scholarly journals Analysis of Genetic Variability among Phalaenopsis Species and Hybrids Using Amplified Fragment Length Polymorphism

2009 ◽  
Vol 134 (1) ◽  
pp. 58-66 ◽  
Author(s):  
Yeun-Kyung Chang ◽  
Richard E. Veilleux ◽  
Muhammad Javed Iqbal
Keyword(s):  
Genetic Variability ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Similarity ◽  
Fragment Length Polymorphism ◽  
Species Conservation ◽  
Amplified Fragment Length Polymorphism ◽  
The United States ◽  
Group Method ◽  
Aflp Analysis

Phalaenopsis is the second most valuable potted plant in the United States. Information on the genetic diversity and relationships among species and hybrids is important for breeding purposes and species conservation. In this study, genetic variability of 16 Phalaenopsis species and hybrids was analyzed using amplified fragment length polymorphism (AFLP) markers. Ten AFLP primer combinations amplified 1353 DNA fragments ranging in size from 100 to 350 bp and 1285 (95%) of them were polymorphic. The genetic similarity among Phalaenopsis species and hybrids ranged from 0.298 to 0.774 based on Dice coefficient. The dendrogram derived by the unweighted pair group method with arithmetic mean analysis clustered the germplasm into two main groups. Bootstrap values for the groups supported 70% of the clustering. A significant linear relationship (r = 0.724, P < 0.0001) was observed between known pedigrees and AFLP-derived genetic similarity for 136 pairwise comparisons of Phalaenopsis species and hybrids. The results of this study demonstrate the usefulness of AFLP analysis in Phalaenopsis and its potential application in breeding and species conservation.

scholarly journals Polymorphism and Genetic Relationships among Tea Genotypes from Turkey Revealed by Amplified Fragment Length Polymorphism Markers

2009 ◽  
Vol 134 (4) ◽  
pp. 428-434 ◽  
Author(s):  
Salih Kafkas ◽  
Sezai Ercişli ◽  
Yıldız Doğan ◽  
Yaşar Ertürk ◽  
Ayhan Haznedar ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Group Method ◽  
Aflp Analysis ◽  
Black Sea Region ◽  
Pair Group

Individuals in most countries around the world drink tea (Camellia sinensis). Tea drinking has attained ceremonial status in many places as a social and medicinal beverage. Although tea is of great importance in Turkey's economy, little is known about the pattern of genetic variation among the various tea genotypes grown in Turkey. A total of 32 tea genotypes found at the Ataturk Tea and Horticulture Research Institute in the eastern Black Sea region of Turkey were sampled. Fluorescent dye amplified fragment length polymorphism (AFLP) markers and capillary electrophoresis were applied for molecular characterization. The AFLP analysis with six primer combinations generated 835 fragments of which 567 were polymorphic, corresponding to 69.8% polymorphism. Resolving powers of the AFLP primers ranged from 62.6 to 81.9, yielding a total of 437.8; the polymorphic information content (PIC) ranged from 0.76 to 0.83, with an average of 0.79. Genetic similarity values ranged from 0.68 to 0.92, with an average of 0.76. The dendrogram derived by unweighted pair group method with arithmetic mean algorithm (UPGMA) and principal coordinate analysis (PCoA) revealed that all tea genotypes could be clearly divided into four distinct clusters. The results of this study will provide valuable information to the tea cultivar breeding program for the purpose of parental selection.

scholarly journals Investigating Parentage and Hybridity of Three Azaleodendrons Using Amplified Fragment Length Polymorphism Analysis

HortScience ◽  
2007 ◽  
Vol 42 (3) ◽  
pp. 740-743 ◽  
Author(s):  
Ryan N. Contreras ◽  
Thomas G. Ranney ◽  
Susana R. Milla-Lewis ◽  
G. Craig Yencho
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Similarity ◽  
Morphological Analysis ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Single Clone ◽  
Similar Appearance

Morphological analysis historically has been used to determine parentage of unknown hybrids. This can be difficult when potential parents have similar appearance, as in the case of three azaleodendron cultivars, Rhododendron L. ‘Fragrans’, ‘Fragrans Affinity’, and ‘Fragrant Affinity’. These cultivars are similar in name and appearance, and all are purported hybrids of R. catawbiense Michx. or R. ponticum L. and R. viscosum (L.) Torr. Amplified fragment length polymorphism (AFLP) analysis was conducted to determine whether the cultivars are synonyms or distinct clones and to elucidate the parental species. The three cultivars, suspected to be hybrids between taxa in subgenera Hymenanthes (Blume) K.Koch (evergreen rhododendrons) and Pentanthera (G.Don) Pojarkova (deciduous azaleas), and related taxa from each subgenus were evaluated using 31 AFLP primer combinations. Genetic similarity, calculated using Jaccard's coefficient, among the hybrids ranged from 53% to 71%, indicating that they are distinct cultivars and not a single clone. Genetic similarity was highest between the hybrids and R. ponticum among the evergreen rhododendrons, and R. viscosum among the deciduous azaleas. A dendrogram generated using the genetic similarity matrix grouped taxa into their respective subgenera, with the three cultivars nested intermediately between subgenera but more closely with subgenus Hymenanthes and particularly R. ponticum, suggesting it is the evergreen rhododendron parent. Furthermore, principle components grouped R. ponticum more closely with the hybrids and there were 18 AFLP fragments unique to R. ponticum and the hybrids. However, no unique AFLP bands were shared exclusively among the hybrids and the purported deciduous azalea parent, R. viscosum, suggesting that the original azalea parents may have been hybrids.

Amplified Fragment Length Polymorphism, Serotyping, and Quinolone Resistance of Campylobacter jejuni and Campylobacter coli Strains from Chicken-Related Samples and Humans in Taiwan

2006 ◽  
Vol 69 (4) ◽  
pp. 775-783 ◽  
Author(s):  
SHAO W. FANG ◽  
CHING J. YANG ◽  
DANIEL Y. C. SHIH ◽  
CHENG C. CHOU ◽  
ROCH C. YU
Keyword(s):  
Campylobacter Jejuni ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Similarity ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Quinolone Resistance ◽  
Aflp Analysis ◽  
Campylobacter Coli

The high-resolution genotyping method of amplified fragment length polymorphism (AFLP) analysis was used to study the genetic relationships between Campylobacter jejuni isolates from chicken-related samples (n = 32) and humans (n = 27) as well as between Campylobacter coli isolates from chicken-related samples (n = 27) and humans (n = 5). These isolates were collected between 1994 and 2003 in Taiwan. All C. jejuni and C. coli isolates showed highly heterogeneous fingerprints. C. jejuni isolates were separated in two distinct genetic clusters (A and B) at 40% genetic similarity and 42 different AFLP types at 90% similarity. However, three clusters at 40% genetic similarity and 33 different AFLP types at 90% similarity were observed in C. coli isolates. These results showed that AFLP analysis could be used to identify individual isolates of two Campylobacter species. Among C. jejuni isolates, the predominant AFLP type 1 was observed in five (7.9%) isolates, and types 5 and 12 in four (6.3%) isolates each. Cluster B consisted of 10 isolates, while the majority of isolates (n = 53) belonged to cluster A. In some AFLP types (1, 5, 12, 14 and 31), AFLP fingerprints of chicken-related isolates were closely related genetically to those of isolates from humans with gastroenteritis. The predominant serotypes in C. jejuni isolates were B:2 and Y:37. All isolates belonging to serotype O:19 grouped into one single AFLP type. Some chicken samples yielded multiple isolates of Campylobacter harboring simultaneously quinolone-resistant and quinolone-sensitive isolates attributed to the same species, or harboring C. jejuni and C. coli that have the characteristics of quinolone resistance.

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 Amplified Fragment Length Polymorphism to Detect Clonal Diversity and Distribution of Mycobacterium Avium Subspecies Paratuberculosis in Selected Minnesota Dairy Cattle

2005 ◽  
Vol 17 (4) ◽  
pp. 311-315 ◽  
Author(s):  
Laura A. Kiehnbaum ◽  
Alongkorn Amonsin ◽  
Scott J. Wells ◽  
Vivek Kapur
Keyword(s):  
Mycobacterium Avium ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Mycobacterium Avium Subspecies Paratuberculosis ◽  
Molecular Ecology ◽  
Clonal Diversity ◽  
Amplified Fragment Length Polymorphism ◽  
The United States ◽  
Aflp Analysis

The molecular ecology of Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne's disease, is not well understood in the United States. In this study, a DNA fingerprinting method, amplified fragment length polymorphism (AFLP), was used to subtype the pathogen and assess the clonal diversity of MAP in Minnesota dairy herds. Fifty-six fecal culture test–positive isolates from various Minnesota counties and culture dates were analyzed in this study. The AFLP identified 11 profiles with 50% of isolates representing 1 major profile. The major profile was distributed across the state. The genetic diversity of bovine MAP clones in Minnesota based on AFLP analysis of this data appears to be relatively low.

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.

Comparative Fingerprinting Analysis ofCampylobacter jejuni subsp. jejuni Strains by Amplified-Fragment Length Polymorphism Genotyping

2000 ◽  
Vol 38 (9) ◽  
pp. 3379-3387 ◽  
Author(s):  
Bjørn-Arne Lindstedt ◽  
Even Heir ◽  
Traute Vardund ◽  
Kjetil K. Melby ◽  
Georg Kapperud
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Epidemiological Surveillance ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Ofcampylobacter Jejuni

Amplified-fragment length polymorphism (AFLP) analysis with the endonucleases BglII and MfeI was used to genotype 91 Campylobacter jejuni subsp. jejunistrains from outbreaks and sporadic cases. AFLP-generated fragments were labeled with fluorescent dye and separated by capillary electrophoresis. The software packages GeneScan and GelCompar II were used to calculate AFLP pattern similarities and to investigate phylogenetic relationships among the genotyped strains. The AFLP method was compared with two additional DNA-based typing methods, pulsed-field gel electrophoresis (PFGE) using SmaI and restriction fragment length polymorphism analysis on PCR products (PCR-RFLP) of theflaA and flaB genes. We found that AFLP analysis of C. jejuni strains is a rapid method that offers better discriminatory power than do both PFGE and PCR-RFLP. AFLP and, to a lesser extent, PCR-RFLP could differentiate strains within the same PFGE profiles, which also makes PCR-RFLP an alternative to PFGE. We were able to clearly distinguish 9 of 10 recognized outbreaks by AFLP and to identify similarities among outbreak and sporadic strains. Therefore, AFLP is suitable for epidemiological surveillance ofC. jejuni and will be an excellent tool for source identification in outbreak situations.

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.

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