scholarly journals Mapping RFLP loci in maize using B-A translocations.

Genetics ◽  
1989 ◽  
Vol 121 (3) ◽  
pp. 583-590 ◽  
Author(s):  
D Weber ◽  
T Helentjaris
Keyword(s):  
Zea Mays L ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Genetic Maps ◽  
Agarose Gels ◽  
Rflp Map ◽  
Genomic Dnas ◽  
Highly Correlated ◽  
Restriction Fragment Length

Abstract Plants hypoploid for specific segments of each of the maize (Zea mays L.) chromosomes were generated using 24 different B-A translocations. Plants carrying each of the B-A translocations were crossed as male parents to inbreds, and sibling progeny hypoploid or not hypoploid for specific chromosomal segments were recovered. Genomic DNAs from the parents, hypoploid progeny, and nonhypoploid (euploid or hyperploid) progeny for each of these B-A translocations were digested with restriction enzymes, electrophoresed in agarose gels, blotted onto reusable nylon membranes, and probed with nick-translated, cloned DNA fragments which had been mapped previously by restriction fragment length polymorphism (RFLP) analysis to the chromosome involved in the B-A translocation. The chromosomal segment on our RFLP map which was uncovered by each of the B-A translocations was determined. This work unequivocally identified the short and long arms of each chromosome on this map, and it also identified the region on each chromosome which contains the centromere. Because the breakpoints of the B-a translocations were previously known on the cytological and the conventional genetic maps, this study also allowed this RFLP map to be more highly correlated with these maps.

scholarly journals Identification of Pneumococcal Serotypes by PCR–Restriction Fragment Length Polymorphism

Diagnostics ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 196 ◽  
Author(s):  
García-Suárez ◽  
González-Rodríguez ◽  
Cima-Cabal ◽  
Yuste ◽  
Vazquez ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Dna Sequences ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Pcr Rflp ◽  
Restriction Fragment Length

Streptococcus pneumoniae shows more than 90 capsular serotypes that can be distinguished by their reactivity against antisera. The main objective of this work was the development of a molecular method for serotyping without the use of antisera. A computer program containing an algorithm was used to search in a database for potentially useful enzymes for Restriction Fragment Length Polymorphism-RFLP typing, in order to maximize the discrimination between different serotypes. DNA sequences of 90 serotypes for the region between dexB and aliA genes were compiled, and a computer screening of restriction enzymes was performed. The wzg–wzh–wzd–wze region and Sse9I restriction predicted unique PCR-RFLP patterns for 39 serotypes and eight serogroups. A second restriction enzyme resolved fragment specific patterns for 25 serotypes. The method was tested with 98 serotype-unknown clinical isolates. PCR-RFLP analysis deduced correct serotypes that were confirmed by Quellung reaction for 78.5% of the isolates.

scholarly journals Formation of Pseudo-Terminal Restriction Fragments, a PCR-Related Bias Affecting Terminal Restriction Fragment Length Polymorphism Analysis of Microbial Community Structure

2003 ◽  
Vol 69 (5) ◽  
pp. 2555-2562 ◽  
Author(s):  
Markus Egert ◽  
Michael W. Friedrich
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
16S Rrna ◽  
Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Restriction Fragments ◽  
Restriction Fragment Length

ABSTRACT Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified genes is a widely used fingerprinting technique in molecular microbial ecology. In this study, we show that besides expected terminal restriction fragments (T-RFs), additional secondary T-RFs occur in T-RFLP analysis of amplicons from cloned 16S rRNA genes at high frequency. A total of 50% of 109 bacterial and 78% of 68 archaeal clones from the guts of cetoniid beetle larvae, using MspI and AluI as restriction enzymes, respectively, were affected by the presence of these additional T-RFs. These peaks were called “pseudo-T-RFs” since they can be detected as terminal fluorescently labeled fragments in T-RFLP analysis but do not represent the primary terminal restriction site as indicated by sequence data analysis. Pseudo-T-RFs were also identified in T-RFLP profiles of pure culture and environmental DNA extracts. Digestion of amplicons with the single-strand-specific mung bean nuclease prior to T-RFLP analysis completely eliminated pseudo-T-RFs. This clearly indicates that single-stranded amplicons are the reason for the formation of pseudo-T-RFs, most probably because single-stranded restriction sites cannot be cleaved by restriction enzymes. The strong dependence of pseudo-T-RF formation on the number of cycles used in PCR indicates that (partly) single-stranded amplicons can be formed during amplification of 16S rRNA genes. In a model, we explain how transiently formed secondary structures of single-stranded amplicons may render single-stranded amplicons accessible to restriction enzymes. The occurrence of pseudo-T-RFs has consequences for the interpretation of T-RFLP profiles from environmental samples, since pseudo-T-RFs may lead to an overestimation of microbial diversity. Therefore, it is advisable to establish 16S rRNA gene sequence clone libraries in parallel with T-RFLP analysis from the same sample and to check clones for their in vitro digestion T-RF pattern to facilitate the detection of pseudo-T-RFs.

Mapping the anther culture response genes in maize (Zea mays L.)

Genome ◽  
1995 ◽  
Vol 38 (5) ◽  
pp. 968-975 ◽  
Author(s):  
V. H. Beaumont ◽  
T. R. Rocheford ◽  
J. M. Widholm
Keyword(s):  
Zea Mays ◽  
Anther Culture ◽  
Plant Hormone ◽  
Zea Mays L ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Culture Process ◽  
Anther Culture Response ◽  
Chromosome Regions ◽  
Restriction Fragment Length

In order to map the genes conditioning the induction of embryos during our anther culture process, we evaluated F2 plants from three different crosses for their anther culture ability and also performed RFLP analysis on these plants. The results showed that six chromosomal regions appear to be associated with the ability to induce embryo-like structures from maize microspores. These regions are located on chromosomes 1 (two regions), 3, 5, 7, and 8. Some of these chromosomes are identical to those found in previous studies and we have localized the regions more precisely. Notably, all chromosome regions identified, except one, are near viviparous mutant loci. Since the viviparous mutations are known to involve the plant hormone abscisic acid (ABA), these results suggest that ABA or its antagonist, gibberellic acid (GA3), might somehow be related to anther culture ability. We also propose some combinations of probes to screen for anther culture ability in the three genotypes studied.Key words: restriction fragment length polymorphism, anther culture, gene mapping, Zea mays L.

scholarly journals PROGRESS TOWARD DEVELOPMENT OF AN RFLP MAP FOR CUCUMBER

HortScience ◽  
1990 ◽  
Vol 25 (9) ◽  
pp. 1159a-1159 ◽  
Author(s):  
Wayne Kennard ◽  
Arian Dijkhuizen ◽  
Michael Havey ◽  
Jack Staub
Keyword(s):  
Genetic Linkage ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Cdna Libraries ◽  
Rflp Map ◽  
Map Construction ◽  
Large Numbers ◽  
Length Polymorphisms ◽  
Resistance Markers ◽  
Restriction Fragment Length

The analysis of genetic linkage in cucumber (Cucumis sativus has primarily involved morphological and disease resistance markers. Linkage analysis in cucumber would benefit from more markers. Restriction fragment length polymorphisms (RFLPs) can occur in relatively large numbers within a single segregating family. Research is presently underway to construct an RFLP map of cucumber. Pst I partial genomic and cDNA libraries of cucumber have been constructed as sources of probes for RFLP analysis. Cucumber DNA from 16 accessions of cucumber and one accession of C. sativus var. hardwickii were digested with either of two restriction enzymes (EcoR I and Hind III). This germplasm allows for the assessment of the variability for RFLPs in cucumber and will provide the parents for map construction.

scholarly journals Rhizoctonia spp. Recovered from Strawberry Roots in Central Coastal California

2000 ◽  
Vol 90 (4) ◽  
pp. 345-353 ◽  
Author(s):  
Frank N. Martin
Keyword(s):  
Polymerase Chain Reaction ◽  
Fragment Length Polymorphism ◽  
Coastal Region ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Molecular Techniques ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Collection Sites ◽  
Restriction Fragment Length

Rhizoctonia spp. were commonly recovered from the roots of strawberry plants growing in nonfumigated soil in the central coastal region of California. With the exception of one multinucleate isolate of R. solani (frequency of recovery of 0.8%), all other isolates were binucleate and were in anastomosis groups (AG) A, G, or I. AGs-A and -I were recovered from all five collection sites, whereas AG-G was recovered from only two sites. AG-A was the most commonly isolated AG, followed by AGs-I and -G. Similar levels of virulence were observed among the different AGs, but differences in virulence were observed among isolates in the same AG. Evaluating anastomosis grouping by pairing isolates recovered from strawberry with known tester isolates did not always yield a positive anastomosis reaction, even though both isolates anastomosed with other members of the same AG. Subsequent investigations with multiple isolates in the same AG from the same collection location confirmed that there was a lack of anastomosis or weak anastomosis reactions for some combinations of pairings, highlighting the need for to use multiple tester isolates or molecular techniques for AG determination. Restriction fragment length polymorphism (RFLP) analysis of a polymerase chain reaction-amplified region of the rDNA was effective for differentiating AGs. Sixteen RFLP groups were observed after cluster analysis with data for the size of the amplified products and fragment sizes after digestion with four restriction enzymes. Although each AG had isolates in multiple RFLP groups, any one individual RFLP group contained isolates of only a single AG. There was no consistent correlation between RFLP group and location of isolate collection.

scholarly journals Differentiation of porcine reproductive and respiratory syndrome virus European vaccine strains from Czech field isolates by restriction fragment length polymorphism analysis of ORF5 gene

2012 ◽  
Vol 47 (No. 10 - 11) ◽  
pp. 295-301 ◽  
Author(s):  
S. Indik ◽  
L. Valíček
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Respiratory Syndrome Virus ◽  
Field Isolates ◽  
Restriction Fragment Length

Restriction fragment length polymorphism (RFLP) analysis of open reading frame 5 was developed for typing of Czech strains of porcine reproductive and respiratory syndrome virus (PRRSV). The set of restriction enzymes Acc I, Hae II and SnaB I allowed the differentiation of heterogeneous Czech strains of PRRSV clustered separately in the phylogenetic tree. The high-passage strain V-502 (164) was also differentiated from its parent strain V-502. The same restriction enzymes could distinguish the European-type vaccine strains Porcilis PRRS and Pyrsvac-183, registered inCzechRepublic, from the Czech field isolates. The published ORF5 nucleotide sequences allowed us to presume that it will also be possible to distinguish most of European field strains from vaccine strains. PCR-based RFLP analysis can become a valuable tool in epidemiological studies of PRRSV inEurope.

scholarly journals Identification of Polymorphisms of the CSN2 Gene Encoding β-Casein in Greek Local Breeds of Cattle

2021 ◽  
Vol 8 (11) ◽  
pp. 257
Author(s):  
Dionysios Antonopoulos ◽  
Despina Vougiouklaki ◽  
George P. Laliotis ◽  
Theofania Tsironi ◽  
Irene Valasi ◽  
...  
Keyword(s):  
Fragment Length Polymorphism ◽  
Restriction Enzymes ◽  
The Other ◽  
Holstein Cows ◽  
Gene Encoding ◽  
Blood Samples ◽  
Agarose Gels ◽  
Detection And Identification ◽  
Pcr Product ◽  
Restriction Fragment Length

This research focused on the detection and identification of genetic polymorphisms in exon 7 of the β-casein CSN2 gene in blood samples from Greek Holstein cows and from local breeds of cattle, such as Vrachykeratiki, Katerinis, and Sykias. For this purpose, DNA was isolated from 780 blood samples obtained from Greek Holstein cows, 86 from three local breeds of cattle, namely Brachyceros, Katerinis, and Sykias, and 14 from Greek buffalo. The desired region of exon 7 was amplified by PCR, resulting in 121 and 251 bp products in bovine and buffalo samples. The PCR product was digested with restriction fragment length polymorphism (RFLP) on agarose gels. The restriction enzymes DdeI and TaqI were used. All of the blood samples had the amplified size. The results showed that 74.4% of the Greek Holstein cows had the A2A2 β-casein genotype, the three native breads Vrachykeratiki had 57.7%, and the other two had 100% of the A2A2 β-casein. From the 14 Greek buffalo ,100% had the A2A2 β-casein.

scholarly journals Autoscreening of Restriction Endonucleases for PCR-Restriction Fragment Length Polymorphism Identification of Fungal Species, with Pleurotus spp. as an Example

2007 ◽  
Vol 73 (24) ◽  
pp. 7947-7958 ◽  
Author(s):  
Zhi-Hui Yang ◽  
Ji-Xiang Huang ◽  
Yi-Jian Yao
Keyword(s):  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Fungal Species ◽  
Restriction Endonucleases ◽  
Its Sequences ◽  
Pcr Rflp ◽  
Average Coefficient ◽  
Identification Of Species ◽  
Restriction Fragment Length

ABSTRACT A molecular method based on PCR-restriction fragment length polymorphism (RFLP) analysis of internal transcribed spacer (ITS) ribosomal DNA sequences was designed to rapidly identify fungal species, with members of the genus Pleurotus as an example. Based on the results of phylogenetic analysis of ITS sequences from Pleurotus, a PCR-RFLP endonuclease autoscreening (PRE Auto) program was developed to screen restriction endonucleases for discriminating multiple sequences from different species. The PRE Auto program analyzes the endonuclease recognition sites and calculates the sizes of the fragments in the sequences that are imported into the program in groups according to species recognition. Every restriction endonuclease is scored through the calculation of the average coefficient for the sequence groups and the average coefficient for the sequences within a group, and then virtual electrophoresis maps for the selected restriction enzymes, based on the results of the scoring system, are displayed for the rapid determination of the candidate endonucleases. A total of 85 haplotypes representing 151 ITS sequences were used for the analysis, and 2,992 restriction endonucleases were screened to find the candidates for the identification of species. This method was verified by an experiment with 28 samples representing 12 species of Pleurotus. The results of the digestion by the restriction enzymes showed the same patterns of DNA fragments anticipated by the PRE Auto program, apart from those for four misidentified samples. ITS sequences from 14 samples (of which nine sequences were obtained in this study), including four originally misidentified samples, confirmed the species identities revealed by the PCR-RFLP analysis. The method developed here can be used for the identification of species of other living microorganisms.

A variable minisatellite sequence in the chloroplast genome of Sorbus L. (Rosaceae: Maloideae)

Genome ◽  
2002 ◽  
Vol 45 (3) ◽  
pp. 570-576 ◽  
Author(s):  
R Andrew King ◽  
Colin Ferris
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Chloroplast Genome ◽  
Length Polymorphism ◽  
Sequence Variation ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Chloroplast Microsatellites ◽  
Sorbus Aucuparia ◽  
Pcr Product ◽  
Restriction Fragment Length

The chloroplast genome is now known to be more variable than was once thought. Reports of RFLP (restriction fragment length polymorphism) and sequence variation, as well as variation in chloroplast microsatellites, are common. Here, data are presented on the variability of a minisatellite sequence in the chloroplast genome of Sorbus species. RFLP analysis of a PCR product comprising the region between the trnM and rbcL genes of nine Sorbus species identified seven size variants. Sequencing revealed the observed size polymorphism to be due to differences in the number of copies of an imperfect 9-bp motif. A more intensive survey of the variability of the minisatellite was undertaken in populations of Sorbus aucuparia. The potential uses of such regions in chloroplast DNA are discussed and a possible mechanism for the evolution of the minisatellite is presented.Key words: atpE, homoplasy, microsatellite, rowan, VNTR.

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