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.

scholarly journals Use of Amplified Fragment Length Polymorphisms for Typing Corynebacterium diphtheriae

2000 ◽  
Vol 38 (10) ◽  
pp. 3843-3845 ◽  
Author(s):  
Aruni De Zoysa ◽  
Androulla Efstratiou
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Corynebacterium Diphtheriae ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms

Amplified fragment length polymorphism (AFLP) was investigated for the differentiation of Corynebacterium diphtheriaeisolates. Analysis using Taxotron revealed 10 distinct AFLP profiles among 57 isolates. Strains with ribotype patterns D1, D4, and D12 could not be distinguished; however, the technique discriminated isolates of ribotype patterns D3, D6, and D7 further. AFLP was rapid, fairly inexpensive, and reproducible and could be used as an alternative to ribotyping.

Amplified fragment length polymorphism analysis reveals three distinct taxa in Carex digitalis sect. Careyanae (Cyperaceae)

2006 ◽  
Vol 84 (9) ◽  
pp. 1444-1452 ◽  
Author(s):  
Bruce A. Ford ◽  
Robert F.C. Naczi ◽  
Habibollah Ghazvini ◽  
Mahmood Iranpour
Keyword(s):  
North Carolina ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Polymorphism Analysis ◽  
Neighbor Joining ◽  
Aflp Data ◽  
Additional Species ◽  
Pair Group

Unweighted pair-group (UPGMA) cluster, neighbor-joining (NJ), and parsimony analyses using amplified fragment length polymorphism (AFLP) data revealed the presence of three taxa within Carex digitalis Willd. (var. digitalis , var. floridana , var. macropoda ). Even when taxa occur syntopically, genetic distinctiveness is maintained (Hertford Co., North Carolina populations of var. macropoda and var. floridana). Clades or clusters corresponding with vars. digitalis and floridana were well supported in all analyses. However, the var. macropoda clade was poorly supported on most trees. Despite our inability to fully resolve taxon relationships, AFLP data substantiate ongoing morphological and phytogeographic studies that show the presence of additional species diversity within sect. Careyanae and the eastern North American Carex flora.

scholarly journals Using Amplified Fragment-length Polymorphisms (AFLPs) to Identify Peach Cultivars

2003 ◽  
Vol 128 (5) ◽  
pp. 672-677 ◽  
Author(s):  
Maria José Aranzana ◽  
Joaquim Carbó ◽  
Pere Arús
Keyword(s):  
Cluster Analysis ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Somatic Mutations ◽  
Prunus Persica ◽  
Fragment Length Polymorphism ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Wide Range ◽  
Plant Characteristics

A sample of 210 cultivars of Prunus persica (L.) Batsch, with a wide range of fruit and plant characteristics, was studied for variability using nine polymorphic amplified fragment length polymorphism (AFLP) primer combinations. Forty-seven AFLPs allowed identification of 196 (93%) different genotypes, 187 of which could be distinguished with three primer combinations. Eleven cultivars with the same AFLP phenotype corresponded to known somatic mutations (sports), but from the four sports of the `Springcrest' group, two (`Maycrest' and `Queencrest') differed at three AFLPs from the others (`Starcrest' and `Early Maycrest'). Cluster analysis allowed differentiation of most cultivars with nonmelting fruit flesh, generally used for canning, from the melting-flesh peach and nectarine cultivars used for fresh consumption.

Phylogenetic relationships among Secale species revealed by amplified fragment length polymorphisms

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 792-801 ◽  
Author(s):  
T Chikmawati ◽  
B Skovmand ◽  
J P Gustafson
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Polymorphism Analysis ◽  
Aflp Data ◽  
Length Polymorphisms

Amplified fragment length polymorphism (AFLP) data were utilized to analyze the phylogenetic relationships among 29 accessions representing 14 of the most commonly recognized ranked species or subspecies in the genus Secale. We observed 789 AFLP markers of 1130 fragments utilizing 18 P-/M- and E-/M- primer combinations. All polymorphic fragments were used to construct phenetic and phylogenetic trees. The resulting phenogram and cladogram had similar tree topologies. Cluster analysis showed that Secale sylvestre was the most distantly related to all other ryes. Annual forms were grouped together, and the perennial forms appeared more closely related to each other. This suggested that life cycle could have played an important role in determining the relationships among Secale species. Secale sylvestre was considered to be the most ancient species, whereas Secale cereale was the most recently evolved species. Amplified fragment length polymorphism analysis clearly separated all Secale species into only 3 major species groups, within the genus Secale: S. sylvestre, Secale montanum (syn. Secale strictum) for perennial forms, and S. cereale for annual forms. This study demonstrated that the AFLP approach is a useful tool for discriminating species differences, and also gave a much better resolution in discerning genetic relationships among Secale species as compared with previous studies using other approaches.Key words: AFLP, Secale, phylogenetic relationship.

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.

Genetic Variability in the Potato Pathogen Colletotrichum coccodes as Determined by Amplified Fragment Length Polymorphism and Vegetative Compatibility Group Analyses

2006 ◽  
Vol 96 (10) ◽  
pp. 1097-1107 ◽  
Author(s):  
Larry J. Heilmann ◽  
Nadav Nitzan ◽  
Dennis A. Johnson ◽  
Julie S. Pasche ◽  
Curt Doetkott ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Vegetative Compatibility ◽  
Colletotrichum Coccodes ◽  
Aflp Analysis ◽  
Aflp Data ◽  
Bootstrap Analysis ◽  
Nit Mutants

Amplified fragment length polymorphism (AFLP) using three primer sets was used to characterize 211 Colletotrichum coccodes isolates from North America, 112 of which were assigned to six vegetative compatibility groups (VCGs) using nitrate nonutilizing (nit) mutants. These isolates clustered into five corresponding groups by unweighted pairgroup method with arithmetic means-based cluster analysis of AFLP banding patterns. Isolates of C. coccodes belonging to NA-VCG1 and NA-VCG3 were closely related, as were isolates belonging to NA-VCG2 and NA-VCG5. Based on bootstrap analysis of AFLP data, the two isolates originally assigned to NA-VCG4 clustered with isolates belonging to NA-VCG2 and NA-VCG5. C. coccodes isolates that clustered with two isolates belonging to NA-VCG6 were the most diverged from other groups, including seven isolates collected from hosts other than potato. As opposed to the bootstrap analysis, a quadratic discriminant analysis (QDA) of AFLP data correctly categorized the two isolates of NA-VCG4. Furthermore, in isolates where VCG determinations had been made, this model correctly classified isolates of all VCGs. QDA classifications were identical to those made by the bootstrap analysis, with the exception of VCG4. Overall, classifications made by the QDA model were strongly correlated (r = 0.970, P < 0.001) to the VCGs assigned by traditional methods. All 99 C. coccodes isolates evaluated only by AFLP also were subjected to QDA, leading to the assignment of a presumptive VCG for each isolate. No isolates of VCG4 or VCG6 were identified by QDA within this population. Symptoms of black dot developed in plants inoculated with isolates collected from both potato and non-potato hosts. However, total yield was not significantly reduced by infection with non-potato isolates. The lack of any additional groups identified by AFLP analysis may be an indicator of a limited level of genetic variation among North American C. coccodes isolates. AFLP is a much more efficient technique for subspecific characterization in C. coccodes than VCG analysis utilizing nit mutants and will provide an effective means by which the population biology of this pathogen can be further investigated worldwide.

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.

scholarly journals Genetic Characterization of Cercospora sorghi from Cultivated and Wild Sorghum and Its Relationship to Other Cercospora Fungi

2004 ◽  
Vol 94 (7) ◽  
pp. 743-750 ◽  
Author(s):  
P. Okori ◽  
P. R. Rubaihayo ◽  
A. Ekwamu ◽  
J. Fahleson ◽  
C. Dixelius
Keyword(s):  
Population Structure ◽  
Genetic Variability ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Small Subunit ◽  
Gray Leaf Spot ◽  
Wild Sorghum ◽  
Aflp Data ◽  
Using Data

Genetic variability and population structure of Cercospora sorghi from wild and cultivated sorghum were investigated to gain insight into their potential impact on epidemics of gray leaf spot of sorghum in Africa. Population structure was examined using data derived from amplified fragment length polymorphism (AFLP) of C. sorghi by Nei's test for population differentiation, GST, and analysis of molecular variation (AMOVA). Two ecological populations of C. sorghi in Uganda were devoid of population structure (GST = 0.03, фFST = 0.01, P = 0.291). AMOVA revealed that genetic variability was due mainly to variations within (99%) rather than between (0.35%) populations, and Nei's genetic distance between the two populations was 0.014. Phenetic analysis based on AFLP data and polymerase chain reaction-restriction fragment length polymorphism analyses of the internal transcribed spacer regions of rDNA and mitochondrial small subunit rDNA separated Cercospora cereal pathogens from dicot pathogens but did not differentiate among C. sorghi isolates from wild and cultivated sorghum. Our results indicate that Ugandan populations of C. sorghi compose one epidemiological unit and suggest that wild sorghum, while not affecting genetic variability of the pathogen population, provides an alternative host for generating additional inoculum.

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