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AFLP Analysis (aflp + analysis)
Selected AbstractsAFLP Analysis of Trichoderma spp. from India Compared with Sequence and Morphological-based DiagnosticsJOURNAL OF PHYTOPATHOLOGY, Issue 7-8 2005H. K. Buhariwalla Abstract Trichoderma species offer considerable potential for controlling aflatoxin contamination in groundnut and other crops. Initial classification of 48 Trichoderma isolates, derived from four different groundnut cultivation sites in India was based on alignment of 28S rDNA sequences to GenBank sequences of ex-type strains. This was found to be substantially more reliable than our routine morphological characterization, but did not provide a comprehensive diagnostic solution, as unique single nucleotide polymorphism (SNP) haplotypes could not be identified for all species. However, all the Trichoderma isolates could be readily distinguished by amplified fragment length polymorphism (AFLP) analysis, based on six primer pair combinations, which generated 234 polymorphic bands. In addition, individual AFLP bands were identified which differentiate closely related species. Similarly, AFLP bands were identified that correlated with different types of antagonism to Aspergillus flavus. The implications of these results for the development of simple polymerase chain reaction (PCR)-based diagnostic assays for antagonistic isolates of Trichoderma is discussed. [source] Biogeographical patterns of genetic differentiation in dung beetles of the genus Trypocopris (Coleoptera, Geotrupidae) inferred from mtDNA and AFLP analysesJOURNAL OF BIOGEOGRAPHY, Issue 7 2004Loredana Carisio Abstract Aim, To examine the phylogeography and population structure of three dung beetle species of the genus Trypocopris (Coleoptera, Geotrupidae). We wanted to test whether genetic differences and genealogies among populations were in accordance with morphologically described subspecies and we aimed to establish times of divergence among subspecies to depict the appropriate temporal framework of their phylogeographical differentiation. We also wished to investigate the historical demographic events and the relative influences of gene flow and drift on the distribution of genetic variability of the different populations. Location, Europe (mostly Italy). Methods, We collected adult males from dung pats from 15 Italian localities over the period 2000,2002. For sequence analysis, some dried specimens from Albania, Croatia, Slovakia and Spain were also used. We applied cytochrome oxidase I mitochondrial DNA sequencing and the amplified fragment length polymorphism (AFLP) technique to determine whether phylogeographical patterns within the three species support the proposed hypotheses of subspecies designations, and to detect further structure among populations that might mediate diversification. Results and main conclusions, The results show a high concordance between the distribution of mtDNA variation and the main morphological groups recognized as subspecies, which thus may represent independent evolutionary units. The degree of mitochondrial divergence suggests that speciation events occurred during the Pliocene, while diversification of the main subspecific lineages took place in the Pleistocene, from c. 0.3 to 1.5 Ma. Mitochondrial and nuclear data also reveal that there is phylogeographical structuring among populations within each of the main groups and that both contemporary and historical processes determined this pattern of genetic structure. Geographical populations form monophyletic clades in both phylogenetic and network reconstructions. Despite the high levels of intrapopulational diversity, FST values indicate moderate but significant genetic differentiation among populations, and a Bayesian clustering analysis of the AFLP data clearly separates the geographical populations. Nucleotide and gene diversity estimates reveal interspecific differences in the degree of diversification among populations that may be related to the different ecological requirements of the three species. [source] Genetic characterization by fluorescent AFLP of Pseudomonas savastanoi pv. savastanoi strains isolated from different host speciesPLANT PATHOLOGY, Issue 3 2007A. Sisto The genetic diversity of 71 Pseudomonas savastanoi pv. savastanoi strains isolated from different host species and from diverse geographical regions was determined by fluorescent amplified fragment length polymorphism (f-AFLP) analysis. The study was carried out using three different selective primer combinations. Strains of P. syringae pv. syringae, P. syringae pv. phaseolicola, P. syringae pv. glycinea, P. syringae pv. tagetis and P. amygdali were also included as outgroups. Based on cluster analysis of f-AFLP data, all P. savastanoi pv. savastanoi strains showed a high degree of similarity, grouping in a cluster and forming a taxon clearly separate from outgroup strains. AFLP analyses failed to support placing strains of P. savastanoi pv. savastanoi, P. syringae pv. phaseolicola and P. syringae pv. glycinea in the same species. Strains of P. savastanoi pv. savastanoi formed subclusters that correlated with the host species. Strains identified within these subclusters were related to the geographical region where the strains were isolated. Strains of P. savastanoi pv. savastanoi from olive were divided into two subclusters. Strains from oleander were differentiated from those from ash and were divided into two additional subclusters, distinct from olive strains. Three strains isolated from jasmine showed a high level of similarity among them but, at a lower Dice similarity coefficient, were linked to a subcluster including olive strains. Finally, two strains isolated from privet were similar to strains from olive and were included in the same subcluster. [source] Natural hybridization in Cardamine (Brassicaceae) in the Pyrenees: evidence from morphological and molecular dataBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2002KAROL MARHOLD FLS While researching Cardamine (Brassicaceae) in the Pyrenees, putative hybrid plants were found at two natural sites. Pollen grain viability, AFLP, and multivariate morphometric analyses were performed in order to assess the plants' presumed hybrid origin, establishing that natural hybridization between the diploids C. crassifolia and C. amara ssp. pyrenaea had occurred. A new diploid nothospecies, C.×enriquei (2n = 2x = 16), is described. Examination of 18 morphological characters showed the intermediacy of the hybrid between the parental taxa in most characters. AFLP analyses of C. amara ssp. amara, ssp. austriaca, ssp. olotensis and C. raphanifolia, demonstrated the close position of the hybrid to C. crassifolia, and revealed that the highest number of markers were shared with the parents. Polymorphism found in the AFLP pattern of the hybrid suggested recurrent origin, segregation and/or backcrosses, although assessment of pollen viability indicated high male sterility. The hybridization event reported here represents the second documented case between the C. pratensis group and C. amara. An account of the nomenclature of C. crassifolia is also presented, including lectotypification of relevant names. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society, 2002, 139, 275,294. [source] Comparison of phenotypic and genotypic markers for characterization of an outbreak of Salmonella serotype Havana in captive raptorsJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2003M.P. Reche Abstract Aims: To establish a typing method for tracing the epidemic relationship of 16 strains of Salmonella serotype Havana isolated from captive raptors showing no symptomatology and residing in a wildlife hospital in Spain. Methods and Results: Antimicrobial susceptibility testing, ribotyping, pulsed field gel electrophoresis (PFGE) and amplified fragment length polymorphism (AFLP) methodology were applied. Ten unrelated strains of serotype Havana were included as a control group to provide a basis of for the efficiency of the different markers used. All outbreak-related strains were resistant to nalidixic acid and streptomycin and showed the same ripotype, pulsotype and AFLP pattern. Conclusions: This is the first time that AFLP analysis has been tested with serotype Havana isolates and it has demonstrated to be the most useful epidemiological tool for discriminating between unrelated and outbreak-related strains of this serotype. The results obtained suggest that all the Salmonella serotype Havana isolates represented a common outbreak strain whose origin of contamination could not be established although it is thought that it was the poultry meat used for raptors'diet. Significance and Impact of the Study: Our study suggests the importance of microbiological analysis of these products in order to prevent contamination and dissemination of Salmonellae in this kind of Hospital. [source] Nestling sex ratios in a population of Bluethroats Luscinia svecica inferred from AFLPÔ analysisJOURNAL OF AVIAN BIOLOGY, Issue 1 2000S. Questiau We studied the sex ratio of Bluethroat Luscinia svecica broods using AFLPs. Our aim was to test whether there is a bias towards males that could be explained by sexual selection theories, or conversely, a bias towards females that could help explain the female-biased sex ratio among juveniles observed at a wintering site. The AFLP technique was reliable in sexing the nestlings from even small initial DNA quantities. Given the large number of polymorphic markers that can be obtained for each primer combination, the probability of detecting a W-chromosome-linked fragment is reasonably high. As a consequence, this method could be used in other species for sex-ratio studies and for other genetic purposes. Among 246 nestlings, we found an overall proportion of males of 50.8% at hatching and the sex-ratio variation using broods as independent units was not significantly different from expectation under a binomial distribution. None of the parental and environmental variables tested changed significantly the deviance to the model. Thus, sex determination in the Bluethroat seems to match the classical Mendelian model of a 1:1 sex ratio and cannot explain the biased sex ratio towards juvenile females found at the wintering site. [source] Genetic and chemical assessment of Arbequina olive cultivar grown in Córdoba province, ArgentinaJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 3 2009Mariela M Torres Abstract BACKGROUND: Thirty-eight accessions of olive (Olea europaea L.) originating from Córdoba province (Argentina) and preliminarily identified as belonging to the Arbequina variety were genotyped using AFLP (amplified fragment length polymorphism) DNA markers. Also, the oil chemical composition was studied during three consecutive crop years. The objectives of the work were (a) to investigate genetic intra-cultivar diversity and (b) to evaluate the oil chemical composition and compare it with that of Arbequina oil produced in Spain. RESULTS: The 19 primer combinations employed to perform the AFLP analysis produced 98 polymorphic bands. A reduced genetic heterogeneity was obtained, confirming that (a) the selected accessions belong to the Arbequina variety and (b) the traditional vegetative propagation practice has caused low genetic erosion in this variety cultivated in Córdoba. The main features that characterise the Argentinian Arbequina oils studied are the lower content of oleic acid and higher levels of phenolics and high-molecular-weight volatile compounds compared with those found in Spanish Arbequina oils. CONCLUSION: In spite of the small proportion of intra-cultivar variability, the Arbequina variety grown in Argentina produces oils with different chemical traits from those obtained in the original Spanish growing region. These differences can be attributed mainly to the particular environmental conditions of the olive-growing areas in these countries. Copyright © 2008 Society of Chemical Industry [source] Comparison of restriction enzyme analysis and amplified fragment length polymorphism typing of Porphyromonas gingivalis isolated from spousesMOLECULAR ORAL MICROBIOLOGY, Issue 6 2007M. C. Rijnsburger Introduction:, In the past, theories on the transmission of Porphyromonas gingivalis between individuals have been based on, among other techniques, restriction enzyme analysis (REA) of bacterial DNA. Currently, amplified fragment length polymorphism (AFLP) may be a more sophisticated alternative. The possibility of automatic pattern analysis and digital storage of the typing data enables the comparison of patterns from a large number of strains in a broad time frame. The aim of this study was to compare REA profiles with AFLP patterns of P. gingivalis strains isolated from periodontitis patients and their spouses. Methods: Forty-two P. gingivalis strains were isolated from different sites in the mouth from six adult patients with periodontitis and their spouses. DNA of the bacterial isolates was subjected to REA and AFLP analysis. Results:, One single type of P. gingivalis was found in each individual with both methods, regardless of the site of isolation. Indistinguishable types were found in four of the six couples with both techniques. Different types were found in two couples with both the REA and the AFLP method. Conclusions:, The AFLP typing technique confirms earlier observations on the transmission of P. gingivalis between spouses. This new technique can replace REA typing. [source] AFLP analysis of genetic variability among Stylosanthes guianensis accessions resistant and susceptible to the stylo anthracnosePLANT BREEDING, Issue 6 2005C.-S. Jiang Abstract Stylosanthes guianensis, belonging to the genus Stylosanthes, is one of the most important tropical forage legumes and is native to South and Central America and Africa. Anthracnose, caused by the fungus Colletotrichum gloeosporioides (Penz.) Sacc., is a major constraint to the extensive use of Stylosanthes as tropical forage. Forty-two accessions of S. guianensis were assessed with amplified fragment length polymorphism (AFLP) for genetic diversity and for resistance to anthracnose. In AFLP analysis, four selective primer combinations screened from 96 primer combinations were used to analyse these accessions, and a total of 225 clear bands were used for genetic similarity (GS) analysis, showing a 95.5% level of polymorphism on average. GS from 31.0% to 95.0% among the accessions was calculated with ntsys -pc software. The dendrogram was constructed with unweighted pair group method of averages (UPGMA) based on the AFLP data, and five clusters were defined at 48% GS. Two typical strains of C. gloeosporioides from Stylosanthes in China were used for anthracnose resistance screening. Most of the plant accessions showed variation in the reaction to two strains, and the correlation of resistance had a value of 0.904 (P < 0.01), suggesting common resistance to the two strains. The resistance accessions were randomly distributed in different groups of UPGMA clustering. These results demonstrate that AFLP analysis is an efficient method for evaluating the genetic diversity among S. guianensis accessions. [source] Molecular and agronomic evaluation of wheat doubled haploid lines obtained through maize pollination and anther culture methodsPLANT BREEDING, Issue 4 2003J. Guzy-Wrobelska Abstract Although maize pollination (MP) and anther culture (AC) are alternative techniques widely used for wheat doubled haploid (DH) production, there is only limited information on the attributes of the plant materials produced through both methods. This study was conducted to evaluate genetic fidelity, transmission of parental gametes, and to compare field performance of DH populations produced by the MP and AC methods from the F1s of two crosses between spring bread wheat cultivars. The DH populations were compared to single seed descent (SSD) lines created from the same crosses. In total, 76 MP and 122 AC lines of the cross between cultivars of divergent origin were subjected to RAPD and AFLP analysis. Only changes in AFLP banding patterns, at similarly low frequencies, 0.18% (MP) and 0.21% (AC), were detected. The frequency of the DH lines affected by the variation, 14.5% (MP) and 14.8% (AC), was similar in both populations. For most of the DH lines, variation in 1-2 loci only, out of several hundreds scored, was observed. A total of 14.3% (MP) and 22.2% (AC) marker loci showed the significant segregation distortion from the expected 1 : 1 ratio, but in at least one polymorphic locus the within-cultivar variation was responsible for the skewed segregation. The field performance of the corresponding MP and AC lines derived from two crosses confirmed the equivalency of both DH populations. In most of the traits analyzed, the MP and AC lines performed the same as the SSD populations created from the same crosses. No, or very small differences in means and ranges, were observed when the best 10% of the lines from all three methods were compared. Moreover, the best 10 % of the lines of the cross between Polish wheat cultivars adapted to the local environment performed significantly better for some traits than different groups of checks used in the study. [source] Assessment of genetic diversity in clover species from Sardinia, Italy, using AFLP analysisPLANT BREEDING, Issue 4 2003S. J. Bennett Abstract Two species, Trifolium glomeratum and T. nigrescens, from Sardinia, Italy, were analysed for genetic diversity using amplified fragment length polymorphism (AFLP). Variation between and within populations was compared between the inbreeder, T. glomeratum, and the outbreeder, T. nigrescens. Four AFLP primer combinations resulted in a total of 292 loci, of which 75% were polymorphic in T. glomeratum and 85% in Trifolium nigrescens. Variation was highest between populations in both species, but the difference between populations was greater in T. glomeratum (Fst = 0.17), compared with T. nigrescens (Fst = 0.02). Cluster analysis and principal coordinates analysis were used to verify the relationships found. The high level of genetic variation within populations in both species is attributed to the movement of sheep between paddocks, the existence of both species in Sardinia for thousands of years and the persistence of a long-lived seedbank due to the production of large numbers of small seeds with high levels of hard seededness. [source] Bacterial leaf blight of strawberry (Fragaria (x) ananassa) caused by a pathovar of Xanthomonas arboricola, not similar to Xanthomonas fragariae Kennedy & King.PLANT PATHOLOGY, Issue 6 2001Description of the causal organism as Xanthomonas arboricola pv. fragariae (pv. nov., comb. nov.) A new bacterial disease of strawberry is described. This disease, called bacterial leaf blight of strawberry, is characterized by dry, brown necrotic leaf spots and large brown V-shaped lesions along the leaf margin, midrib and major veins. Symptoms are different from angular leaf spot of strawberry caused by the bacterium Xanthomonas fragariae. Strains of the bacterial leaf blight pathogen were characterized in a polyphasic approach by biochemical tests, fatty acid analysis, protein electrophoresis, serology, PCR, pigment analysis, ice-nucleation activity, AFLP analysis, DNA:DNA hybridization, pathogenicity and host range tests, and compared with a number of reference strains of X. fragariae and other Xanthomonas species. Bacterial leaf blight strains formed a homogeneous group in all tests, completely different from X. fragariae. They were the only strains causing leaf blight of strawberry upon artificial inoculation into strawberry. Fatty acid and protein electrophoretic analysis showed that the strains belong to the phenon X. campestris (sensu latu, including pathovars now classified as belonging to X. arboricola). AFLP analysis and DNA:DNA hybridization further clarified their taxonomic position as belonging to X. arboricola. The name X. arboricola pv. fragariae is proposed for the bacterium causing leaf blight of strawberry with strain PD2780 (LMG 19145) as pathovar type strain. Criteria for routine identification are given and the taxonomic status is discussed. [source] Application of various DNA extraction methodologies on abalone, Haliotis midae, larvae and juveniles for fluorescent AFLP analysisAQUACULTURE RESEARCH, Issue 5 2007Daleen Badenhorst First page of article [source] | ||||||||||