Genetic structuring of the stream lily Helmholtzia glaberrima (Philydraceae) within Toolona Creek, south-eastern Queensland

2004 ◽  
Vol 52 (2) ◽  
pp. 201 ◽  
Author(s):  
Peter J. Prentis ◽  
A. Vesey ◽  
N. M. Meyers ◽  
P. B. Mather
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
Fragment Length Polymorphism ◽  
Metapopulation Model ◽  
Genetic Structuring ◽  
Mantel Tests ◽  
Riparian Species ◽  
Site Diversity ◽  
Non Equilibrium

The distribution of genetic variation among five isolated sites of the riparian species Helmholtzia glaberrima (J.D.Hook) was examined in Toloona Creek (28�13′S, 153�07′E) by using dominant amplified fragment length polymorphism (AFLP) markers. From the 137 fragments assessed, analysis of molecular variance (AMOVA) showed that most genetic variability occurred within sites (68%), although high (32%) variation also occurred among sites. Highly significant pairwise θ estimates among all sampled sites suggest that gene flow is restricted in H. glaberrima. Levels of within-site diversity were intermediate and significantly different across the sampled sites. Significant levels of linkage disequilibrium were detected at all sites except TC3. Differences in linkage disequilibrium and genetic diversity among the sites suggest that sites may have been founded by different numbers of colonists. Mantel tests found no correlation between geographic and genetic distance and significant levels of linkage disequilibrium were detected at the total site level, supporting a non-equilibrium model of population structure. The observed pattern of non-equilibrium population structure and genetic variation in H. glaberrima are best explained by a classical metapopulation model.

Population structure in two geographically sympatric and congeneric ectoparasites (Cimex adjunctus and Cimex lectularius) in the North American Great Lakes region

2017 ◽  
Vol 95 (12) ◽  
pp. 901-907 ◽  
Author(s):  
Benoit Talbot ◽  
Maarten J. Vonhof ◽  
Hugh G. Broders ◽  
M. Brock Fenton ◽  
Nusha Keyghobadi
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Geographic Area ◽  
Abundant Species ◽  
Cimex Lectularius ◽  
Genetic Structuring ◽  
The North ◽  
Genetic Clusters

Subdivided populations can be described by different models of population structure that reflect population organization, dynamics, and connectivity. We used genetic data to investigate population structure in two geographically sympatric, congeneric species of generalist ectoparasites of warm-blooded animals. We characterized the spatial genetic structure of the eastern bat bug (Cimex adjunctus Barber, 1939), an understudied and fairly abundant species, using microsatellite markers at a spatial scale representing contemporary dispersal of the species. We found seven genetic clusters, global [Formula: see text] of 0.2, 33% of genetic variation among sites, and nonsignificant isolation-by-distance. We compared these results with the common bed bug (Cimex lectularius L., 1758), a closely related but conversely well-known species, in the same geographic area. We found stronger genetic structuring in C. lectularius than in C. adjunctus, with 11 genetic clusters, [Formula: see text] of 0.7, 57% of genetic variation among sites, and significant but weak isolation-by-distance (R2 = 0.09). These results suggest that while both species can be described as having classic metapopulation structure, C. adjunctus leans more towards a patchy population and C. lectularius leans more towards a nonequilibrium metapopulation. The difference in population structure between these species may be attributable to differences in movement potential and extinction–colonization dynamics.

SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium

2013 ◽  
Vol 126 (5) ◽  
pp. 1285-1303 ◽  
Author(s):  
Cristina Esteras ◽  
Gelsomina Formisano ◽  
Cristina Roig ◽  
Aurora Díaz ◽  
José Blanca ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
Snp Genotyping

scholarly journals Genetic variation, population structure and linkage disequilibrium in peach commercial varieties

BMC Genetics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 69 ◽  
Author(s):  
Maria Aranzana ◽  
El-Kadri Abbassi ◽  
Werner Howad ◽  
Pere Arús
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Linkage Disequilibrium

scholarly journals Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers

Hereditas ◽  
2016 ◽  
Vol 153 (1) ◽  
Author(s):  
Yu Zhang ◽  
Haidong Yan ◽  
Xiaomei Jiang ◽  
Xiaoli Wang ◽  
Linkai Huang ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
Ssr Markers

scholarly journals Genetic variation and population structure in China summer maize germplasm

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guoping Shu ◽  
Gangqiang Cao ◽  
Niannian Li ◽  
Aifang Wang ◽  
Fang Wei ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
Germplasm Collection ◽  
Genotyping By Sequencing ◽  
Inbred Lines ◽  
Summer Maize ◽  
Heterotic Groups ◽  
Breeding Germplasm

AbstractMaize (Zea mays L.) germplasm in China Summer maize ecological region (CSM) or central corn-belt of China is diverse but has not been systematically characterized at molecular level. In this study, genetic variation, genome diversity, linkage disequilibrium patterns, population structure, and characteristics of different heterotic groups were studied using 525,141 SNPs obtained by Genotyping-By-Sequencing (GBS) for 490 inbred lines collected from researchers at CSM region. The SNP density is lower near centromere, but higher near telomere region of maize chromosome, the degree of linkage disequilibrium (r2) vary at different chromosome regions. Majority of the inbred lines (66.05%) show pairwise relative kinship near zero, indicating a large genetic diversity in the CSM breeding germplasm. Using 4849 tagSNPs derived from 3618 haplotype blocks, the 490 inbred lines were delineated into 3 supergroups, 6 groups, and 10 subgroups using ADMIXTURE software. A procedure of assigning inbred lines into heterotic groups using genomic data and tag-SNPs was developed and validated. Genome differentiation among different subgroups measured by Fst, and the genetic diversity within each subgroup measured by GD are both large. The share of heterotic groups that have significant North American germplasm contribution: P, SS, IDT, and X, accounts about 54% of the CSM breeding germplasm collection and has increased significantly in the last two decades. Two predominant types of heterotic pattern in CSM region are: M-Reid group × TSPT group, and X subgroup × Local subgroups.

AFLP analyses of genetic variation of Eupatorium adenophorum (Asteraceae) populations in China

2009 ◽  
Vol 89 (1) ◽  
pp. 119-126 ◽  
Author(s):  
W. K. Huang ◽  
F. H. Wan ◽  
J. Y. Guo ◽  
B. D. Gao ◽  
B. Y. Xie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Shannon Index ◽  
Eupatorium Adenophorum ◽  
Data Set

The Eupatorium adenophorum is one of the most widespread invasive alien species in China. In the present study, the genetic variation and population structure of this species were analyzed using amplified fragment length polymorphism (AFLP) markers. Nine primer pairs were selected for the analysis and 685 bands were produced, among which 474 bands were polymorphic (PPB = 69.2%). Diversity levels within populations were relatively high (mean expected heterozygosity = 0.188, mean Shannon index = 0.296). Regression analysis showed a significant positive relationship between Shannon genetic diversity and altitude (R2 = 0.31). However, there was a negative correlation between Shannon genetic diversity and latitude (R2 = 0.16), as well as between Shannon genetic diversity and longitude (R2 = 0.45). Cluster analysis grouped the majority of the weed populations into three main clusters that corresponded with the geographic regions. At the regional level, the AMOVA indicated that about 70% of the variations in the data set were from genotypic variations within populations, 13.3% of the variations were due to regional differences, and the remaining 16.6% were due to differences among populations within the provincial regions. The results imply that most individuals tested in the present study should have been produced through seeds, and the process of colonization resulted in progressive loss of genetic diversity from the southwest to the northeast of China. Key words: Amplified fragment length polymorphism, invasive species, Eupatorium adenophorum, diversity, genetic variation, population structure

Genetic variation, population structure, and linkage disequilibrium in European elite germplasm of perennial ryegrass

Plant Science ◽  
2011 ◽  
Vol 181 (4) ◽  
pp. 412-420 ◽  
Author(s):  
Gintaras Brazauskas ◽  
Ingo Lenk ◽  
Morten Greve Pedersen ◽  
Bruno Studer ◽  
Thomas Lübberstedt
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
Perennial Ryegrass ◽  
Elite Germplasm

scholarly journals Investigating the Genetic Structure of Phytophthora capsici Populations

2011 ◽  
Vol 101 (9) ◽  
pp. 1061-1073 ◽  
Author(s):  
L. M. Quesada-Ocampo ◽  
L. L. Granke ◽  
M. R. Mercier ◽  
J. Olsen ◽  
M. K. Hausbeck
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Association Studies ◽  
Phytophthora Capsici ◽  
Geographic Origin ◽  
The United States ◽  
Diagnostic Tools ◽  
Bayesian Clustering ◽  
Genetic Structuring

Phytophthora capsici Leonian is a destructive soilborne pathogen that infects economically important solanaceous, cucurbitaceous, fabaceous, and other crops in the United States and worldwide. The objective of this study was to investigate the genetic structure of 255 P. capsici isolates assigned to predefined host, geographical, mefenoxam-sensitivity, and mating-type categories. Isolates from six continents, 21 countries, 19 U.S. states, and 26 host species were genotyped for four mitochondrial and six nuclear loci. Bayesian clustering revealed some population structure by host, geographic origin, and mefenoxam sensitivity, with some clusters occurring more or less frequently in particular categories. Bayesian clustering, split networks, and statistical parsimony genealogies also detected the presence of non-P. capsici individuals in our sample corresponding to P. tropicalis (n = 9) and isolates of a distinct cluster closely related to P. capsici and P. tropicalis (n = 10). Our findings of genetic structuring in P. capsici populations highlight the importance of including isolates from all detected clusters that represent the genetic variation in P. capsici for development of diagnostic tools, fungicides, and host resistance. The population structure detected will also impact the design and interpretation of association studies in P. capsici. This study provides an initial map of global population structure of P. capsici but continued genotyping of isolates will be necessary to expand our knowledge of genetic variation in this important plant pathogen.

scholarly journals Assessment of the Genetic Diversity and Population Structure of Lotus Cultivars Grown in China by Amplified Fragment Length Polymorphism

2011 ◽  
Vol 136 (5) ◽  
pp. 339-349 ◽  
Author(s):  
Jie Fu ◽  
Qiaoyan Xiang ◽  
Xianbao Zeng ◽  
Mei Yang ◽  
Ying Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Group I ◽  
Population Structure Analysis ◽  
Morphological Criteria

To assess the genetic diversity among lotus (Nelumbo) accessions and evaluate the correlation between genetic variation and morphological classification, we sampled 138 accessions: two of N. lutea, 112 of N. nucifera, 17 of hybrids between N. nucifera and N. lutea, and seven Japanese cultivars. The 11 selected combinations of amplified fragment length polymorphism (AFLP) primers produced 138 polymorphic loci, and the percentage of polymorphism was 28.7%. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram clustered all the accessions into two groups: Group I comprised N. lutea and its hybrids with N. nucifera; Group II included N. nucifera and its hybrids with N. lutea and Japanese cultivars. Population structure analysis identified four main clusters: N. lutea clustered mainly in C1, whereas N. nucifera clustered in C2, C3, and C4, which was consistent with the UPGMA and principal coordinate analysis results. The Japanese cultivars were related more closely to N. nucifera (genetic similarity coefficient = 0.74) than to N. lutea (0.46); hence, the Japanese cultivars can be classified as N. nucifera. Moreover, rhizome lotuses formed a separate subclade, whereas seed lotuses were interspersed among flower lotuses, which demonstrated that rhizome lotuses were distinct from flower and seed lotuses. Plant size, flower color, and other morphological criteria used commonly to classify lotuses were correlated with genetic variation to a certain extent but not sufficiently for accurate classification. It appears that it is necessary to use both DNA markers and morphological characteristics to classify lotus species and cultivars.

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