Genetic diversity of Echinacea species based upon amplified fragment length polymorphism markers

Genome ◽  
2004 ◽  
Vol 47 (1) ◽  
pp. 102-111 ◽  
Author(s):  
D -H Kim ◽  
D Heber ◽  
D W Still
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Fragment Length ◽  
Echinacea Purpurea ◽  
Morphological Characters ◽  
Pairwise Distance ◽  
Neighbor Joining ◽  
Aflp Data ◽  
Phenetic Relationships ◽  
Length Polymorphisms

The taxonomy of Echinacea is based on morphological characters and has varied depending on the monographer. The genus consists of either nine species and four varieties or four species and eight varieties. We have used amplified fragment length polymorphisms (AFLP) to assess genetic diversity and phenetic relationships among nine species and three varieties of Echinacea (sensu McGregor). A total of 1086 fragments, of which approximately 90% were polymorphic among Echinacea taxa, were generated from six primer combinations. Nei and Li's genetic distance coefficient and the neighbor-joining algorithm were employed to construct a phenetic tree. Genetic distance results indicate that all Echinacea species are closely related, and the average pairwise distance between populations was approximately three times the intrapopulation distances. The topology of the neighbor-joining tree strongly supports two major clades, one containing Echinacea purpurea, Echinacea sanguinea, and Echinacea simulata and the other containing the remainder of the Echinacea taxa (sensu McGregor). The species composition within the clades differs between our AFLP data and the morphometric treatment offered by Binns and colleagues. We also discuss the suitability of AFLP in determining phylogenetic relationships.Key words: Echinacea, AFLP, genetic distance, phylogeny.

scholarly journals Measuring the Genetic Diversity of Xanthomonas axonopodis pv. manihotis Within Different Fields in Colombia

2000 ◽  
Vol 90 (7) ◽  
pp. 683-690 ◽  
Author(s):  
S. Restrepo ◽  
C. M. Vélez ◽  
V. Verdier
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Dna Polymorphism ◽  
Fragment Length Polymorphism ◽  
Close Association ◽  
Aflp Data ◽  
Cassava Bacterial Blight ◽  
Xanthomonas Axonopodis ◽  
Phenetic Relationships

Cassava bacterial blight, caused by Xanthomonas axonopodis pv. manihotis, is a widespread disease that affects cassava (Manihot esculenta). We collected 238 X. axonopodis pv. manihotis strains by intensively sampling single fields in four edaphoclimatic zones (ECZs) in Colombia. DNA polymorphism of different X. axonopodis pv. manihotis populations was assessed by restriction fragment length polymorphism (RFLP) analyses, repetitive sequence-based polymerase chain reaction (rep-PCR), and amplified fragment length polymorphism (AFLP) assays. Genetic diversity, phenetic relationships among strains, and the coefficient of genetic differentiation were determined. All strains were tested for aggressiveness on the susceptible cassava cv. MCOL 1522. Strains were also tested for virulence on cassava differentials adapted to the strains' respective ECZs. Our study showed that the Colombian X. axonopodis pv. manihotis population has a high degree of genetic diversity. The hierarchical analysis of diversity showed genotypic differentiation at all levels, among ECZs, among fields within ECZs, and among strains within fields planted to several cassava genotypes. New RFLP haplotypes were detected, leading to the characterization of a new pathotype. Dendrograms from AFLP were more robust than those from RFLP data. A close association between the strains' geographical origin and DNA polymorphism was obtained using RFLP and AFLP data. We suggest that the host played a role in causing pathogen differentiation.

Systematic relationships in Lathyrus sect. Lathyrus (Fabaceae) based on amplified fragment length polymorphism (AFLP) data

2002 ◽  
Vol 80 (9) ◽  
pp. 962-969 ◽  
Author(s):  
Abdelfattah Badr ◽  
Hanaa El Shazly ◽  
Haddad El Rabey ◽  
Linda E Watson
Keyword(s):  
Phylogenetic Tree ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Neighbor Joining ◽  
Aflp Data ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Close Relationship ◽  
Systematic Relationships

Amplified fragment length polymorphisms (AFLP) were utilized to examine systematic relationships in Lathyrus L. sect. Lathyrus (Fabaceae). In addition to a parsimony-based phylogenetic tree, AFLP-based trees were constructed using Dice, Jaccard, and mean character difference coefficients to produce distance-based trees using the UPGMA and neighbor-joining methods. All trees clearly show a close relationship among accessions of the same species, confirming the monophyly of the species examined. All analyses indicate that species of the section Lathyrus are distinct from species of other sections. These findings confirm the monophyly of the section and contradict proposals to split it. They do not support the segregation of L. gorgoni in the section Gorgonia. Within the section Lathyrus, several relationships are present but are only weakly supported. The use of AFLP data to resolve systematic relationships in the genus Lathyrus is further demonstrated.Key words: Lathyrus, Fabaceae, systematics, AFLP.

Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates

Genome ◽  
2010 ◽  
Vol 53 (4) ◽  
pp. 302-310 ◽  
Author(s):  
Doris Herrmann ◽  
Bénédicte N. Poncet ◽  
Stéphanie Manel ◽  
Delphine Rioux ◽  
Ludovic Gielly ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Fragment Length ◽  
Population Genetic ◽  
Selection Criteria ◽  
Genetic Parameters ◽  
Data Set ◽  
Marker Selection ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Population Genetic Parameters

A reliable data set is a fundamental prerequisite for consistent results and conclusions in population genetic studies. However, marker scoring of genetic fingerprints such as amplified fragment length polymorphisms (AFLPs) is a highly subjective procedure, inducing inconsistencies owing to personal or laboratory-specific criteria. We applied two alternative marker selection algorithms, the newly developed script scanAFLP and the recently published AFLPScore, to a large AFLP genome scan to test how population genetic parameters and error rates were affected. These results were confronted with replicated random selections of marker subsets. We show that the newly developed marker selection criteria reduced the mismatch error rate and had a notable influence on estimates of genetic diversity and differentiation. Both effects are likely to influence biological inference. For example, genetic diversity (HS) was 29% lower while genetic differentiation (FST) was 8% higher when applying scanAFLP compared with AFLPScore. Likewise, random selections of markers resulted in substantial deviations of population genetic parameters compared with the data sets including specific selection criteria. These randomly selected marker sets showed surprisingly low variance among replicates. We conclude that stringent marker selection and phenotype calling reduces noise in the data set while retaining patterns of population genetic structure.

Evaluating the Taxonomic Status of the Globally Rare Carex roanensis and Allied Species Using Morphology and Amplified Fragment Length Polymorphisms

2008 ◽  
Vol 33 (3) ◽  
pp. 525-535 ◽  
Author(s):  
Tyler W. Smith ◽  
Marcia J. Waterway
Keyword(s):  
Fragment Length ◽  
Taxonomic Status ◽  
Principal Coordinate Analysis ◽  
Species Level ◽  
Morphological Data ◽  
Aflp Data ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
The Common ◽  
Geographic Regions

We used a combination of amplified fragment length polymorphisms (AFLP) and morphological data from 272 individuals from 59 populations to investigate the species-level taxonomy of Carex roanensis and allied species. There were two taxonomic problems in this group: identifying the appropriate taxonomic status for Carex roanensis, and clarifying the distinctions (if any) between C. virescens and C. swanii. Principal coordinate analysis of the morphological data suggested four entities corresponding to C. aestivalis, C. roanensis, C. swanii, and C. virescens, but clear discrimination was not possible. In contrast, the AFLP data showed marked discontinuities among these four species, placing even morphological intermediates into one of four groups. Analysis of molecular variance revealed significant population differentiation within each species, but only C. virescens had any detectable differentiation between geographic regions. This study confirms the species-level distinction between the common and widespread taxa C. swanii and C. virescens, as well as that of the globally rare Appalachian endemic C. roanensis.

AFLP-based molecular characterization of Brassica rapa and diversity in Canadian spring turnip rape cultivars

2008 ◽  
Vol 6 (1) ◽  
pp. 11-21 ◽  
Author(s):  
S. I. Warwick ◽  
T. James ◽  
K. C. Falk
Keyword(s):  
Genetic Diversity ◽  
Brassica Rapa ◽  
Genetic Relationships ◽  
Aflp Data ◽  
Distance Information ◽  
Breeding Lines ◽  
Cultivar Development ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Aa Genome

Information on genetic diversity and genetic relationships among taxa of Brassica rapa (n = 10, AA genome) is currently limited. Grown for oil, vegetable and fodder use in Europe and Asia, previous studies have indicated western and eastern groups corresponding to independent centres of origin. This study evaluated patterns and levels of genetic diversity in 93 accessions [includes 25 Agriculture and Agri-Food Canada (AAFC) breeding lines (BL)] of B. rapa based on 307 amplified fragment length polymorphisms (AFLP), testing subspecific separateness and the affiliation of four previously unassigned AA genome species (B. perviridis, B. purpuraria, B. ruvo and B. septiceps). AFLP data revealed three main clusters (I, II, III) corresponding to European (I), Indian (III), and a mixed Asian/European/Indian (II) purported origins of the taxa, with several subclusters observed in I and II. Mean AFLP polymorphism levels for Asian, European, Indian and AAFC-BL accessions were 79, 74, 66 and 62%, respectively. Few of the subspecies formed unique clusters and some, particularly subspecies chinensis and pekinensis, were assigned to several clusters. AFLP-based genetic distance information can be used by breeders to select diverse genotypes for cultivar development and fingerprinting of genotypes/cultivars. For example, a single AFLP primer pair was sufficient to uniquely identify all breeding lines in the AAFC B. rapa breeding programme.

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