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AFLP Profiles (aflp + profile)
Selected AbstractsGenetic variations among Mycoplasma bovis strains isolated from Danish cattleFEMS MICROBIOLOGY LETTERS, Issue 1 2000Lughano J.M. Kusiluka Abstract The genetic heterogeneity of Mycoplasma bovis strains isolated in Denmark over a 17-year period was investigated. Forty-two field strains isolated from different geographic locations and specimens, including strains from 21 herds involved in two outbreaks of M. bovis -induced mastitis, and the type strain of M. bovis (PG45T) were assayed for variations in the BglII and MfeI restriction sites in the chromosomal DNA by using the amplified fragment length polymorphism (AFLP) fingerprinting technique. The obtained genomic fingerprints consisted of 62,68 AFLP fragments in the size range of 50,500 bp. Among the analyzed strains, 18 different AFLP profiles were detected. The similarity between individual fingerprints, calculated by Dice similarity coefficient, ranged from 0.9 to 1.0. Twenty-five strains, including 23 which were isolated during two outbreaks of M. bovis -induced mastitis which occurred 2 years apart, showed indistinguishable AFLP patterns. More genetic diversity was observed among the recent strains. The similarity of the genotypes of the field strains to that of the M. bovis type strain (PG45T) was 97.7%. The results of this study have demonstrated a remarkable genomic homogeneity of Danish strains of M. bovis that were probably epidemiologically related and which have remained stable for a considerable length of time. Furthermore, this study has demonstrated that AFLP can be used for genomic fingerprinting and discrimination of M. bovis strains. [source] Amplified fragment length polymorphism (AFLP) and biochemical typing of Photobacterium damselae subsp. damselaeJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2002S. Botella Aims: The aim of the present study was to characterize subspecifically Photobacterium damselae subsp. damselae strains isolated from cultured Sparus aurata and Dicentrarchus labrax by means of phenotypic and molecular typing techniques (amplified fragment length polymorphism, AFLP). Methods and Results: Seventy-one strains of P. damselae subsp. damselae were isolated from 38 cultured fishes at different fish farms located on the Mediterranean coast near Valencia, Spain. Most fish studied were asymptomatic and some were recovered during infectious outbreaks. Phenotypic characterization revealed a considerable degree of variability within the subspecies, including some characters, such as production of urease, which are used to differentiate P. damselae subsp. damselae from P. damselae subsp. piscicida. Genetic characterization was conducted on a selection of 33 strains, including two reference strains. Dice coefficient (Sd) and the unweighted pair group method with average linkage (UPGMA) were used for numerical analysis of banding patterns. AFLP type was defined on the basis of 100% similarity in the dendrogram obtained, yielding 24 distinct AFLP profiles. At 70% similarity, 13 clusters were defined, thus confirming the great variability observed for the phenotypic traits. Conclusions: The AFLP variability shown by the isolates was high enough to discriminate between different strains which colonize the same fish. However, closely related AFLP types were usually derived from strains isolated at the same fish farm, indicating an epidemiological relationship. Significance and Impact of the Study: This study has confirmed that the AFLP technique allows discrimination of individual strains within P. damselae subsp. damselae for epidemiological studies, and that this subspecies exhibits greater variability than that described for subspecies piscicida. [source] Genetic diversity in pollen beetles (Meligethes aeneus) in Sweden: role of spatial, temporal and insecticide resistance factorsAGRICULTURAL AND FOREST ENTOMOLOGY, Issue 4 2007Nadiya Kazachkova Abstract 1,Pollen beetles Meligethes aeneus are pests of oilseed Brassica crops that are subject to intensive chemical control. Resistance to pyrethroids has been reported. Although this insect is of great economic importance, little is known about its genetic properties and population structure. 2,Amplified fragment length polymorphism (AFLP) analysis with the restriction endonuclease combination EcoRI and PstI was performed on 133 samples of groups of three pollen beetles collected during 2001,04 from five different provinces of Sweden. Both susceptible and resistant insects were studied. Using one primer combination, more than 450 polymorphic DNA fragments were obtained and, in total, four primer combinations were used for analysis. A subsample of 59 single beetles was analysed using one primer combination. 3,AFLP profiles were analysed by similarity measures using the Nei and Li coefficient and Neighbour-joining dendrograms were generated. The dendrogram built using 133 samples showed three distinct groups, each containing beetles representing one generation. Statistical analysis using analysis of molecular variance of single beetle samples showed no evidence of significant genetic difference between resistant and susceptible beetles. Instead, a clear difference between samples, depending on time of collection and generation, was observed. 4,The expected regional population structure, although statistically significant, explained little of the variation. The levels of genetic variation within populations were very high. There appears to be a high rate of gene flow between pollen beetle populations. The implications of this in the context of insecticide resistance are discussed. [source] Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionistsMOLECULAR ECOLOGY, Issue 18 2007A. Bonin Abstract Recently, the amplified fragment length polymorphism (AFLP) technique has gained a lot of popularity, and is now frequently applied to a wide variety of organisms. Technical specificities of the AFLP procedure have been well documented over the years, but there is on the contrary little or scattered information about the statistical analysis of AFLPs. In this review, we describe the various methods available to handle AFLP data, focusing on four research topics at the population or individual level of analysis: (i) assessment of genetic diversity; (ii) identification of population structure; (iii) identification of hybrid individuals; and (iv) detection of markers associated with phenotypes. Two kinds of analysis methods can be distinguished, depending on whether they are based on the direct study of band presences or absences in AFLP profiles (,band-based' methods), or on allelic frequencies estimated at each locus from these profiles (,allele frequency-based' methods). We investigate the characteristics and limitations of these statistical tools; finally, we appeal for a wider adoption of methodologies borrowed from other research fields, like for example those especially designed to deal with binary data. [source] Geographic distribution and genetic diversity of Fusarium graminearum and F. asiaticum on wheat spikes throughout ChinaPLANT PATHOLOGY, Issue 1 2008B. Qu A large number of Fusarium graminearum and F. asiaticum isolates were collected from wheat spikes from all regions in China with a history of fusarium head blight (FHB) epidemics. Isolates were analysed to investigate their genetic diversity and geographic distribution. Sequence characterized amplified region (SCAR) analyses of 437 isolates resolved both species, with 21% being F. graminearum (SCAR type 1) and 79% being F. asiaticum (SCAR type 5). AFLP profiles clearly resolved two groups, A and B, that were completely congruent with both species. However, more diversity was detected by AFLP, revealing several subgroups within each group. In many cases, even for isolates from the same district, AFLP haplotypes differed markedly. Phylogenetic analyses of multilocus DNA sequence data indicated that all isolates of SCAR type 1, AFLP group A were F. graminearum, whilst isolates of SCAR type 5, AFLP group B were F. asiaticum, demonstrating that it is an efficient method for differentiating these two species. Both species seem to have different geographic distributions within China. Fusarium graminearum was mainly obtained from wheat growing in the cooler regions where the annual average temperature was 15°C or lower. In contrast, the vast majority of F. asiaticum isolates were collected from wheat growing in the warmer regions where the annual average temperature is above 15°C and where FHB epidemics occur most frequently. This is the first report of the distribution of, and genetic diversity within, F. graminearum and F. asiaticum on wheat spikes throughout China. [source] Efficacy of the R2 resistance gene as a component for the durable management of potato late blight in FrancePLANT PATHOLOGY, Issue 6 2005F. Pilet Many race-specific resistance genes to potato late blight are overcome in France, but the disease appears later on genotypes carrying the R2 gene. This study examined whether R2 could contribute to durable late-blight control in France, and analysed the conditions of its performance. Plants grown from tubers of different physiological ages showed no difference in R2 expression in field and climate-chamber experiments, demonstrating that the delay in epidemic onset provided by R2 was not the result of gene inactivation in old plants. Among isolates collected at one site, those virulent on R2 were classified into three AFLP profiles. AFLP-VII comprised exclusively isolates virulent to R2, whereas AFLP-IV and AFLP-V included both virulent and avirulent isolates. No significant aggressiveness differences were observed between virulent and avirulent isolates from AFLP-V; however, isolates from AFLP-VII were significantly less aggressive than virulent isolates from AFLP-V. These results indicate that: (i) the delayed onset of epidemics on R2 cultivars is the result of the breakdown of R2 by virulent isolates; (ii) aggressiveness of isolates virulent to R2 depends primarily on the genetic background of the pathogen where the mutation to virulence occurs; and (iii) this mutation does not lead per se to lower pathogenic fitness. It is suggested that R2 is unlikely to make a lasting contribution to late-blight control in France, and that diversification strategies such as cultivar mixtures might not considerably increase its durability. [source] | ||||||||||