scholarly journals Characterization of Verticillium albo-atrum Field Isolates Using Pathogenicity Data and AFLP Analysis

Plant Disease ◽  
2003 ◽  
Vol 87 (6) ◽  
pp. 633-638 ◽  
Author(s):  
Sebastjan Radišek ◽  
Jernej Jakše ◽  
Andrej Simončič ◽  
Branka Javornik
Keyword(s):  
Fragment Length Polymorphism ◽  
Economic Losses ◽  
Aflp Analysis ◽  
Mild Form ◽  
Aflp Data ◽  
Green Pepper ◽  
Clear Separation ◽  
Pathogenicity Tests ◽  
Verticillium Albo Atrum

Since 1997, hop wilt induced by a virulent pathotype of Verticillium albo-atrum has caused considerable economic losses in hop fields in Slovenia. In all, 20 isolates of V. albo-atrum, including 12 from plants affected with the lethal form (PG2) of hop wilt, 6 from plants with the mild form (PG1), 1 from cucumber, and 1 from petunia, as well as 1 isolate of V. dahliae each from hop and green pepper, were analyzed by amplified fragment length polymorphism (AFLP). Differences in the virulence of hop isolates were confirmed by pathogenicity tests on hop cultivars. The AFLP method was optimized for analysis of these fungi and 7 of 39 primer combinations tested were used for the analysis of polymorphism among isolates. Cluster analysis of AFLP data divided the isolates into two, well-separated V. albo-atrum and V. dahliae clusters, confirming that the two species are genetically distinct. Within the V. albo-atrum cluster, isolates were further separated into two distinct groups: the A1 group contained PG1 hop pathotype and cucumber and petunia isolates, and the A2 group all hop isolates of the PG2 pathotype. Minor genetic variation was detected within pathotype-associated AFLP groups, but the clear separation of V. albo-atrum hop isolates according to their level of virulence shows genetic differentiation among hop V. albo-atrum pathotypes.

scholarly journals Fourier Transform Infrared and Raman Spectroscopy for Characterization of Listeria monocytogenes Strains

2006 ◽  
Vol 72 (1) ◽  
pp. 228-232 ◽  
Author(s):  
Astrid Oust ◽  
Trond Møretrø ◽  
Kristine Naterstad ◽  
Ganesh D. Sockalingum ◽  
Isabelle Adt ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Raman Spectroscopy ◽  
Fourier Transform ◽  
Listeria Monocytogenes ◽  
Fragment Length Polymorphism ◽  
Fourier Transform Infrared ◽  
Aflp Analysis ◽  
Aflp Data ◽  
Infrared And Raman Spectroscopy

ABSTRACT The purpose of this study was to characterize the variation in biochemical composition of 89 strains of Listeria monocytogenes with different susceptibilities towards sakacin P, using Fourier transform infrared (FTIR) spectroscopy and Raman spectroscopy. The strains were also analyzed using amplified fragment length polymorphism (AFLP) analysis. Based on their susceptibilities to sakacin P, the 89 strains have previously been divided into two groups. Using the FTIR spectra and AFLP data, the strains were basically differentiated into the same two groups. Analyses of the FTIR and Raman spectra revealed that the strains in the two groups contained differences in the compositions of carbohydrates and fatty acids. The relevance of the variation in the composition of carbohydrates with respect to the variation in the susceptibility towards sakacin P for the L. monocytogenes strains is discussed.

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.

scholarly journals Characterization of a New Subgroup of Rhizoctonia solani Anastomosis Group 1 (AG-1-ID), Causal Agent of a Necrotic Leaf Spot on Coffee

2001 ◽  
Vol 91 (11) ◽  
pp. 1054-1061 ◽  
Author(s):  
Achmadi Priyatmojo ◽  
Verma E. Escopalao ◽  
Naomi G. Tangonan ◽  
Cecilia B. Pascual ◽  
Haruhisa Suga ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Fragment Length Polymorphism ◽  
Hyphal Growth ◽  
Anastomosis Group ◽  
Fatty Acid Profiles ◽  
Pathogenicity Tests ◽  
Necrotic Spots ◽  
Random Amplified Polymorphism Dna ◽  
Group 1

A new foliar disease on coffee leaves was observed in Mindanao, Philippines, in 1996. The symptoms appeared as large circular or irregularly shaped necrotic areas with small circular necrotic spots (1 mm or less in diameter) usually found around the periphery of the large necrotic areas. Rhizoctonia solani was consistently isolated from these diseased coffee leaves. Isolates obtained were multinucleate (3 to 12 nuclei per hyphal cell), had an optimum temperature for hyphal growth at 25°C, prototrophic for thiamine, and anastomosed with tester isolates belonging to R. solani anastomosis group 1 (AG-1). Mature cultures on potato dextrose agar (PDA) were light to dark brown. Sclerotia, light brown to brown, were formed on the surface of PDA and covered the whole mature colony culture. Individual sclerotia often aggregated into large clumps (3 to 8 mm in diameter) and their color was brown to dark brown. In pathogenicity tests, isolates from coffee caused necrotic symptoms on coffee leaves, whereas isolates of AG-1-IA (not isolated from coffee), 1-IB, and 1-IC did not. The results of analyses of restriction fragment length polymorphism of ribosomal DNA internal transcribed spacer, random amplified polymorphism DNA, and fatty acid profiles showed that R. solani isolates from coffee are a population of AG-1 different from AG-1-IA, 1-IB, and 1-IC. These results suggest that R. solani isolates from coffee represent a new subgroup distinct from AG-1-IA, 1-IB, and 1-IC. A new subgroup ID (AG-1-ID) is proposed.

Genetic structure of the Anthyllis vulneraria L. s. l. species complex in Estonia based on AFLPs

2008 ◽  
Vol 3 (4) ◽  
pp. 442-450 ◽  
Author(s):  
Egle Köster ◽  
Elena Bitocchi ◽  
Roberto Papa ◽  
Silvia Pihu
Keyword(s):  
Species Complex ◽  
Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Data Sets ◽  
Geographic Scale ◽  
Aflp Data ◽  
Anthyllis Vulneraria ◽  
Directional Variation ◽  
Intraspecific Structure ◽  
Cryptic Taxa

AbstractAnthyllis vulneraria L. (Fabaceae) s. lato includes many cryptic taxa, ranging from 25 to 60 subspecies according to different authors. The delimitation of intraspecific taxa of A. vulneraria s. lato has always been complicated and inconsistent. Different data sets (multivariate analyses of morphological variation, allozymes, chloroplast SSRs and ITS) have not resolved the existing problem with distinguishing some subspecies. We used the amplified fragment length polymorphism (AFLP) analysis to describe the differentiation in this species complex and to characterize variation on a geographic scale. Some correlation was found between genetic variability and geographic distribution (western-eastern directional variation), but AFLP data analysis did not reveal clear intraspecific structure of the seven analysed taxa. The analysed specimens did not comprise groups correlated with the subspecies.

scholarly journals Characterization, Genetic Structure, and Pathogenicity of Rhizoctonia spp. Associated with Rice Sheath Diseases in India

2007 ◽  
Vol 97 (3) ◽  
pp. 373-383 ◽  
Author(s):  
Parissa Taheri ◽  
Sam Gnanamanickam ◽  
Monica Höfte
Keyword(s):  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Geographic Region ◽  
Dominant Factor ◽  
Chain Reaction ◽  
Aflp Data ◽  
Pathogenicity Tests ◽  
Polymerase Chain ◽  
Geographic Regions ◽  
Pathogen Populations

Isolates of Rhizoctonia spp. were obtained from rice in India during 2000-2003. Characterization by conventional techniques and polymerase chain reaction showed that from 110 isolates, 99 were R. solani and 11 were R. oryzae-sativae. Of 99 isolates identified as R. solani, 96 were AG1-IA, 1 was AG1-IB, and 2 were AG1-IC. Amplified fragment length polymorphism (AFLP) analyzes were used to determine genetic relationships in Rhizoctonia pathogen populations collected from different geographic regions. Cluster analysis based on the AFLP data separated isolates belonging to the three different intraspecific groups of R. solani AG1 and differentiated R. solani from R. oryzae-sativae. Analysis of molecular variance (AMOVA) revealed that geographic region was the dominant factor determining population structure of R. solani AG1-1A; host cultivar had no significant effect. Pathogenicity tests on Oryza sativa cv. Zenith revealed that isolates of R. solani AG1-1A and AG1-1B were more virulent than R. solani AG1-IC and R. oryzae-sativae isolates.

scholarly journals Characterization of a New Anastomosis Group (AG-W) of Binucleate Rhizoctonia, Causal Agent for Potato Stem Canker

Plant Disease ◽  
2015 ◽  
Vol 99 (12) ◽  
pp. 1757-1763 ◽  
Author(s):  
Y. G. Yang ◽  
C. Zhao ◽  
Z. J. Guo ◽  
X. H. Wu
Keyword(s):  
Fragment Length Polymorphism ◽  
Stem Canker ◽  
Anastomosis Group ◽  
Northeastern China ◽  
Binucleate Rhizoctonia ◽  
Rdna Its ◽  
Its Regions ◽  
Pathogenicity Tests ◽  
Reference Strains

Two binucleate Rhizoctonia (BNR) isolates were recovered from potato cankered stems in Heilongjiang Province, northeastern China. Their cultural appearance on potato dextrose agar remained whitish as the cultures aged. White monilioid cells formed in the fluffy aerial hyphae, whereas no sclerotia appeared during the incubation. The two isolates could anastomose with each other, but they failed to anastomose with reference strains of BNR from AG-A to AG-Q, and AG-U. Analyses of restriction fragment length polymorphism (RFLP) of internal transcribed spacer of ribosomal DNA (rDNA-ITS) regions confirmed that these two isolates differed from the reference strains. The phylogenetic tree based on the sequences of rDNA-ITS regions showed that they were located in a distinct clade from other BNR AGs. These collective results suggested that the isolates recovered from potato in this study belonged to a new BNR AG designated as AG-W. Pathogenicity tests under glasshouse conditions revealed that both isolates were able to cause brown, dry, and slightly sunken lesions on potato subterranean stems. To our knowledge, this is the first report of the AG-W causing potato disease in China as well as worldwide.

Extent and pattern of genetic differentiation within and between phenotypic populations of Leymus chinensis (Poaceae) revealed by AFLP analysis

2007 ◽  
Vol 85 (9) ◽  
pp. 813-821 ◽  
Author(s):  
Lei Gong ◽  
Xinxin Song ◽  
Mu Li ◽  
Wanli Guo ◽  
Lanjuan Hu ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Fragment Length Polymorphism ◽  
Green Leaf ◽  
Leymus Chinensis ◽  
Aflp Analysis ◽  
Natural Habitats ◽  
Aflp Data ◽  
Original Population ◽  
Naturally Occurring ◽  
Mantel’S Test

The extent and pattern of genetic differentiation between two naturally occurring phenotypes, grey–green leaf (GGL) and yellow–green leaf (YGL), of Leymus chinensis (Trin.) Tzvel., which colonize distinct habitats in the Songnen Prairie in northeast China, were investigated by amplified fragment length polymorphism (AFLP) analysis. Twelve selected AFLP primer pairs amplified 593 reproducible bands, of which 148 (24.96%) were polymorphic among 69 individuals taken from three populations: two natural ones (YGL and GGL1) and one transplanted (GGL2). Cluster analysis based on the AFLP data categorized the plants into distinct groups that are in line with their phenotypes and population origins, thus denoting clear genetic differentiation between the two phenotypes. This, together with their adaptation to contrasting natural habitats, suggests that the two phenotypes probably represent stabilized ecotypes. The grouping was supported by multiple statistical analyses including Mantel’s test, principal coordinate analysis (PCOORDA), and analysis of molecular variance (AMOVA). The GGL phenotype harbors a higher level of within-population genetic diversity than YGL, possibly reflecting selection by habitat heterogeneity. Although GGL2 is largely similar to its original population (GGL1), further diversification since transplantation was evident. Sequence analysis of a subset of phenotype-specific or phenotype-enriched AFLP bands implicated diverse biological functions being involved in ecological adaptation and formation of the two phenotypes.

scholarly journals Genotypic Analysis of Escherichia coli Strains from Poultry Carcasses and Their Susceptibilities to Antimicrobial Agents

2001 ◽  
Vol 67 (4) ◽  
pp. 1940-1944 ◽  
Author(s):  
Ifigenia Geornaras ◽  
John W. Hastings ◽  
Alexander von Holy
Keyword(s):  
Escherichia Coli ◽  
South African ◽  
Length Polymorphism ◽  
Antimicrobial Agents ◽  
Susceptibility Testing ◽  
Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Aflp Data ◽  
Genotypic Analysis ◽  
Plasmid Profiling

ABSTRACT Plasmid profiling and amplified fragment length polymorphism (AFLP) analysis were used to genotype 50 Escherichia coli strains from poultry carcasses. Thirty different plasmid profiles were evident, and clustering of the AFLP data showed that they were a distinctly heterogeneous group of strains. Susceptibility testing against five antimicrobial agents used in the South African poultry industry showed all strains to be susceptible to danofloxacin and colistin, while the majority (96%) were resistant to two tetracyclines.

Characterization of AFLP markers in damselflies: prevalence of codominant markers and implications for population genetic applications

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 677-684 ◽  
Author(s):  
A Wong ◽  
M R Forbes ◽  
M L Smith
Keyword(s):  
Population Genetic ◽  
Genetic Parameters ◽  
Fragment Length Polymorphism ◽  
Population Studies ◽  
Natural Populations ◽  
Aflp Analysis ◽  
Polymorphic Markers ◽  
Dominant Markers ◽  
Nehalennia Irene

Amplified fragment length polymorphism (AFLP) analysis is becoming increasingly popular as a method for generating molecular markers for population genetic applications. For practical considerations, it is generally assumed in population studies that AFLPs segregate as dominant markers, i.e., that present and absent are the only possible states of a given locus. We tested the assumption of dominance in natural populations of the damselfly Nehalennia irene (Hagen) (Odonata: Coenagrionidae). Electro-blotted AFLP products from 21 samples were probed with individual markers. Eleven markers were analyzed, of which two were monomorphic and nine were polymorphic. Only two of the polymorphic markers behaved in a strictly dominant manner. The remaining seven polymorphic markers displayed various degrees of codominance, with 2–10 visible alleles in the sample. Of the three markers displaying the highest degree of variability, two contained microsatellite repeat tracts. Our results suggest that the assumption of dominance is unfounded. As a result, AFLP analysis may be unsuitable for estimating several important population genetic parameters, including genetic diversity.Key words: AFLP, population genetics, dominant markers, microsatellite, insect, damselfly.

scholarly journals Identification and characterization of the contact zone between short-tailed shrews (Blarina) in Iowa and Missouri

2011 ◽  
Vol 89 (4) ◽  
pp. 278-288 ◽  
Author(s):  
C.W. Thompson ◽  
R.S. Pfau ◽  
J.R. Choate ◽  
H.H. Genoways ◽  
E.J. Finck
Keyword(s):  
Fragment Length Polymorphism ◽  
Putative Hybrid ◽  
Aflp Analysis ◽  
Contact Zones ◽  
Blarina Brevicauda ◽  
Field Identification ◽  
The One ◽  
Blarina Hylophaga ◽  
Identification And Characterization

Short-tailed shrews (genus Blarina Gray, 1838) are characterized by divergent karyotypes and are genetically distinct. Blarina species are similar morphologically but, in most cases, can be distinguished morphometrically. Blarina distributions tend to be parapatric along well-defined contact zones; however, it has been suggested that the northern short-tailed shrew ( Blarina brevicauda (Say, 1823)) and Elliot’s short-tailed shrew ( Blarina hylophaga Elliot, 1899) occur sympatrically in Iowa and Missouri. To evaluate this possibility, 179 specimens were collected in southwestern Iowa and northwestern Missouri. Karyotypes and total length were used for field identification, and amplified fragment length polymorphism (AFLP) analysis was used to verify field identifications and to investigate the extent of hybridization. One hundred seventy-eight of 179 specimens were identified to species. The one exception had a karyotype of B. brevicauda (2n = 50, FN = 48); however, AFLP analysis indicated that this individual was likely an F1 hybrid. No backcrosses were detected, so it appears that introgression is minimal. The putative hybrid was trapped at a locality with B. brevicauda just north of a locality having only B. hylophaga. No locality contained both species. Therefore, these species are not broadly sympatric as has been suggested, but rather exhibit a distribution similar to the pattern of parapatry seen in most of the contact zones of Blarina.

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