The population of Sclerotinia sclerotiorum in Brazil is structured by mycelial compatibility groups

Plant Disease ◽  
2021 ◽  
Author(s):  
Rhaphael Alves Silva ◽  
Camila Geovana Ferro ◽  
Miller da Silva Lehner ◽  
Trazilbo José Paula Júnior ◽  
Eduardo S. G. Mizubuti
Keyword(s):  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
Genetic Structure ◽  
Sclerotinia Sclerotiorum ◽  
Total Population ◽  
Random Mating ◽  
Genetic Groups ◽  
Close Relationship ◽  
Mycelial Compatibility ◽  
Variable Population

The genetic structure of the population of Sclerotinia sclerotiorum was analyzed using 238 individuals collected from different hosts. Individuals were characterized for microsatellite genotypes and mycelial compatibility groups (MCGs). A total of 22 MCGs and 64 multilocus lineages (MLLs) were identified. There was a close relationship between the MCGs and MLLs, but there was no association between MLLs and hosts or regions. At least 39 MCGs are present in Brazil and 68.5% of the isolates were assigned to either MCG 1 or 2. Eight new MCGs were found. Seven genetic groups were identified and associated with MCGs. Most genetic variation (70.0%) was due to differences among MCGs. High values of estimates of linkage disequilibrium among loci were more frequent in the total population (all MCGs). In contrast, there was evidence of random mating in subpopulations defined by MCGs 1 and 2. Additionally, there was evidence of outcrossing in the population of S. sclerotiorum in Brazil. The population was structured by MCGs, lineages originated from asexual reproduction or selfing prevail and are widely distributed in space, are persistent in time and affect many hosts, but there is evidence of some degree of outcrossing which may lead to a more genetically variable population in the future.

scholarly journals Genetic Diversity and Recombination in the Plant Pathogen Sclerotinia sclerotiorum Detected in Sri Lanka

Pathogens ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 306
Author(s):  
Thirega Mahalingam ◽  
Weidong Chen ◽  
Chandima Shashikala Rajapakse ◽  
Kandangamuwa Pathirannahalage Somachandra ◽  
Renuka Nilmini Attanayake
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Sri Lanka ◽  
Sclerotinia Sclerotiorum ◽  
Genetic Recombination ◽  
Multiple Infections ◽  
Tropical Country ◽  
High Genetic Diversity ◽  
Principal Coordinates ◽  
Mycelial Compatibility

Sclerotinia sclerotiorum is an important fungal pathogen on many economically important crops including cabbage worldwide. Even though population structure and genetic diversity of S. sclerotiorum is well studied in temperate climatic conditions, only a few studies have been conducted in tropical countries. It is also not clear whether the populations are clonal or recombining in the tropics. In filling this information gap, 47 isolates of S. sclerotiorum were collected from commercial cabbage (Brassica oleracea L.) fields in Nuwara Eliya district of Sri Lanka, where the disease has been previously reported. All the isolates were subjected to genetic diversity study using mycelial compatibility grouping and microsatellite markers. Fourteen mycelial compatibility groups (MCGs) and 23 multilocus haplotypes (MLHs) were recorded. Mean expected heterozygosity of the population was 0.56. MLHs were weakly correlated with MCGs. Population genetic structure analysis and principal coordinates identified three genetic clusters. Genetic recombination was inferred within each genetic cluster when isolates were subjected to clone correction. There was evidence of multiple infections on single plant as detected by the presence of more than one MCG on each cabbage plant. However, multiple infections did not increase the disease severity in detached leaf assay. We found high genetic diversity and recombination of S. sclerotiorum population in a tropical country, Sri Lanka. Importance of detecting genetic structure when inferring recombination was also highlighted.

scholarly journals Mycelial Compatibility Groups and Microsatellite Markers Reveal Genetic Diversity Within and Among Populations of Sunflower Sclerotinia Sclerotiorum in China

2014 ◽  
Vol 3 (1) ◽  
pp. 21-31
Author(s):  
Yujie Wang ◽  
Yaguang Hou ◽  
Haoyu Bo ◽  
Hongyou Zhou ◽  
Lan Jing ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Microsatellite Markers ◽  
Sclerotinia Sclerotiorum ◽  
Inner Mongolia ◽  
Test Results ◽  
Marker Data ◽  
Microsatellite Haplotype ◽  
Mycelial Compatibility ◽  
Geographic Populations ◽  
Geographic Regions

The genetic variability and differentiation among 101 sunflower Sclerotinia sclerotiorum isolates collected from four different geographic regions of China were analyzed using mycelial compatibility groupings (MCGs) and microsatellite markers. Twenty three MCGs were identified among all tested isolates. The majority of isolates collected from the same region were grouped in to the same MCGs, indicating less genetic variation of S. sclerotiorum within the same region. But there still have exceptions for some isolates. Also microsatellite marker data revealed that all tested isolates from four geographic populations could be divided into three distinct clusters, isolates from Inner Mongolia and Ninxia regions formed cluster I, isolates from Heilongjiang and Xinjiang formed separate clusters II and III . The percentage of variance within and among different geographic populations was 84.54% and 15.46% respectively and both variances were significantly different from each other (p0.01). Meanwhile, association between the microsatellite haplotype and MCGs was observed but not so significant; majority isolates from the same MCG showed the same haplotype, but certain samples showed different haplotypes, although they belonged to the same MCG. Based on the virulence test results, we also found that MCGs not only represent the genetic variation of tested isolates, but also reflect their pathogenic ability to a certain extent.

scholarly journals Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Babu Valliyodan ◽  
Anne V. Brown ◽  
Juexin Wang ◽  
Gunvant Patil ◽  
Yang Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Glycine Max ◽  
Linkage Disequilibrium ◽  
Genetic Structure ◽  
Glycine Soja ◽  
Geographic Location ◽  
High Similarity ◽  
Genetic Diversity And Structure ◽  
Selection Of

AbstractWe report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.

scholarly journals Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kelly B. Klingler ◽  
Joshua P. Jahner ◽  
Thomas L. Parchman ◽  
Chris Ray ◽  
Mary M. Peacock
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Sierra Nevada ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Thermal Sensitivity ◽  
Genomic Variation ◽  
Genome Wide ◽  
A Genome ◽  
American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

scholarly journals Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 457-467 ◽  
Author(s):  
Z W Luo ◽  
S H Tao ◽  
Z-B Zeng
Keyword(s):  
Linkage Disequilibrium ◽  
Allele Frequency ◽  
Random Mating ◽  
Natural Populations ◽  
Polymorphic Marker ◽  
Marker Locus ◽  
Model Parameters ◽  
Phenotypic Variance ◽  
Wide Range ◽  
Trait Locus

Abstract Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

scholarly journals Pleiotropy and multilocus polymorphisms.

Genetics ◽  
1992 ◽  
Vol 130 (1) ◽  
pp. 223-227
Author(s):  
A Gimelfarb
Keyword(s):  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
Stabilizing Selection ◽  
Additive Genetic Variation ◽  
Very High

Abstract It is demonstrated that systems of two pleiotropically related characters controlled by additive diallelic loci can maintain under Gaussian stabilizing selection a stable polymorphism in more than two loci. It is also shown that such systems may have multiple stable polymorphic equilibria. Stabilizing selection generates negative linkage disequilibrium, as a result of which the equilibrium phenotypic variances are quite low, even though the level of allelic polymorphisms can be very high. Consequently, large amounts of additive genetic variation can be hidden in populations at equilibrium under stabilizing selection on pleiotropically related characters.

scholarly journals Deep genetic structure at a small spatial scale in the endangered land snail Xerocrassa montserratensis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Cristina Català ◽  
Vicenç Bros ◽  
Xavier Castelltort ◽  
Xavier Santos ◽  
Marta Pascual
Keyword(s):  
Genetic Structure ◽  
Land Snail ◽  
Snail Species ◽  
Small Spatial Scale ◽  
Geographic Ranges ◽  
Genetic Groups ◽  
Species Of Conservation Concern ◽  
Conservation Actions ◽  
Conservation Concern ◽  
Single Locality

AbstractSpecies with small geographic ranges do not tend to have a high genetic structure, but some land snail species seem to be an exception. Xerocrassa montserratensis, an endangered land snail endemic to Catalonia (northeastern Iberian Peninsula), is an excellent model to study the processes affecting the phylogeography of specialized species of conservation concern. This species is restricted to xerophilous stony slopes and occurs within a small and fragmented area of ca. 500 km2. We sequenced the COI barcode region of 152 individuals from eight sites covering the entire range of the species. We found four genetic groups mostly coincident with their geographic distribution: a central ancestral group containing shared haplotypes among five localities and three groups restricted to a single locality each. Two of these derived groups were geographically and genetically isolated, while the third and most differentiated group was not geographically isolated. Geomorphologic and paleoclimatic processes during the Pleistocene can explain the divergence found between populations of this low dispersal species with historical fragmentation and secondary contacts. Nonetheless, recent passive large dispersal through streams was also detected in the central group. Overall, our study uncovered four evolutionary units, partially matching morphologically described subspecies, which should be considered in future conservation actions.

Genetic Relationships of Cory's Shearwater: Parentage, Mating Assortment, and Geographic Differentiation Revealed by DNA Fingerprinting

The Auk ◽  
2000 ◽  
Vol 117 (3) ◽  
pp. 651-662 ◽  
Author(s):  
Corinne Rabouam ◽  
Vincent Bretagnolle ◽  
Yves Bigot ◽  
Georges Periquet
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Dna Fingerprinting ◽  
Genetic Relatedness ◽  
Isolation By Distance ◽  
Genetic Relationships ◽  
Cory’S Shearwater ◽  
Genetic Structure Of Populations ◽  
The Social ◽  
Calonectris Diomedea

Abstract We used DNA fingerprinting to assess genetic structure of populations in Cory's Shearwater (Calonectris diomedea). We analyzed mates and parent-offspring relationships, as well as the amount and distribution of genetic variation within and among populations, from the level of subcolony to subspecies. We found no evidence of extrapair fertilization, confirming that the genetic breeding system matches the social system that has been observed in the species. Mates were closely related, and the level of genetic relatedness within populations was within the range usually found in inbred populations. In contrast to previous studies based on allozymes and mtDNA polymorphism, DNA fingerprinting using microsatellites revealed consistent levels of genetic differentiation among populations. However, analyzing the two subspecies separately revealed that the pattern of genetic variation among populations did not support the model of isolation by distance. Natal dispersal, as well as historic and/or demographic events, probably contributed to shape the genetic structure of populations in the species.

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