Genetic Diversity and Structure in RegionalCercospora beticolaPopulations fromBeta vulgarissubsp.vulgarisSuggest Two Clusters of Separate Origin

Cercospora leaf spot, caused by Cercospora beticola, is a highly destructive disease of Beta vulgaris subsp. vulgaris worldwide. C. beticola populations are usually characterized by high genetic diversity, but little is known of the relationships among populations from different production regions around the world. This information would be informative of population origin and potential pathways for pathogen movement. For the current study, the genetic diversity, differentiation, and relationships among 948 C. beticola isolates in 28 populations across eight geographic regions were investigated using 12 microsatellite markers. Genotypic diversity, as measured by Simpson’s complement index, ranged from 0.18 to 1.00, while pairwise index of differentiation values ranged from 0.02 to 0.42, with the greatest differentiation detected between two New York populations. In these populations, evidence for recent expansion was detected. Assessment of population structure identified two major clusters: the first associated with New York, and the second with Canada, Chile, Eurasia, Hawaii, Michigan, North Dakota, and one population from New York. Inferences of gene flow among these regions suggested that the source for one cluster likely is Eurasia, whereas the source for the other cluster is not known. These results suggest a shared origin of C. beticola populations across regions, except for part of New York, where population divergence has occurred. These findings support the hypothesis that dispersal of C. beticola occurs over long distances.

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Genetic Dissimilarity in Conyza sumatrensis Revealed by Simple Sequence Repeat (SSR) Markers

Planta Daninha ◽

10.1590/s0100-83582020380100018 ◽

2020 ◽

Vol 38 ◽

Author(s):

T. SCHNEIDER ◽

M.A. RIZZARDI ◽

S.P. BRAMMER ◽

S.M. SCHEFFER-BASSO ◽

A.L. NUNES

Keyword(s):

Genetic Diversity ◽

Management Strategies ◽

Rapid Evolution ◽

Jaccard Coefficient ◽

Mechanisms Of Resistance ◽

High Genetic Diversity ◽

Resistance To Herbicides ◽

Geographic Regions ◽

Genetic Dissimilarity ◽

Simple Sequence

ABSTRACT: In view of the rapid evolution of Conyza sumatrensis populations resistant to glyphosate, it is necessary to understand the genetic diversity aimed to improve strategies for managing this weed. We investigated the genetic dissimilarity among 15 biotypes of C. sumatrensis from different geographic regions using microsatellite loci. The biotypes, were cultivated in a greenhouse to obtain vegetal material for DNA extraction. Nineteen microsatellite markers (SSR), were developed for C. sumatrensis biotypes. The genetic dissimilarity was estimated by the Jaccard coefficient (JC) and the biotypes grouped by the UPGMA method. The results demonstrated a high dissimilarity (JC = 7.14 to 82.62) of the analyzed material, with the biotypes forming five groups, being one group formed just by the susceptible biotype and in the others grouped by biotypes from distinct locations in the same group The high genetic diversity of C. sumatrensis indicates that the biotypes may show different responses to different management strategies, and that the mechanisms of resistance to herbicides and characteristics of evolution of populations due to adaptability may be some of the factors involved in the genetic variability of the species.

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Genetic Diversity and Structure of Latvian Tilia cordata Populations

Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences. ◽

10.2478/prolas-2021-0039 ◽

2021 ◽

Vol 75 (4) ◽

pp. 261-267

Author(s):

Dainis Edgars Ruņģis ◽

Baiba Krivmane

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Vegetative Reproduction ◽

Growth Conditions ◽

Climatic Conditions ◽

Tilia Cordata ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

Broadleaf Tree ◽

Broadleaf Species

Abstract Changing climatic conditions are transforming the ecological and silvicultural roles of broadleaf tree species in northern Europe. Small-leaved lime (Tilia cordata Mill.) is distributed throughout most of Europe, and is a common broadleaf species in Latvia. This species can tolerate a broad range of environmental and ecological conditions, including temperature, water availability, and soil types. The aim of this study was to assess the genetic diversity and differentiation of Latvian T. cordata populations using nuclear microsatellite markers developed for Tilia platyphyllos. After testing of 15 microsatellite markers, Latvian T. cordata samples were genotyped at 14 micro-satellite loci. Latvian T. cordata populations had high genetic diversity, and were not overly isolated from each other, with moderate gene flow between populations. No highly differentiated populations were identified. Vegetative reproduction was identified in most analysed populations, and almost one-third of analysed individuals are of clonal origin. T. cordata has high timber production potential under the current climatic and growth conditions in Latvia, and therefore this species has potential for use in forestry, as well as playing a significant role in maintaining biodiversity and other ecosystem services.

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Genetic Diversity and Population Divergence of a Rare, Endemic Grass (Elymus breviaristatus) in the Southeastern Qinghai-Tibetan Plateau

Sustainability ◽

10.3390/su11205863 ◽

2019 ◽

Vol 11 (20) ◽

pp. 5863 ◽

Cited By ~ 2

Author(s):

Qingqing Yu ◽

Qian Liu ◽

Yi Xiong ◽

Yanli Xiong ◽

Zhixiao Dong ◽

...

Keyword(s):

Genetic Diversity ◽

Tibetan Plateau ◽

Isolation By Distance ◽

Genetic Distances ◽

Conservation Strategy ◽

Conservation Strategies ◽

Grass Species ◽

Population Divergence ◽

High Genetic Diversity ◽

Widespread Species

Elymus breviaristatus is a grass species only distributed in the southeast of Qinghai-Tibetan Plateau (QTP), which has suffered from serious habitat fragmentation. Therefore, understanding patterns of genetic diversity within and among natural E. breviaristatus populations could provide insight for future conservation strategies. In this study, sequence-related amplified polymorphism markers were employed to investigate the genetic diversity and hierarchical structure of seven E. breviaristatus populations from QTP, China. Multiple measures of genetic diversity indicated that there is low to moderate genetic variation within E. breviaristatus populations, consistent with its presumed mating system. In spite of its rarity, E. breviaristatus presented high genetic diversity that was equivalent to or even higher than that of widespread species. Bayesian clustering approaches, along with clustering analysis and principal coordinate analysis partitioned the studied populations of E. breviaristatus into five genetic clusters. Differentiation coefficients (Fst, GST, etc.) and AMOVA analysis revealed considerable genetic divergence among different populations. BARRIER analyses indicated that there were two potential barriers to gene flow among the E. breviaristatus populations. Despite these patterns of differentiation, genetic distances between populations were independent of geographic distances (r = 0.2197, p = 0.2534), indicating little isolation by distance. Moreover, despite detecting a common outlier by two methods, bioclimatic factors (altitude, annual mean temperature, and annual mean precipitation) were not related to diversity parameters, indicating little evidence for isolation caused by the environment. These patterns of diversity within and between populations are used to propose a conservation strategy for E. breviaristatus.

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First Insight into a Nationwide Genotypic Diversity ofMycobacterium tuberculosisamong Previously Treated Pulmonary Tuberculosis Cases in Benin, West Africa

Canadian Journal of Infectious Diseases and Medical Microbiology ◽

10.1155/2017/3276240 ◽

2017 ◽

Vol 2017 ◽

pp. 1-6 ◽

Cited By ~ 5

Author(s):

Dissou Affolabi ◽

N’Dira Sanoussi ◽

Sergio Codo ◽

Fréderic Sogbo ◽

Prudence Wachinou ◽

...

Keyword(s):

Genetic Diversity ◽

Genotypic Diversity ◽

Molecular Study ◽

Drug Susceptibility ◽

Drug Susceptibility Testing ◽

Resistance Rate ◽

High Genetic Diversity ◽

Pulmonary Tb ◽

Previously Treated ◽

Insight Into

Background. Molecular studies on tuberculosis (TB) are rare in low-resource countries like Benin, where data on molecular study on previously treated TB cases is unavailable.Materials and Methods. From January to December 2014, all smear- and culture-positive previously treated pulmonary TB patients from all TB clinics were systematically recruited. Drug susceptibility testing and spoligotyping were performed on all isolates.Results. Of the 100 patients recruited, 71 (71.0%) were relapse cases and 24 (24.0%) were failure cases, while 5 (5.0%) were default cases. Resistance rate to any first-line drug was 40.0%, while 12.0% of strains were multidrug-resistant (MDR) and no strain was extensively drug-resistant (XDR). A total of 40 distinct spoligotypes were found to be corresponding to a genotypic diversity of 40.0%. ST61 was the most predominant spoligotype with prevalence of 33.0%. In all, 31 single spoligotypes and nine clusters were observed with 2 to 33 strains per cluster giving a clustering rate of 69.0%. Euro-American (Lineage 4) was the most prevalent lineage (74.0%) and Lineage 2 was associated with resistance to streptomycin.Conclusion. This first insight into genetic diversity of previously treated pulmonary TB patients in Benin showed a relatively high genetic diversity ofMycobacterium tuberculosis.

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Using Random Amplified Polymorphic DNA to Assess Genetic Diversity and Structure of NaturalCalophyllum brasiliense(Clusiaceae) Populations in Riparian Forests

International Journal of Forestry Research ◽

10.1155/2014/305286 ◽

2014 ◽

Vol 2014 ◽

pp. 1-8

Author(s):

Evânia Galvão Mendonça ◽

Anderson Marcos de Souza ◽

Fábio de Almeida Vieira ◽

Regiane Abjaud Estopa ◽

Cristiane Aparecida Fioravante Reis ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Random Amplified Polymorphic Dna ◽

Natural Populations ◽

Rio Grande ◽

Shannon Index ◽

High Genetic Diversity ◽

Family Structures ◽

Genetic Diversity And Structure ◽

Kinship Coefficients

The objective of this study was to assess the genetic variability in two natural populations ofCalophyllum brasilienselocated along two different rivers in the state of Minas Gerais, Brazil, using RAPD molecular markers. Eighty-two polymorphic fragments were amplified using 27 primers. The values obtained for Shannon index (I) were 0.513 and 0.530 for the populations located on the margins of the Rio Grande and Rio das Mortes, respectively, demonstrating the high genetic diversity in the studied populations. Nei’s genetic diversity (He) was 0.341 for the Rio Grande population and 0.357 for the Rio das Mortes population. These results were not significantly different between populations and suggest a large proportion of heterozygote individuals within both populations. AMOVA showed that 70.42% of the genetic variability is found within populations and 29.58% is found among populations (ФST=0.2958). The analysis of kinship coefficients detected the existence of family structures in both populations. Average kinship coefficients between neighboring individuals were 0.053 (P<0.001) in Rio das Mortes and 0.040 (P<0.001) in Rio Grande. This could be due to restricted pollen and seed dispersal and the history of anthropogenic disturbance in the area. These factors are likely to contribute to the relatedness observed among these genotypes.

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Genotypic Diversity and Resistance to Azoxystrobin of Cercospora beticola on Processing Table Beet in New York

Plant Disease ◽

10.1094/pdis-09-15-1014-re ◽

2016 ◽

Vol 100 (7) ◽

pp. 1466-1473 ◽

Cited By ~ 22

Author(s):

Niloofar Vaghefi ◽

Frank S. Hay ◽

Julie R. Kikkert ◽

Sarah J. Pethybridge

Keyword(s):

New York ◽

Spore Germination ◽

Microsatellite Loci ◽

Point Mutations ◽

Allelic Diversity ◽

Genotypic Diversity ◽

Cercospora Beticola ◽

Mating Types ◽

Cercospora Leaf Spot ◽

Quinone Outside Inhibitor

Cercospora leaf spot (CLS), caused by Cercospora beticola, is one of the major diseases affecting productivity and profitability of beet production worldwide. Fungicides are critical for the control of this disease and one of the most commonly used products is the quinone outside inhibitor (QOI) azoxystrobin. In total, 150 C. beticola isolates were collected from two commercial processing table beet fields in Batavia, NY in 2014. The mating types of the entire population were determined, and genetic diversity of a subset of samples (n = 48) was assessed using five microsatellite loci. Sensitivity to azoxystrobin was tested using a spore germination assay. The cytochrome b gene was sequenced to check for the presence of point mutations known to confer QOI resistance in fungi. High allelic diversity (He = 0.50) and genotypic diversity (D* = 0.96), gametic equilibrium of the microsatellite loci, and equal ratios of mating types were suggestive of a mixed mode of reproduction for C. beticola. Resistance to azoxystrobin was prevalent because 41% of the isolates had values for effective concentrations reducing spore germination by 50% (EC50) > 0.2 μg/ml. The G143A mutation, known to cause QOI resistance in C. beticola, was found in isolates with EC50 values between 0.207 and 19.397 μg/ml. A single isolate with an EC50 of 0.272 μg/ml carried the F129L mutation, known to be associated with low levels of QOI resistance in fungi. This is the first report of the F129L mutation in C. beticola. The implications of these findings for the epidemiology and control of CLS in table beet fields in New York are discussed.

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Temporal Genetic Differentiation of Cercospora beticola Populations in New York Table Beet Fields

Plant Disease ◽

10.1094/pdis-01-18-0175-re ◽

2018 ◽

Vol 102 (11) ◽

pp. 2074-2082 ◽

Cited By ~ 10

Author(s):

Noel L. Knight ◽

Niloofar Vaghefi ◽

Zachariah R. Hansen ◽

Julie R. Kikkert ◽

Sarah J. Pethybridge

Keyword(s):

New York ◽

Genetic Differentiation ◽

Temporal Stability ◽

Cropping System ◽

Genotypic Diversity ◽

Cercospora Beticola ◽

Multilocus Genotype ◽

Cercospora Leaf Spot ◽

Corrected Data

Annual epidemics of Cercospora leaf spot (CLS), caused by the fungus Cercospora beticola, can result in substantial defoliation in table beet fields in New York. High allelic and genotypic diversity have been described within C. beticola populations; however, information on the temporal stability of populations is lacking. C. beticola isolates were obtained from symptomatic leaves in three table beet fields in successive years. Two of the fields were organic mixed-cropping farms and the third was managed conventionally in a broad-acre cropping system. C. beticola isolates (n = 304) were genotyped using 12 microsatellite markers. Genotypic diversity (Simpson’s complement index = 0.178 to 0.990), allele frequencies, and indices of differentiation between years varied. Pairwise index of differentiation values ranged from 0.02 to 0.25 for clone-corrected data, and indicated significant genetic differentiation at Farm 2. No multilocus genotype was shared between years. The shift in multilocus genotypes between years questions the role of clonally reproducing primary inoculum. Collectively, these results suggest that a dominant inoculum source for initiating annual CLS epidemics is external to the field of interest. These findings have implications for CLS disease management in conventional and organic table beet production.

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Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci

PeerJ ◽

10.7717/peerj.10327 ◽

2020 ◽

Vol 8 ◽

pp. e10327

Author(s):

Ricardo M. Landínez-García ◽

Juan Carlos Narváez ◽

Edna J. Márquez

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Freshwater Fish ◽

Microsatellite Loci ◽

Natural Populations ◽

Genetic Stock ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

Genetic Stocks ◽

Species Specific

Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.

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Genetic Diversity and Dispersal of Aspergillus fumigatus in Arctic Soils

Genes ◽

10.3390/genes13010019 ◽

2021 ◽

Vol 13 (1) ◽

pp. 19

Author(s):

Gregory A. Korfanty ◽

Mykaelah Dixon ◽

Haoran Jia ◽

Heather Yoell ◽

Jianping Xu

Keyword(s):

Genetic Diversity ◽

Aspergillus Fumigatus ◽

Opportunistic Pathogen ◽

Ecological Niches ◽

Ecological Distribution ◽

Resistant Genotype ◽

Arctic Regions ◽

Arctic Soils ◽

The World ◽

Geographic Regions

Aspergillus fumigatus is a saprophytic mold and an opportunistic pathogen with a broad geographic and ecological distribution. A. fumigatus is the most common etiological agent of aspergillosis, affecting over 8,000,000 individuals worldwide. Due to the rising number of infections and increasing reports of resistance to antifungal therapy, there is an urgent need to understand A. fumigatus populations from local to global levels. However, many geographic locations and ecological niches remain understudied, including soil environments from arctic regions. In this study, we isolated 32 and 52 A. fumigatus strains from soils in Iceland and the Northwest Territories of Canada (NWT), respectively. These isolates were genotyped at nine microsatellite loci and the genotypes were compared with each other and with those in other parts of the world. Though significantly differentiated from each other, our analyses revealed that A. fumigatus populations from Iceland and NWT contained evidence for both clonal and sexual reproductions, and shared many alleles with each other and with those collected from across Europe, Asia, and the Americas. Interestingly, we found one triazole-resistant strain containing the TR34 /L98H mutation in the cyp51A gene from NWT. This strain is closely related to a triazole-resistant genotype broadly distributed in India. Together, our results suggest that the northern soil populations of A. fumigatus are significantly influenced by those from other geographic regions.

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Genetic Diversity and Differentiation inPhoma betaePopulations on Table Beet in New York and Washington States

Plant Disease ◽

10.1094/pdis-09-18-1675-re ◽

2019 ◽

Vol 103 (7) ◽

pp. 1487-1497 ◽

Cited By ~ 4

Author(s):

Lori B. Koenick ◽

Niloofar Vaghefi ◽

Noel L. Knight ◽

Lindsey J. du Toit ◽

Sarah J. Pethybridge

Keyword(s):

Genetic Diversity ◽

New York ◽

Mating Type ◽

Gene Diversity ◽

Management Strategies ◽

Allelic Diversity ◽

Genotypic Diversity ◽

Reproduction Mode ◽

Inoculum Source ◽

Seed Crops

Phoma betae is an important seedborne pathogen of table beet worldwide that is capable of causing foliar, root, and damping-off diseases. Ten microsatellite and mating type markers were developed to investigate the genetics of P. betae populations in table beet root crops in New York and in table beet seed crops in Washington, from where table beet seed is predominantly sourced. The markers were used to characterize 175 isolates comprising five P. betae populations (two from New York and three from Washington), and they were highly polymorphic with an allelic range of 4 to 33 and an average of 11.7 alleles per locus. All populations had high genotypic diversity (Simpson’s complement index = 0.857 to 0.924) and moderate allelic diversity (Nei’s unbiased gene diversity = 0.582 to 0.653). Greater differentiation observed between populations from the two states compared with populations within the same state suggested that an external inoculum source, such as windblown ascospores, may be homogenizing the populations. However, most genetic diversity (87%) was among individual isolates within populations (pairwise index of population differentiation = 0.127; P = 0.001), suggesting that local within-field inoculum source(s), such as infested field debris or infected weeds, may also be important in initiating disease outbreaks. Standardized index of association, proportion of compatible pairs of loci, and mating type ratio calculations showed evidence for a mixed reproduction mode in all populations. These findings could be useful in designing more effective management strategies for diseases caused by P. betae in table beet production.

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