scholarly journals Evaluation of genetic stability in olive callus-induced and meristem-induced shoots using flow cytometry and amplified fragment length polymorphism techniques

Plant Methods ◽  
2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Leila Mirzaei ◽  
Abbas Yadollahi ◽  
Maryam Jafarkhani Kermani ◽  
Masoud Naderpour ◽  
Ali Asghar Zeinanloo ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Stability ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Growth Indices ◽  
Axillary Shoots ◽  
Olive Cultivars

Abstract Background In vitro culture of olive, as an economically valuable tree, has fundamentally a genotype-dependant low micropropagation rate which needs to be improved in already established and newly released cultivars. Various plant tissue culture media, planting systems and growth factors were evaluated in two promissing Iranian olive cultivars ˈAminˈ and ˈMeshkatˈ and the commercial Spanish cultivar ˈArbequinaˈ. Results The results showed that cultivars have their specific optimal media, i.e. ˈAminˈ in the MS with 4 mg/L zeatin, ˈArbequinaˈ in the OM with 1 mg/L zeatin, and ˈMeshkatˈ in the OM and MS with 2 mg/L zeatin, which produced significantly a higher number of axillary shoots than other media. The results also indicated a significant improvement in the growth indices of ˈAminˈ (number of axillary shoots) when cultured using periodical mini bioreactor (PMB) in the VS medium. In comparison with VS, OM did not reveal any significant differences when both culturing systems (PMB and semi-solid media (SSM)) were used. Regarding the effect of carbon source and light intensity, mannitol and 2000 cd sr m−2 greatly enhanced ˈArbequinaˈ growth indices (main shoot length and growth quality). The results of genetic stability of callus induced shoots (CIS) and meristem induced shoots (MIS) revealed that 2C DNA value assessed by partec flow cytometery (FCM) had 0.01, 0.03 and 0.08 pg discrepencies in ˈAminˈ, ˈArbequinaˈ and ˈMeshkatˈ, repectively. The Amplified Fragment Length Polymorphism (AFLP) results also indicated that the cultivars were classified regardless of the micropropagation origin (CIS or MIS), except for ˈArbequinaˈ. The AFLP findings showed that ˈArbequinaˈ had the highest dispersal (7–38%) in CIS and MIS, while the Iranian cultivar of ˈMeshkatˈ (5–9%) had the highest stability. Conclusions This study indicated the importance of in vitro growth parameters for improving the micropropagation indices of olive cultivars. It showed that optimized protocols (OM, PMB, zeatin, mannitol and 2000 cd sr m−2) co-produced larger calli resulting in indirect organogenesis. Based on FCM and AFLP analysis, it can be concluded that true-to-typeness of micropropagated olive was cultivar-dependent.

scholarly journals Evaluation of Genetic Stability in Olive Callus-induced and Meristem-induced Shoots using Flow Cytometry and Amplified Fragment Length Polymorphism Techniques

2020 ◽  
Author(s):  
Leila Mirzaei ◽  
Abbas Yadollahi ◽  
Maryam Jafarkhani Kermani ◽  
Masoud Naderpour ◽  
Ali Asghar Zeinanloo ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Genetic Stability ◽  
Fragment Length Polymorphism ◽  
Culture Media ◽  
Carbon Sources ◽  
Amplified Fragment Length Polymorphism ◽  
Dna Amount ◽  
Indirect Organogenesis

Abstract BackgroundIn vitro culture of olive, as an economically valuable tree, has fundamentally genotype-dependant low micropropagation rate which need to be improved in already established cultivars, while needing to be struggled in firstly considered cultivars. Various plant tissue culture media, planting systems and growth factors were evaluated in two promissing Iranian olive cultivars ˈAminˈ and ˈMeshkatˈ plus a commercial Spanish cultivar ˈArbequinaˈ. ResultsThe results showed that in ˈAminˈ cultivar MS enriched with zeatin (4 mg/L), in ˈArbequinaˈ cultivar OM enriched with zeatin (1 mg/L) and in ˈMeshkatˈ cultivar OM and MS enriched with zeatin (2 mg/L) produced reasonably healthier in vitro plantlets. The results indicated that using Periodical Mini Bioreactor (PMB) system in the presence of VS medium in ˈAminˈ cultivar resulted in growth indicies amelioration compared to semi-solid media. Regarding carbon sources and light intensities, mannitol and 2000 cd·sr·m-² greatly enhancedˈArbequinaˈ growth indices. The genetic stability of callus induced shoots (CIS) was compared with meristem induced shoots (MIS) using Amplified Fragment Length Polymorphism (AFLP) marker and flow cytometery (FCM). The results revealed that 2C DNA value assessed by partec FCM was mostly depended on the cultivars rather than the origin of generation -callus or meristem-. The AFLP results also showed that the cultivars were classified regardless of the micropropagation origin (CIS or MIS), except for ˈArbequinaˈ. However, ˈArbequinaˈ CIS and MIS still had 62- 80% of genetic similarity with three other categories and the highest resemblance (97%) was seen with MIS of ˈAminˈ cultivar. ConclusionsBriefly,olive in vitro propagation optimization co-produced large volume and percent of calli resulting in more undesired indirect organogenesis. True to typeness of CIS was assessed showing that no changes in DNA amount occurred. Nonetheless, in phylogenetic analysis cultivars were clustered separately even some discrepancies were seen in ˈArbequinaˈ MIS and CIS, however, ˈAminˈ and ˈMeshkatˈ cultivars were more stable in clustering.

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.

scholarly journals Amplified fragment length polymorphism analysis of Mycobacterium avium complex isolates recovered from southern California

2007 ◽  
Vol 56 (9) ◽  
pp. 1152-1160 ◽  
Author(s):  
Stacy L. Pfaller ◽  
Timothy W. Aronson ◽  
Alan E. Holtzman ◽  
Terry C. Covert
Keyword(s):  
Mycobacterium Avium ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Southern California ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Amplified Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Environmental Isolates

Fine-scale genotyping methods are necessary in order to identify possible sources of human exposure to opportunistic pathogens belonging to the Mycobacterium avium complex (MAC). In this study, amplified fragment length polymorphism (AFLP) analysis was evaluated for fingerprinting 159 patient and environmental MAC isolates from southern California. AFLP analysis accurately identified strains belonging to M. avium and Mycobacterium intracellulare and differentiated between strains within each species. The method was also able to differentiate strains that were presumed to be genetically identical in two previous studies using large RFLP analysis with PFGE, or PCR-amplification of DNA segments located between insertion sequences IS1245 and IS1311. For M. avium, drinking-water isolates clustered more closely with each other than with patient or food isolates. Patient isolates were more genetically diverse. None of the environmental isolates shared identical AFLP patterns with patient isolates for either species. There were, however, environmental isolates that shared identical patterns, and patient isolates that shared identical patterns. A subset of the isolates, which are referred to as MX isolates due to their ambiguous identification with the Gen-Probe system, produced AFLP patterns similar to those obtained from M. intracellulare isolates. Sequence analysis of 16S rDNA obtained from the MX isolates suggests that they are strains of M. intracellulare that were not correctly identified by the M. intracellulare AccuProbe from Gen-Probe.

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