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.

scholarly journals Amplified Fragment Length Polymorphism Analysis Provides Strategies for Improvement of Bitter Gourd (Momordica charantia L.)

HortScience ◽  
2008 ◽  
Vol 43 (1) ◽  
pp. 127-133 ◽  
Author(s):  
Ambika B. Gaikwad ◽  
Tusar Kanti Behera ◽  
Anand K. Singh ◽  
Devanshi Chandel ◽  
Jawahir L. Karihaloo ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Momordica Charantia ◽  
Bitter Gourd ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Diversity Assessment

Monoecious bitter gourd (Momordica charantia L. var. minima and maxima Williams & Ng), a cucurbit of major economic importance, is widely cultivated in India, China, Africa, and South America. Although the morphology (i.e., growth habit and fruit shape, size, color, and surface texture) of Indian bitter gourd is diverse and gynoecious sex forms exist, a comprehensive diversity assessment of ecotypes has not been performed. Therefore, the genetic relatedness of 38 Indian cultigens (commercial varieties and cultivated landraces originating from different agroecological zones) was determined by amplified fragment length polymorphism (AFLP) analysis. Six primer combinations yielded a total of 519 bands of which 404 (77.8%) were polymorphic among the cultigens examined. Unweighted pair group cluster analyses were performed using Jaccard's genetic similarities to define genetic relationships among cultigens. Genetic similarities among cultigens ranged between 0.44 and 0.88, indicating that the bitter gourd cultigens examined were genetically diverse. Moreover, putative AFLP loci defined genetic relationships that allowed for partitioning of cultigens into two distinct groups [Group 1 and Group II (node 1); bootstrap = 100%] after cluster analysis. With rare exception, cultigens were grouped with respect to geographical region, in which cultigens within a group and subgroups possessed high degrees of genetic similarity. The relatively high marker indices (6.2 to 19.4), polymorphic information content of the markers used (0.20 to 0.25), and multiplex ratios (28.9 to 77.4) collectively indicate that the AFLP markers used are discriminatory in bitter gourd and that the analysis of the broad-based cultigens described provides valuable baseline information for advancing initial breeding strategies for this crop species.

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 Amplified Fragment Length Polymorphism Analysis for Studying Genetic Relationships among Mangifera Species in Thailand

2000 ◽  
Vol 125 (2) ◽  
pp. 160-164 ◽  
Author(s):  
Wichan Eiadthong ◽  
Keizo Yonemori ◽  
Shinya Kanzaki ◽  
Akira Sugiura ◽  
Naoki Utsunomiya ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Interspecific Variation ◽  
Polymorphism Analysis ◽  
Important Species ◽  
Cashew Nut ◽  
Grouping Method

The phylogenetic relationships among 14 Mangifera L. species including three economically important species, i.e., common mango (M. indica L.), horse mango (M. foetida Lour.) and kwini (M. odorata Griff.), were analyzed by comparing 217 amplified fragment length polymorphism (AFLP) markers. The unweighted pair grouping method using arithmetic averages (UPGMA) and neighbor-joining (NJ) method were used and two outgroup taxa, cashew nut (Anacardium occidentale L.) and gandaria (Bouea macrophylla Griff.), were added to both analyses. The common mango was closely related to banana mango (M. sylvatica Roxb.), M. laurina Bl., and M. oblongifolia Hook.f. Intraspecific variation among seven cultivars of common mango was much smaller than interspecific variation and these cultivars were classified into one M. indica group using both methods. Mangifera macrocarpa Bl., M. foetida, and M. odorata were also related to M. indica in both UPGMA and NJ trees, although these three species are classified into a different subgenus (subgenus Limus) from the subgenus Mangifera to which M. indica belongs. Also, in both UPGMA and NJ trees, M. gedebe Miq. and M. griffithii Hk.f. were placed in distant positions among the Mangifera species tested, indicating these two species are related distantly to M. indica. The AFLP technique was confirmed to be useful for phylogenetic analysis.

scholarly journals Fluorescent Amplified Fragment Length Polymorphism Analysis of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis Isolates

2004 ◽  
Vol 70 (2) ◽  
pp. 1068-1080 ◽  
Author(s):  
Karen K. Hill ◽  
Lawrence O. Ticknor ◽  
Richard T. Okinaka ◽  
Michelle Asay ◽  
Heather Blair ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Bacillus Cereus ◽  
Bacillus Anthracis ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Phenotypic Traits ◽  
Polymorphism Analysis ◽  
Aflp Data

ABSTRACT DNA from over 300 Bacillus thuringiensis, Bacillus cereus, and Bacillus anthracis isolates was analyzed by fluorescent amplified fragment length polymorphism (AFLP). B. thuringiensis and B. cereus isolates were from diverse sources and locations, including soil, clinical isolates and food products causing diarrheal and emetic outbreaks, and type strains from the American Type Culture Collection, and over 200 B. thuringiensis isolates representing 36 serovars or subspecies were from the U.S. Department of Agriculture collection. Twenty-four diverse B. anthracis isolates were also included. Phylogenetic analysis of AFLP data revealed extensive diversity within B. thuringiensis and B. cereus compared to the monomorphic nature of B. anthracis. All of the B. anthracis strains were more closely related to each other than to any other Bacillus isolate, while B. cereus and B. thuringiensis strains populated the entire tree. Ten distinct branches were defined, with many branches containing both B. cereus and B. thuringiensis isolates. A single branch contained all the B. anthracis isolates plus an unusual B. thuringiensis isolate that is pathogenic in mice. In contrast, B. thuringiensis subsp. kurstaki (ATCC 33679) and other isolates used to prepare insecticides mapped distal to the B. anthracis isolates. The interspersion of B. cereus and B. thuringiensis isolates within the phylogenetic tree suggests that phenotypic traits used to distinguish between these two species do not reflect the genomic content of the different isolates and that horizontal gene transfer plays an important role in establishing the phenotype of each of these microbes. B. thuringiensis isolates of a particular subspecies tended to cluster together.

scholarly journals Amplified Fragment Length Polymorphism Analysis ofCampylobacter jejuni Strains Isolated from Chickens and from Patients with Gastroenteritis or Guillain-Barr� or Miller Fisher Syndrome

2000 ◽  
Vol 66 (9) ◽  
pp. 3917-3923 ◽  
Author(s):  
Birgitta Duim ◽  
C. Wim Ang ◽  
Alex van Belkum ◽  
Alan Rigter ◽  
Nan W. J. van Leeuwen ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Miller Fisher Syndrome ◽  
Group Method ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Fisher Syndrome

ABSTRACT The high-resolution genotyping method of amplified fragment length polymorphism (AFLP) analysis was used to study the genetic relationships between Campylobacter jejuni strains infecting chickens (n = 54) and those causing gastroenteritis in humans (n = 53). In addition,C. jejuni strains associated with the development of Guillain-Barr� syndrome (GBS) (n = 14) and Miller Fisher syndrome (MFS) (n = 4), two related acute paralytic syndromes in human, were included. Strains were isolated between 1989 and 1998 in The Netherlands. The AFLP banding patterns were analyzed with correlation-based and band-based similarity coefficients and UPGMA (unweighted pair group method using average linkages) cluster analysis. All C. jejuni strains showed highly heterogeneous fingerprints, and no fingerprints exclusive for chicken strains or for human strains were obtained. All strains were separated in two distinct genetic groups. In group A the percentage of human strains was significantly higher and may be an indication that genotypes of this group are more frequently associated with human diseases. We conclude that C. jejuni from chickens cannot be distinguished from human strains and that GBS or MFS related strains do not belong to a distinct genetic group.

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