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 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.

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 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.

scholarly journals High-Resolution Genotyping of Streptococcus pyogenesSerotype M1 Isolates by Fluorescent Amplified-Fragment Length Polymorphism Analysis

1999 ◽  
Vol 37 (6) ◽  
pp. 1948-1952 ◽  
Author(s):  
Meeta Desai ◽  
Androulla Efstratiou ◽  
Robert George ◽  
John Stanley
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Geographic Origin ◽  
Amplified Fragment Length Polymorphism ◽  
Discriminatory Power ◽  
Polymorphism Analysis ◽  
Worldwide Distribution ◽  
High Discriminatory Power ◽  
Typing Methods

We have used fluorescent amplified-fragment length polymorphism (FAFLP) analysis to subtype clinical isolates of Streptococcus pyogenes serotype M1. Established typing methods define most M1 isolates as members of a clone that has a worldwide distribution and that is strongly associated with invasive diseases. FAFLP analysis simultaneously sampled 90 to 120 loci throughout the M1 genome. Its discriminatory power, precision, and reproducibility were compared with those of other molecular typing methods. Irrespective of disease symptomatology or geographic origin, the majority of the clinical M1 isolates shared a single ribotype, pulsed-field gel electrophoresis macrorestriction profile, and emm1 gene sequence. Nonetheless, among these isolates, FAFLP analysis could differentiate 17 distinct profiles, including seven multi-isolate groups. The FAFLP profiles of M1 isolates reproducibly exhibited between 1 and more than 20 amplified fragment differences. The high discriminatory power of genotyping by FAFLP analysis revealed genetic microheterogeneity and differentiated otherwise “identical” M1 isolates as members of a clone complex.

scholarly journals Genomic Relatedness of ChlamydiaIsolates Determined by Amplified Fragment Length Polymorphism Analysis

1999 ◽  
Vol 181 (15) ◽  
pp. 4469-4475 ◽  
Author(s):  
Adam Meijer ◽  
Servaas A. Morré ◽  
Adriaan J. C. Van Den Brule ◽  
Paul H. M. Savelkoul ◽  
Jacobus M. Ossewaarde
Keyword(s):  
Cluster Analysis ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Chlamydia Psittaci ◽  
Rrna Genes ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Genomic Relatedness

ABSTRACT The genomic relatedness of 19 Chlamydia pneumoniaeisolates (17 from respiratory origin and 2 from atherosclerotic origin), 21 Chlamydia trachomatis isolates (all serovars from the human biovar, an isolate from the mouse biovar, and a porcine isolate), 6 Chlamydia psittaci isolates (5 avian isolates and 1 feline isolate), and 1 Chlamydia pecorum isolate was studied by analyzing genomic amplified fragment length polymorphism (AFLP) fingerprints. The AFLP procedure was adapted from a previously developed method for characterization of clinical C. trachomatis isolates. The fingerprints of all C. pneumoniae isolates were nearly identical, clustering together at a Dice similarity of 92.6% (± 1.6% standard deviation). The fingerprints of the C. trachomatis isolates of human, mouse, and swine origin were clearly distinct from each other. The fingerprints of the isolates from the human biovar could be divided into at least 12 different types when the presence or absence of specific bands was taken into account. The C. psittacifingerprints could be divided into a parakeet, a pigeon, and a feline type. The fingerprint of C. pecorum was clearly distinct from all others. Cluster analysis of selected isolates from all species revealed groups other than those based on sequence data from single genes (in particular, omp1 and rRNA genes) but was in agreement with available DNA-DNA hybridization data. In conclusion, cluster analysis of AFLP fingerprints of representatives of all species provided suggestions for a grouping of chlamydiae based on the analysis of the whole genome. Furthermore, genomic AFLP analysis showed that the genome of C. pneumoniae is highly conserved and that no differences exist between isolates of respiratory and atherosclerotic origins.

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