United States

2021 ◽  
Author(s):  
Kyle M Lewald ◽  
Antoine Abrieux ◽  
Derek A Wilson ◽  
Yoosook Lee ◽  
William R Conner ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Weather Conditions ◽  
The United States ◽  
Future Research ◽  
Drosophila Suzukii ◽  
Significant Damage ◽  
Wide Range ◽  
Multiple Invasions

Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native to East Asia, D. suzukii infestations started in the United States a decade ago, occupying a wide range of climates. To better understand invasion ecology of this pest, knowledge of past migration events, population structure, and genetic diversity is needed. To improve on previous studies examining genetic structure of D. suzukii, we sequenced whole genomes of 237 individual flies collected across the continental U.S., as well as several representative sites in Europe, Brazil, and Asia, to identify hundreds of thousands of genetic markers for analysis. We analyzed these markers to detect population structure, to reconstruct migration events, and to estimate genetic diversity and differentiation within and among the continents. We observed strong population structure between West and East Coast populations in the U.S., but no evidence of any population structure North to South, suggesting there is no broad-scale adaptations occurring in response to the large differences in regional weather conditions. We also find evidence of repeated migration events from Asia into North America have provided increased levels of genetic diversity, which does not appear to be the case for Brazil or Europe. This large genomic dataset will spur future research into genomic adaptations underlying D. suzukii pest activity and development of novel control methods for this agricultural pest.

scholarly journals Contrasting Patterns of Genetic Diversity and Population Structure of Armillaria mellea sensu stricto in the Eastern and Western United States

2010 ◽  
Vol 100 (7) ◽  
pp. 708-718 ◽  
Author(s):  
Kendra Baumgartner ◽  
Renaud Travadon ◽  
Johann Bruhn ◽  
Sarah E. Bergemann
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Los Angeles ◽  
The United States ◽  
Sensu Stricto ◽  
Western United States ◽  
Eastern United States ◽  
Armillaria Mellea ◽  
Genetic Pools

Armillaria mellea infects hundreds of plant species in natural and managed ecosystems throughout the Northern hemisphere. Previously reported nuclear genetic divergence between eastern and western U.S. isolates is consistent with the disjunct range of A. mellea in North America, which is restricted mainly to both coasts of the United States. We investigated patterns of population structure and genetic diversity of the eastern (northern and southern Appalachians, Ozarks, and western Great Lakes) and western (Berkeley, Los Angeles, St. Helena, and San Jose, CA) regions of the United States. In total, 156 diploid isolates were genotyped using 12 microsatellite loci. Absence of genetic differentiation within either eastern subpopulations (θST = –0.002, P = 0.5 ) or western subpopulations (θST = 0.004, P = 0.3 ) suggests that spore dispersal within each region is sufficient to prevent geographic differentiation. In contrast to the western United States, our finding of more than one genetic cluster of isolates within the eastern United States (K = 3), revealed by Bayesian assignment of multilocus genotypes in STRUCTURE and confirmed by genetic multivariate analyses, suggests that eastern subpopulations are derived from multiple founder sources. The existence of amplifiable and nonamplifiable loci and contrasting patterns of genetic diversity between the two regions demonstrate that there are two geographically isolated, divergent genetic pools of A. mellea in the United States.

Genetic diversity studies of alfalfa germplasm (Medicago sativa L. subsp. sativa) of United States origin using microsatellite analysis

2017 ◽  
Author(s):  
Shuying Yin ◽  
Yanrong Wang ◽  
Zhibiao Nan
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Polymorphic Information Content ◽  
The United States ◽  
Microsatellite Analysis ◽  
Information Index ◽  
Diversity Studies ◽  
Two Populations

This study aimed to understand the genetic diversity and population structure of alfalfa germplasm from the United States. In this study, the population structure and genetic diversity of six alfalfa cultivars of United States origin were investigated by microsatellite analysis with 40 individuals per cultivar. A total of 312 discernible alleles were amplified from the whole genome with an average of 31.2 alleles per locus. The average values of polymorphic information content and Shannon’s information index were 0.928 and 0.133, respectively, showing high levels of genetic diversity. Two populations were identified by STRUCTURE software with principal coordinate analysis and neighbour-joining clustering. Analysis of molecular variance analysis (AMOVA) revealed that the majority of genetic variation was within cultivars (96.42%) rather than between cultivars (3.58%). In conclusion, analyses of genetic diversity and population structure may be useful for the genetic analysis and utilization of genetic variation in alfalfa breeding.

scholarly journals Genetic Diversity and Population Structure of Fusicladium effusum on Pecan in the United States

Plant Disease ◽  
2014 ◽  
Vol 98 (7) ◽  
pp. 916-923 ◽  
Author(s):  
C. H. Bock ◽  
B. W. Wood ◽  
K. L. Stevenson ◽  
R. S. Arias
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Gene Diversity ◽  
The United States ◽  
Individual Tree ◽  
Pecan Scab ◽  
The Individual ◽  
Average Gene

Fusicladium effusum causes pecan scab, which is the most destructive disease of pecan orchards in the United States. Conidia of the pathogen are spread by rain splash and wind. The fungus is pathogenically diverse; yet there is no information on its genetic diversity or population genetics. Universally primed polymerase chain reaction (UP-PCR) was used to investigate the genetic diversity and population structure on a hierarchical sample of 194 isolates collected from 11 orchard locations from Florida to Texas, consisting of three to four isolates from each of five to six trees at each location. Genetic variation was high throughout the region, with all but nine of the multilocus haplotypes being unique. Nei's average gene diversity ranged from 0.083 for a population from Mississippi to 0.160 for a population from Kansas. An analysis of molecular variance of the hierarchically sampled populations found that the majority of the genetic variability (82.6%) occurred at the scale of the individual tree and only relatively small amounts among populations in trees from an orchard (5.0%) or within groups (i.e., orchard location populations) (12.5%). The results suggest little population differentiation in F. effusum in the southeastern United States, although φpt values of genetic distance for pairwise comparisons indicated some populations could be differentiated from others. There was evidence of linkage disequilibrium in certain populations, and the common occurrence of asexual reproduction in F. effusum could lead to measurable linkage disequilibrium under certain circumstances. However, the degree of genetic diversity and the scale over which diversity is distributed is evidence that F. effusum undergoes regular recombination despite no known sexual stage.

scholarly journals Genetic diversity and population structure of Alternaria species from tomato and potato in North Carolina and Wisconsin

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tika B. Adhikari ◽  
Norman Muzhinji ◽  
Dennis Halterman ◽  
Frank J. Louws
Keyword(s):  
Genetic Diversity ◽  
North Carolina ◽  
Population Structure ◽  
Genetic Variation ◽  
Dna Sequences ◽  
Random Mating ◽  
Population Expansion ◽  
The United States ◽  
Population Subdivision ◽  
The Impact

AbstractEarly blight (EB) caused by Alternaria linariae or Alternaria solani and leaf blight (LB) caused by A. alternata are economically important diseases of tomato and potato. Little is known about the genetic diversity and population structure of these pathogens in the United States. A total of 214 isolates of A. alternata (n = 61), A. linariae (n = 96), and A. solani (n = 57) were collected from tomato and potato in North Carolina and Wisconsin and grouped into populations based on geographic locations and tomato varieties. We exploited 220 single nucleotide polymorphisms derived from DNA sequences of 10 microsatellite loci to analyse the population genetic structure between species and between populations within species and infer the mode of reproduction. High genetic variation and genotypic diversity were observed in all the populations analysed. The null hypothesis of the clonality test based on the index of association $$\left( {\overline{r}_{d} } \right)$$ r ¯ d was rejected, and equal frequencies of mating types under random mating were detected in some studied populations of Alternaria spp., suggesting that recombination can play an important role in the evolution of these pathogens. Most genetic differences were found between species, and the results showed three distinct genetic clusters corresponding to the three Alternaria spp. We found no evidence for clustering of geographic location populations or tomato variety populations. Analyses of molecular variance revealed high (> 85%) genetic variation within individuals in a population, confirming a lack of population subdivision within species. Alternaria linariae populations harboured more multilocus genotypes (MLGs) than A. alternata and A. solani populations and shared the same MLG between populations within a species, which was suggestive of gene flow and population expansion. Although both A. linariae and A. solani can cause EB on tomatoes and potatoes, these two species are genetically differentiated. Our results provide new insights into the evolution and structure of Alternaria spp. and can lead to new directions in optimizing management strategies to mitigate the impact of these pathogens on tomato and potato production in North Carolina and Wisconsin.

scholarly journals Genetic Diversity and Structure of the Apiosporina morbosa Populations on Prunus spp.

2005 ◽  
Vol 95 (8) ◽  
pp. 859-866 ◽  
Author(s):  
Jinxiu Zhang ◽  
W. G. Dilantha Fernando ◽  
William. R. Remphrey
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Gene Flow ◽  
Host Species ◽  
Population Differentiation ◽  
The United States ◽  
Flow Rates ◽  
Geographic Locations ◽  
Genetic Diversity And Structure ◽  
Geographic Populations

Populations of Apiosporina morbosa collected from 15 geographic locations in Canada and the United States and three host species, Prunus virginiana, P. pensylvanica, and P. padus, were evaluated using the sequence-related amplified polymorphism (SRAP) technique to determine their genetic diversity and population differentiation. Extensive diversity was detected in the A. morbosa populations, including 134 isolates from Canada and the United States, regardless of the origin of the population. The number of polymorphic loci varied from 6.9 to 82.8% in the geographic populations, and from 41.4 to 79.3% in the populations from four host genotypes based on 58 polymorphic fragments. In all, 44 to 100% of isolates in the geographic populations and 43.6 to 76.2% in populations from four host genotypes represented unique genotypes. Values of heterozygosity (H) varied from 2.8 to 28.3% in the geographic populations and 10.2 to 26.1% in the populations from four host genotypes. In general, the A. morbosa populations sampled from wild chokecherry showed a higher genetic diversity than those populations collected from other host species, whereas the populations isolated from cultivated chokecherry, P. virginiana ‘Shubert Select’, showed a reduction of genetic diversity compared with populations from wild P. virginiana. Significant population differentiation was found among both the geographic populations (P < 0.05) and populations from different host genotypes (P < 0.02). In the geographic populations, most of populations from cultivated and wild P. virginiana were closely clustered, and no population differentiation was detected except for the populations from Morris, Morden, and Winnipeg, Manitoba, Canada. Furthermore, the populations from P. virginiana in the same geographic locations had higher genetic identity and closer genetic distance to each other compared with those from different locations. Four populations from P. virginiana, P. pensylvanica, and P. padus, were significantly differentiated from each other (P < 0.02), except there was no differentiation between the Shubert Select and wild chokecherry populations (>P> = 0.334). Indirect estimation of gene flow showed that significant restricted gene flow existed between populations from different regions and host species. Gene flow rates (Nm) varied from <1 to 12.5, with higher gene flow rates among population pairs from the same host species (P = 1.000). The analysis of molecular variance revealed that a major genetic variance source came from the genetic variation among isolates within populations regardless of the origin and host genotype of the population. Although some locations had a limited number of isolates, the results of this study clearly showed that the genetic diversity and population differentiation of A. morbosa were closely associated with host genotypes and geographic locations, but mostly with the former.

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