scholarly journals Phylogenetic relationships and population structure ofRalstonia solanacearumisolated from diverse origins in Taiwan

2014 ◽  
Vol 63 (6) ◽  
pp. 1395-1403 ◽  
Author(s):  
C.-H. Lin ◽  
K.-C. Tsai ◽  
P. Prior ◽  
J.-F. Wang
Keyword(s):  
Population Structure ◽  
Phylogenetic Relationships

scholarly journals Population structure and phylogenetic relationships in Brassica rapa L. subspecies by using isozyme markers

2020 ◽  
Author(s):  
R. H. Sammour ◽  
M. A. Karam ◽  
Y. S. Morsi ◽  
R. M. Ali
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Brassica Rapa ◽  
Phylogenetic Relationships ◽  
Fixation Index ◽  
Distribution Area ◽  
Enzyme Analysis ◽  
Breeding Programs ◽  
Expected Heterozygosity ◽  
Wide Range

Abstract The present study aimed to assess population structure and phylogenetic relationships of nine subspecies of Brassica rapa L. represented with thirty-five accessions cover a wide range of species distribution area using isozyme analysis in order to select more diverse accessions as supplementary resources that can be utilized for improvement of B. napus. Enzyme analysis resulted in detecting 14 putative polymorphic loci with 27 alleles. Mean allele frequency 0.04 (rare alleles) was observed in Cat4A and Cat4B in sub species Oleifera accession CR 2204/79 and in subspecies trilocularis accessions CR 2215/88 and CR 2244/88. The highest genetic diversity measures were observed in subspecies dichotoma, accession CR 1585/96 (the highest average of observed (H0) and expected heterozygosity (He), and number of alleles per locus (Ae)). These observations make this accession valuable genetic resource to be included in breeding programs for the improvement of oilseed B. napus. The average fixation index (F) is significantly higher than zero for the analysis accessions indicating a significant deficiency of heteozygosity. The divergence among subspecies indicated very great genetic differentiation (FST = 0.8972) which means that about 90% of genetic diversity is distributed among subspecies, while 10% of the diversity is distributed within subspecies. This coincides with low value of gene flow (Nm = 0.0287). B. rapa ssp. oleifera (turnip rape) and B. rapa ssp. trilocularis (sarson) were grouped under one cluster which coincides with the morphological classification.

scholarly journals Population Structure and Phylogenetic Relationships in a Diverse Panel of Brassica rapa L.

2017 ◽  
Vol 8 ◽  
Author(s):  
Kevin A. Bird ◽  
Hong An ◽  
Elodie Gazave ◽  
Michael A. Gore ◽  
J. Chris Pires ◽  
...  
Keyword(s):  
Population Structure ◽  
Brassica Rapa ◽  
Phylogenetic Relationships

scholarly journals Global phylogenetic relationships, population structure and gene flow estimation of Trialeurodes vaporariorum (Greenhouse whitefly)

2017 ◽  
Vol 108 (1) ◽  
pp. 5-13 ◽  
Author(s):  
J.M. Wainaina ◽  
P. De Barro ◽  
L. Kubatko ◽  
M. A. Kehoe ◽  
J. Harvey ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
The Netherlands ◽  
Phylogenetic Relationships ◽  
Virus Transmission ◽  
Sequence Divergence ◽  
Trialeurodes Vaporariorum ◽  
Greenhouse Whitefly ◽  
Population Structure Analysis ◽  
Clade 1

AbstractTrialeurodes vaporariorum (Westwood, 1856) (Greenhouse whitefly) is an agricultural pest of global importance. It is associated with damage to plants during feeding and subsequent virus transmission. Yet, global phylogenetic relationships, population structure, and estimation of the rates of gene flow within this whitefly species remain largely unexplored. In this study, we obtained and filtered 227 GenBank records of mitochondrial cytochrome c oxidase I (mtCOI) sequences of T. vaporariorum, across various global locations to obtain a final set of 217 GenBank records. We further amplified and sequenced a ~750 bp fragment of mtCOI from an additional 31 samples collected from Kenya in 2014. Based on a total of 248 mtCOI sequences, we identified 16 haplotypes, with extensive overlap across all countries. Population structure analysis did not suggest population differentiation. Phylogenetic analysis indicated the 2014 Kenyan collection of samples clustered with a single sequence from the Netherlands to form a well-supported clade (denoted clade 1a) nested within the total set of sequences (denoted clade 1). Pairwise distances between sequences show greater sequence divergence between clades than within clades. In addition, analysis using migrate-n gave evidence for recent gene flow between the two groups. Overall, we find that T. vaporariorum forms a single large group, with evidence of further diversification consisting primarily of Kenyan sequences and one sequence from the Netherlands forming a well-supported clade.

Population structure and phylogenetic relationships of Ceutorhynchus neglectus (Coleoptera: Curculionidae)

2005 ◽  
Vol 137 (6) ◽  
pp. 672-684 ◽  
Author(s):  
R. D. Laffin ◽  
L. M. Dosdall ◽  
F.A.H. Sperling
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
North America ◽  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Isolation By Distance ◽  
Coi Gene ◽  
Restricted Gene Flow ◽  
Species Variation ◽  
Internal Transcribed Spacer Region

AbstractCeutorhynchus neglectus Blatchley is a weevil that is native to, and widely distributed in, North America. It has life-history characteristics similar to its alien invasive congener, Ceutorhynchus obstrictus (Marsham), the cabbage seedpod weevil. Our study was undertaken to compare the population structure of C. neglectus in North America to that of C. obstrictus, which, in contrast, was introduced only recently to North America and might be expected to have a simpler population structure. We also compared the population structure of C. neglectus to that of Pissodes strobi (Peck), which is known to possess high levels of intraspecific variation and is also a Nearctic weevil. We sequenced a 790-bp fragment of mtDNA (cytochrome oxidase I (COI) gene) and a 117-bp fragment of nuclear DNA (internal transcribed spacer region 1 (ITS1)). Nested clade analysis inferred contiguous range expansion and restricted gene flow with isolation by distance. Analysis of molecular variance also supported restricted gene flow between geographically distant populations. However, within-species variation in C. neglectus was lower than that for other weevil species including C. obstrictus. We also examined DNA divergences and phylogenetic relationships among 10 species of Ceutorhynchus using parsimony analysis of a 2.3-kb fragment of mtDNA (COI–COII) and a 541-bp fragment of nuclear DNA (elongation factor 1α).

Population structure and phylogenetic relationships of a new shallow-water Antarctic phyllodocid annelid

2018 ◽  
Vol 47 (6) ◽  
pp. 714-726 ◽  
Author(s):  
Carlos Leiva ◽  
Ana Riesgo ◽  
Conxita Avila ◽  
Greg W. Rouse ◽  
Sergi Taboada
Keyword(s):  
Population Structure ◽  
Shallow Water ◽  
Phylogenetic Relationships

scholarly journals Genetic Diversity and Population Structure Analysis of Citrus Germplasm with Single Nucleotide Polymorphism Markers

2018 ◽  
Vol 143 (6) ◽  
pp. 399-408
Author(s):  
Yuan Yu ◽  
Chunxian Chen ◽  
Ming Huang ◽  
Qibin Yu ◽  
Dongliang Du ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Phylogenetic Relationships ◽  
Snp Array ◽  
Poncirus Trifoliata ◽  
Citrus Paradisi ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Population Structure Analysis

Citrus (Citrus sp.) germplasm collections are a valuable resource for citrus genetic breeding studies, and further utilization of the resource requires knowledge of their genotypic and phylogenetic relationships. Diverse citrus accessions, including citron (Citrus medica), mandarin (Citrus reticulata), pummelo (Citrus maxima), papeda (Papeda sp.), trifoliate orange (Poncirus trifoliata), kumquat (Fortunella sp.), and related species, have been housed at the Florida Citrus Arboretum, Winter Haven, FL, but the accessions in the collection have not been genotyped. In this study, a collection of 80 citrus accessions were genotyped using 1536 sweet orange–derived single nucleotide polymorphism (SNP) markers, to determine their SNP fingerprints and to assess genetic diversity, population structure, and phylogenetic relationships, and thereby to test the efficiency of using the single genotype-derived SNP chip with relatively low cost for these analyses. Phylogenetic relationships among the 80 accessions were determined by multivariate analysis. A model-based clustering program detected five basic groups and revealed that C. maxima introgressions varied among mandarin cultivars and segregated in mandarin F1 progeny. In addition, reciprocal differences in C. maxima contributions were observed among citranges (Citrus sinensis × P. trifoliata vs. P. trifoliata × C. sinensis) and may be caused by the influence of cytoplasmic DNA and its effect on selection of cultivars. Inferred admixture structures of many secondary citrus species and important cultivars were confirmed or revealed, including ‘Bergamot’ sour orange (Citrus aurantium), ‘Kinkoji’ (C. reticulata × Citrus paradisi), ‘Hyuganatsu’ orange (Citrus tamurana), and palestine sweet lime (Citrus aurantifolia). The relatively inexpensive SNP array used in this study generated informative genotyping data and led to good consensus and correlations with previously published observations based on whole genome sequencing (WGS) data. The genotyping data and the phylogenetic results may facilitate further exploitation of interesting genotypes in the collection and additional understanding of phylogenetic relationships in citrus.

Sign in / Sign up

Export Citation Format

Share Document