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Journal articles on the topic 'RFLP analysis'

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Published: 4 June 2021
Last updated: 4 February 2022

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1

Trevisan, Giovani, Aditi Sharma, Phillip Gauger, Karen M. Harmon, Jianqiang Zhang, Rodger Main, Michael Zeller, Leticia C. M. Linhares, and Daniel C. L. Linhares. "PRRSV2 genetic diversity defined by RFLP patterns in the United States from 2007 to 2019." Journal of Veterinary Diagnostic Investigation 33, no. 5 (June 28, 2021): 920–31. http://dx.doi.org/10.1177/10406387211027221.

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The genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV) increases over time. In 1998, restriction-fragment length polymorphism (RFLP) pattern analysis was introduced to differentiate PRRSV wild-type strains from VR2332, a reference strain from which a commercial vaccine (Ingelvac PRRS MLV) was derived. We have characterized here the PRRSV genetic diversity within selected RFLP families over time and U.S. geographic space, using available ISU-VDL data from 2007 to 2019. The 40,454 ORF5 sequences recovered corresponded to 228 distinct RFLPs. Four RFLPs [2-5-2 (21.2%), 1-7-4 (15.6%), 1-4-4 (11.8%), and 1-8-4 (9.9%)] represented 58.5% of all ORF5 sequences and were used for cluster analysis. Over time, there was increased detection of RFLPs 2-5-2, 1-7-4, 1-3-4, 1-3-2, and 1-12-4; decreased detection of 1-4-2, 1-18-4, 1-18-2, and 1-2-2; and different detection trends for 1-8-4, 1-4-4, 1-26-1, 1-22-2, and 1-2-4. An over-time cluster analysis revealed a single cluster for RFLP 2-5-2, supporting that sequences within RFLP 2-5-2 are still relatively conserved. For 1-7-4, 1-4-4, and 1-8-4, there were multiple clusters. State-wise cluster analysis demonstrated 4 main clusters for RFLP 1-7-4 and 1-8-4, and 6 for RFLP 1-4-4. For the other RFLPs, there was a significant genetic difference within them, particularly between states. RFLP typing is limited in its ability to discriminate among different strains of PRRSV. Understanding the magnitude of genetic divergence within RFLPs helps develop PRRSV regional control programs, placement, herd immunization strategies, and design of appropriate animal movements across borders to minimize the risk of PRRSV transmission.
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2

Deynze, A. E. Van, B. S. Landry, and K. P. Pauls. "The identification of restriction fragment length polymorphisms linked to seed colour genes in Brassica napus." Genome 38, no. 3 (June 1, 1995): 534–42. http://dx.doi.org/10.1139/g95-069.

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Restriction fragment length polymorphisms (RFLPs) linked to genes controlling seed colour were identified in rapeseed (Brassica napus). The efficiency of the RFLP analysis was enhanced by utilizing bulked segregant analysis, DNA clones that had previously been used to construct a RFLP map of B. napus, and a doubled-haploid (DH) population segregating for seed colour. Markers for two of the three seed colour genes segregating in the DH population were identified on the basis of χ2 analyses of marker distributions among visually classified black-, brown-, and yellow-seeded DH lines as well as ANOVA and quantitative trait locus analysis of light-reflectance measurements from seeds of the DH lines. The RFLP markers linked to seed colour that were identified in the present study will allow breeding strategies based on genotype selection to be developed for seed colour in rapeseed.Key words: RFLP markers, seed colour genes, rapeseed.
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3

Hulbert, S. H., T. W. Ilott, E. J. Legg, S. E. Lincoln, E. S. Lander, and R. W. Michelmore. "Genetic analysis of the fungus, Bremia lactucae, using restriction fragment length polymorphisms." Genetics 120, no. 4 (December 1, 1988): 947–58. http://dx.doi.org/10.1093/genetics/120.4.947.

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Abstract Restriction fragment length polymorphisms (RFLPs) were developed as genetic markers for Bremia lactucae, the biotrophic Oomycete fungus which causes lettuce downy mildew. By using 55 genomic and cDNA probes, a total of 61 RFLP loci were identified among three heterothallic isolates of B. lactucae. Of these 61 RFLP loci, 53 were heterozygous in at least one of the three strains and thus were informative for linkage analysis in at least one of two F1 crosses that were performed. Analysis of the cosegregation of these 53 RFLPs, eight avirulence loci and the mating type locus allowed the construction of a preliminary genetic linkage map consisting of 13 small linkage groups. Based on the extent of linkage detected among probes, the genome of B. lactucae can be estimated to be approximately 2000 cM. Linkage was detected between a RFLP locus and an avirulence gene, providing a potential starting point for chromosome walking to clone an avirulence gene. The high frequency of DNA polymorphism in naturally occurring isolates and the proper Mendelian segregation of loci detected by low copy number probes indicates that it will be possible to construct a detailed genetic map of B. lactucae using RFLPs as markers. The method of analysis employed here should be applicable to many other outbreeding, heterozygous species for which defined inbred lines are not available.
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4

Garcia, G. M., H. T. Stalker, and G. Kochert. "Introgression analysis of an interspecific hybrid population in peanuts (Arachis hypogaea L.) using RFLP and RAPD markers." Genome 38, no. 1 (February 1, 1995): 166–76. http://dx.doi.org/10.1139/g95-021.

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Forty-six introgression lines (F10C9) from a cross between Arachis hypogaea L. (2n = 4x = 40) and A. cardenasii Krapov. &W.C. Gregory (2n = 2x = 20) were analyzed for the introgression of A. cardenasii chromosome segments. Seventy-three RFLP probes and 70 RAPD primers, expressing from one to four A. cardenasii-specific bands, were used to evaluate the set of introgression lines. Thirty-four RFLP probes and 45 RAPD primers identified putative A. cardenasii introgressed chromosome segments in one or more lines. Introgressed segments were detected by RFLP analysis in 10 of the 11 linkage groups; the smallest introgressed fragments were detected by single RFLP markers and the largest were detected by three or four adjacent markers and represented introgressed segments of 30–40 cM. Similar results were obtained with RAPD markers, although markers detecting introgressed fragments could not be placed on the peanut linkage map. Introgression into both A. hypogaea genomes was detected and its implication in breeding for disease resistance is discussed.Key words: peanut, Arachis hypogaea, Arachis cardenasii, RFLPs, RAPDs, introgression, reciprocal recombination, translocation, alien gene transfer, wide cross.
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5

Waleron, M., K. Waleron, and E. Łojkowska. "Genotypic characterisation of the Erwinia genus by PCR-RFLP analysis of rpoS gene." Plant Protection Science 38, SI 2 - 6th Conf EFPP 2002 (December 31, 2017): 288–90. http://dx.doi.org/10.17221/10470-pps.

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Genotypic characterisation of the members of the genus Erwinia, based on the PCR-RFLP analysis of a fragment of the rpoS gene was done. PCR primers deduced from described rpoS gene sequences of E. carotovora allowed the amplification of about 880 bp DNA fragments from all tested Erwinia species. The rpoS fragments, amplified from 20 species of the studied Erwinia genus, were compared by RFLP analysis with 4 enzymes (AluI, Hin6I, HinfI, and Tru1I). Restriction analysis allowed drawing 63 common profiles of RFLP products for all tested Erwinia. From 1 to 3 specific RFLP profiles were identified among most of the species tested. However, in two cases: E. chrysanthemi and E. c. subsp. carotovora 15 and 20 specific RFLP groups were detected, respectively. High variability of genetic profiles of the E. chrysanthemi and E. c. subsp. carotovora can be explained by the wide spectrum of plants, which they infect. The results indicated that rpoS PCR-RFLP analysis is a useful tool for identification of species and subspecies belonging to the former Erwinia genus, as well as for differentiation of strains within E. c. subsp. carotovora and E. chrysanthemi.
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6

Ozbes, G., Ertas HB, and A. Muzo. "Restriction fragment length polymorphism analysis of isolates of infectious bursal disease viruses from Turkey." Veterinární Medicína 48, No. 12 (March 30, 2012): 359–62. http://dx.doi.org/10.17221/5790-vetmed.

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Infectious bursal disease Virus (IBDV) specific reverse transcriptase/polymerase chain recation (RT/PCR) positive 40 broiler bursa fabricius samples obtained from a commercially reared flock were investigated for genetic diversity by PCR-RFLP assay. The assay amplifies a 743 bp fragment of the IBDV VP2 gene. The RFLP profiles of 40 of these positive samples were determined using the enzyme MboI. Most of the viruses had the same RFLP with the MboI enzyme. RFLP analysis of the isolates produced two different band profiles. The results of this study showed that little genetic heterogeneity exists among IBDV strains in a infected flock.
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7

Seldin, M. F., H. C. Morse, J. P. Reeves, C. L. Scribner, R. C. LeBoeuf, and A. D. Steinberg. "Genetic analysis of autoimmune gld mice. I. Identification of a restriction fragment length polymorphism closely linked to the gld mutation within a conserved linkage group." Journal of Experimental Medicine 167, no. 2 (February 1, 1988): 688–93. http://dx.doi.org/10.1084/jem.167.2.688.

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A linkage map of distal mouse chromosome 1 was generated using restriction fragment length polymorphism (RFLP) analysis of DNA prepared from 95 [C3H-gld/gld X Mus spretus)F1 X C3H-gld/gld] backcross mice. The gene order was: (centromere) C4bp, Ren-1,2, Ly-5, [At-3/gld], Apoa-2/Ly-17, Spna-1 (telomere). All mice expressing the phenotype of gld homozygotes were homozygous for the At-3 RFLP characteristic of C3H mice and none of the mice heterozygous for At-3 RFLPs had characteristics of gld homozygotes, demonstrating close linkage between these genes. The identification of an RFLP closely linked to the gld gene provides a starting point for the identification of a genetic defect that results in abnormal T cells and autoimmune disease.
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8

Kennard, Wayne, Arian Dijkhuizen, Michael Havey, and Jack Staub. "PROGRESS TOWARD DEVELOPMENT OF AN RFLP MAP FOR CUCUMBER." HortScience 25, no. 9 (September 1990): 1159a—1159. http://dx.doi.org/10.21273/hortsci.25.9.1159a.

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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.
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9

Noli, Enrico, Silvio Salvi, and Roberto Tuberosa. "Comparative analysis of genetic relationships in barley based on RFLP and RAPD markers." Genome 40, no. 5 (October 1, 1997): 607–16. http://dx.doi.org/10.1139/g97-080.

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Genetic relationships have seldom been analyzed with different types of molecular markers in order to compare the information provided by each marker class. We investigated genetic relationships among nine barley cultivars using separate cluster analyses based on restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNAs (RAPDs). Genomic DNA restricted with three enzymes and hybridized with 68 probes revealed 415 RFLPs (74.2% of all bands). Among the 128 primers used for RAPD analysis, 100 provided a reproducible profile, 89 of which revealed 202 polymorphic and 561 monomorphic bands (26.5 and 73.5%, respectively). A nonrandom distribution of 62 RAPDs with a tendency to cluster near centromeric regions was produced when these RAPDs were mapped using 76 doubled-haploid lines derived from a cross between two of the nine cultivars. The correlation between the RFLP and RAPD similarity matrices computed for the 36 pairwise comparisons among the nine cultivars was equal to 0.83. The dendrograms obtained by cluster analyses of the RFLP and RAPD data differed. These results indicate that in barley the information provided by RFLPs and RAPDs is not equivalent, most likely as a consequence of the fact that the two marker classes explore, at least in part, different portions of the genome.Key words: Hordeum vulgare L., genetic distance, molecular markers, cluster analysis.
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10

Jackson, C. J., A. J. Fox, D. R. A. Wareing, D. N. Hutchinson, and D. M. Jones. "The application of genotyping techniques to the epidemiological analysis ofCampylobacter jejuni." Epidemiology and Infection 117, no. 2 (October 1996): 233–44. http://dx.doi.org/10.1017/s0950268800001400.

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SummaryCampylobacter jejuniserogroup reference strains and collections of sporadic and outbreak- associated isolates were examined for restriction fragment length polymorphisms (RFLPs), usingC. jejunirandom chromosomal and 16S rRNA gene probes. A collection of 48 Penner (HS) and 14 Lior (HL) serogroup reference strains, plus 10 clinical isolates, generated 35 RFLP and 26 ribotype patterns. In combination the two loci generated 48 distinct genotypes. Both probes were able to differentiate between certain random isolates of the same HS/HL serogroups but greater discrimination was obtained with RFLP than with ribotyping. Genotyping distinguished accurately between related and unrelated strains when applied to several outbreaks. Genotypic analysis ofC. jejuniby restriction fragment length polymorphisms is a valuable technique for epidemiological typing. Chromosomal variation detected by the two unlinked probe loci provides some information about the genetic relationship between isolates.
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11

Reed, Elaine, Peter McManus, and Nicole Suciu-Foca. "RFLP analysis of HLA-DR5 haplotypes." Tissue Antigens 37, no. 2 (February 1991): 66–73. http://dx.doi.org/10.1111/j.1399-0039.1991.tb01847.x.

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12

MOLNAR, STEPHEN J., ROGER WHEATCROFT, and GEORGE FEDAK. "RFLP analysis of Hordeum species relationships1." Hereditas 116 (February 14, 2008): 87–91. http://dx.doi.org/10.1111/j.1601-5223.1992.tb00804.x.

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13

MOLNAR, STEPHEN J., ROGER WHEATCROFT, and GEORGE FEDAK. "RFLP analysis of Hordeum species relationships1." Hereditas 116, no. 1-2 (February 14, 2008): 87–91. http://dx.doi.org/10.1111/j.1601-5223.1992.tb00209.x.

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14

Scholz, Holger Christian, Angela Witte, Herbert Tomaso, Sascha Al Dahouk, and Heinrich Neubauer. "Genotyping ofChromobacterium violaceumisolates byrecAPCR-RFLP analysis." FEMS Microbiology Letters 244, no. 2 (March 2005): 347–52. http://dx.doi.org/10.1016/j.femsle.2005.02.005.

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15

Pourzand, Charareh, and Peter Cerutti. "Genotypic mutation analysis by RFLP/PCR." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 288, no. 1 (July 1993): 113–21. http://dx.doi.org/10.1016/0027-5107(93)90213-y.

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16

Noreen, H. J., M. L. Davidson, E. A. van der Hagen, and M. Segall. "Heterogeneity of HLA-DR5: RFLP analysis." Human Immunology 23, no. 2 (January 1988): 127. http://dx.doi.org/10.1016/0198-8859(88)90217-0.

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17

Pecorara, M., L. Casarino, PG Mori, M. Morfini, G. Mancuso, AM Scrivano, E. Boeri, AC Molinari, R. De Biasi, and N. Ciavarella. "Hemophilia A: carrier detection and prenatal diagnosis by DNA analysis." Blood 70, no. 2 (August 1, 1987): 531–35. http://dx.doi.org/10.1182/blood.v70.2.531.531.

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Abstract In this study, we used DNA polymorphisms for carrier detection and prenatal diagnosis of hemophilia A in a large group of Italian families. The restriction fragment length polymorphisms (RFLPs) investigated were the intragenic polymorphic Bc/I site within the factor VIII gene; the extragenic multiallelic Taq I system at the St14 locus; and the extragenic Bg/II site at the DX13 locus. The factor VIII probe was informative in 30%, St14 in 82%, and DX13 in 60% of obligate carriers. The combination of factor VIII-Bc/I and St14-Taq I showed that 91% of obligate carriers were heterozygotes for one or both; with all three probes, only 4% of obligate carriers were noninformative. In families clearly segregating for hemophilia A, RFLP analysis allowed us to define the carrier status for the hemophilia A gene in all 27 women tested. RFLP analysis allowed us to exclude the carrier status in 39 of 45 female relatives of sporadic patients. The combination of RFLP analysis and biological assay of factor VIII allowed us to identify a de novo mutation in the maternal grandfather in 7 of 12 of the families with sporadic cases, for which members of three generations were available for study. Nine of 10 couples requesting prenatal diagnosis provided informative RFLP DNA pattern. Carrier status was excluded in two women, two fetuses were shown to be female, and prenatal diagnosis was carried out in five pregnancies by DNA analysis. Prenatal testing was successful in three instances and failed in two because a sufficient amount of chorionic villous DNA was not obtained for the analysis.
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18

Pecorara, M., L. Casarino, PG Mori, M. Morfini, G. Mancuso, AM Scrivano, E. Boeri, AC Molinari, R. De Biasi, and N. Ciavarella. "Hemophilia A: carrier detection and prenatal diagnosis by DNA analysis." Blood 70, no. 2 (August 1, 1987): 531–35. http://dx.doi.org/10.1182/blood.v70.2.531.bloodjournal702531.

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In this study, we used DNA polymorphisms for carrier detection and prenatal diagnosis of hemophilia A in a large group of Italian families. The restriction fragment length polymorphisms (RFLPs) investigated were the intragenic polymorphic Bc/I site within the factor VIII gene; the extragenic multiallelic Taq I system at the St14 locus; and the extragenic Bg/II site at the DX13 locus. The factor VIII probe was informative in 30%, St14 in 82%, and DX13 in 60% of obligate carriers. The combination of factor VIII-Bc/I and St14-Taq I showed that 91% of obligate carriers were heterozygotes for one or both; with all three probes, only 4% of obligate carriers were noninformative. In families clearly segregating for hemophilia A, RFLP analysis allowed us to define the carrier status for the hemophilia A gene in all 27 women tested. RFLP analysis allowed us to exclude the carrier status in 39 of 45 female relatives of sporadic patients. The combination of RFLP analysis and biological assay of factor VIII allowed us to identify a de novo mutation in the maternal grandfather in 7 of 12 of the families with sporadic cases, for which members of three generations were available for study. Nine of 10 couples requesting prenatal diagnosis provided informative RFLP DNA pattern. Carrier status was excluded in two women, two fetuses were shown to be female, and prenatal diagnosis was carried out in five pregnancies by DNA analysis. Prenatal testing was successful in three instances and failed in two because a sufficient amount of chorionic villous DNA was not obtained for the analysis.
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19

Vinay, Oraon, Prasad Bhupendra, and Singh Kiran. "16S rDNA-RFLP analysis of phylogenetic tree of Rhizobium bacteria." Indian Journal of Applied Research 3, no. 12 (October 1, 2011): 474–76. http://dx.doi.org/10.15373/2249555x/dec2013/145.

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20

NENENG, Liswara, Rudy Agung NUGROHO, Yukio KOMAI, Naru TAKAYAMA, and Koji KAWAMURA. "Water Quality Measurements with a Simple Molecular Analysis (PCR-RFLP) of the Microbiome in a Metropolitan River System in Japan." Walailak Journal of Science and Technology (WJST) 17, no. 3 (July 22, 2019): 257–68. http://dx.doi.org/10.48048/wjst.2020.5869.

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Urbanization has affected natural freshwater environments by contamination with sewage, toxic chemicals, and excess nutrients, which cause algal bloom, pollution, and ecosystem degradation. To ensure sustainable use of natural waters, appropriate monitoring methods are required. This study aims to investigate the diversity of the microbial community in a metropolitan river system in Japan using a low-cost DNA-based approach, PCR (Polymerase Chain Reaction)-RFLP (Restriction Fragment Length Polymorphism), as a potential bioindicator of environmental change. Surface waters were sampled in seven sites in a river system. Water chemical parameters and concentrations of heavy metals were determined. Microbial DNA was extracted from the samples, ribosomal RNA was amplified with universal primers, and RFLP was scored by agarose gels. Water chemical analyses showed that surface water at the inflow point of a sewage treatment plant had signs of eutrophication. Heavy metal concentrations in surface water were low (< 0.01 ppm) in all sites. The PCR-RFLP analysis showed polymorphisms both in 16S and 18S rRNAs, indicating that the method can detect at least a part of the microbiome changes in a river system. Sequencing of some fragments found the sequence close to a ciliate isolated in wastewater treatment plants, implying contamination from sewage. Principal component analysis (PCA) identified the RFLPs associated with chemical water parameters, which could be bioindicators of environmental pollution. We also found the RFLPs independent of water quality parameters, suggesting that this simple DNA-based analysis can also detect biological changes in water ecosystems that are not quantified by chemical measurements of water quality.
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21

Molnar, S. J., and A. McKay. "Restriction fragment analysis of hordein genes in western Canadian two-rowed barleys." Canadian Journal of Plant Science 75, no. 1 (January 1, 1995): 191–93. http://dx.doi.org/10.4141/cjps95-033.

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Restriction fragment length polymorphisms (RFLP) at the hordein loci were compared with hordein protein patterns for discrimination of barley cultivars. RFLP banding patterns documented extensive polymorphism for B and C hordein gene families in eight closely related western Canadian two-rowed barley cultivars, five parental cultivars and a U.K. cultivar. RFLP results were compared with published protein pattern data on the same cultivars. The power to discriminate cultivars by the two methods is similar. Key words: RFLP, hordein, barley, Hordeum vulgare, cultivar identification
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22

Clemans, Daniel L., Carl F. Marrs, Mayuri Patel, Michelle Duncan, and Janet R. Gilsdorf. "Comparative Analysis of Haemophilus influenzae hifA(Pilin) Genes." Infection and Immunity 66, no. 2 (February 1, 1998): 656–63. http://dx.doi.org/10.1128/iai.66.2.656-663.1998.

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ABSTRACT Adherence of Haemophilus influenzae to epithelial cells plays a central role in colonization and is the first step in infection with this organism. Pili, which are large polymorphic surface proteins, have been shown to mediate the binding of H. influenzae to cells of the human respiratory tract. Earlier experiments have demonstrated that the major epitopes of H. influenzae pili are highly conformational and immunologically heterogenous; their subunit pilins are, however, immunologically homogenous. To define the extent of structural variation in pilins, which polymerize to form pili, the pilin genes (hifA) of 26 type a to f and 16 nontypeable strains of H. influenzae were amplified by PCR and subjected to restriction fragment length polymorphism (RFLP) analysis with AluI and RsaI. Six different RFLP patterns were identified. Four further RFLP patterns were identified from published hifA sequences from five nontypeableH. influenzae strains. Two patterns contained only nontypeable isolates; one of these contained H. influenzaebiotype aegyptius strains F3031 and F3037. Another pattern contained predominantly H. influenzae type f strains. All other patterns were displayed by a variety of capsular and noncapsular types. Sequence analysis of selected hifA genes confirmed the 10 RFLP patterns and showed strong identity among representatives displaying the same RFLP patterns. In addition, the immunologic reactivity of pili with antipilus antisera correlated with the groupings of strains based on hifA RFLP patterns. Those strains that show greater reactivity with antiserum directed againstH. influenzae type b strain M43 pili tend to fall into one RFLP pattern (pattern 3); while those strains that show equal or greater reactivity with antiserum directed against H. influenzae type b strain Eagan pili tend to fall in a different RFLP pattern (pattern 1). Sequence analysis of representative HifA pilins from typeable and nontypeable H. influenzaeidentified several highly conserved regions that play a role in bacterial pilus assembly and other regions with considerable amino acid heterogeneity. These regions of HifA amino acid sequence heterogeneity may explain the immunologic diversity seen in intact pili.
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23

Prince, James P., Vincent K. Lackney, Carmichael Angeles, James R. Blauth, and Molly M. Kyle. "A survey of DNA polymorphism within the genus Capsicum and the fingerprinting of pepper cultivars." Genome 38, no. 2 (April 1, 1995): 224–31. http://dx.doi.org/10.1139/g95-027.

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Interspecific genetic variation was examined in the genus Capsicum based on shared restriction fragments in Southern analyses. Four distinct clusters were delineated among 21 accessions of cultivated and wild pepper (C. annuum, C. baccatum, C. chacoense, C. chinense, and C. frutescens). Three tight clusters comprised of accessions belonging to C. annuum, C. frutescens, and C. baccatum, respectively, were formed, along with a fourth cluster comprised of one accession each of C. chinense and C. chacoense. All accessions were differentiated by this technique, and the clusters corresponded closely to previous morphology-based classification. Sufficient DNA polymorphism exists among these accessions that segregating populations useful for restriction fragment length polymorphism (RFLP) mapping could be constructed using any two pepper accessions as parents. Regression analysis indicates that genetic distance is a good predictor (R2 = 0.872) of the level of mappable DNA polymorphism in Capsicum. Intraspecific variability was examined among four C. annuum cultivars (NuMex R Naky, Jupiter, Perennial, and Criollo de Morelos 334) using both RFLPs and randomly amplified polymorphic DNA (RAPDs), allowing a comparative evaluation of the two techniques. Seventeen percent of the clones used singly in RFLP analyses were sufficient for the differentiation of these varieties, as were 12.5% of the RAPD PCR amplifications. Dendrograms constructed from RFLP and RAPD analyses of the intraspecific data are similar but not identical. Southern analysis and RAPD PCR should be useful for DNA fingerprinting and the discrimination of closely related C. annuum genotypes.Key words: cluster analysis, restriction fragment length polymorphism, RFLP, DNA fingerprinting, randomly amplified polymorphic DNA, RAPD, germplasm.
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24

Jena, K. K., G. S. Khush, and G. Kochert. "Comparative RFLP mapping of a wild rice, Oryza officinalis, and cultivated rice, O. sativa." Genome 37, no. 3 (June 1, 1994): 382–89. http://dx.doi.org/10.1139/g94-054.

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A comparative RFLP map was constructed in a wild rice, Oryza officinalis, by using 139 genomic and cDNA probes that had been used previously to map RFLPs in O. sativa. Nine of the 12 chromosomes of O. officinalis were highly homosequential to those of O. sativa. A major rearrangement of gene order was detected in chromosome 1 and small inversions were found in chromosomes 3 and 11. Fourteen translocated RFLP markers were found, and chromosome 11 contained a high frequency of such translocated segments. Results were consistent with meiotic and trisomie analysis, which suggested that the genomes of O. officinalis and O. sativa were similar. Applications of comparative maps in plant breeding and gene cloning are discussed.Key words: Oryza, rice, wild rice, RFLP, genetic map.
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25

De Baere, Thierry, Richard Summerbell, Bart Theelen, Teun Boekhout, and Mario Vaneechoutte. "Evaluation of internal transcribed spacer 2-RFLP analysis for the identification of dermatophytes." Journal of Medical Microbiology 59, no. 1 (January 1, 2010): 48–54. http://dx.doi.org/10.1099/jmm.0.013870-0.

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A total of 95 isolates, belonging to 33 species of five dermatophyte genera, i.e. Arthroderma (15 species), Chrysosporium (two), Epidermophyton (one), Microsporum (three) and Trichophyton (12), were studied using internal transcribed spacer 2 (ITS2)-PCR-RFLP analysis (ITS2-RFLP), consisting of amplification of the ITS2 region, restriction digestion with BstUI (CG/CG) and restriction fragment length determination by capillary electrophoresis. ITS2-RFLP analysis proved to be most useful for identification of species of the genera Arthroderma, Chrysosporium and Epidermophyton, but could not distinguish between several Trichophyton species. The identification results are in agreement with established and recent taxonomical insights into the dermatophytes; for example, highly related species also had closely related and sometimes difficult-to-discriminate ITS2-RFLP patterns. In some cases, several ITS2-RFLP groups could be distinguished within species, again mostly in agreement with the taxonomic delineations of subspecies and/or genomovars, confirming the relevance of ITS2-RFLP analysis as an identification technique and as a useful taxonomic approach.
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Bin, Chen, Zheng Si-Ping, Zhou Li-Juan, Lin Zhi-Min, Song Ya-Na, and Zheng Wei-Wen. "Genetic diversity analysis of diazotrophs in the rice rhizosphere." Chinese Journal of Agricultural Biotechnology 4, no. 3 (December 2007): 253–58. http://dx.doi.org/10.1017/s1479236207001982.

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SUMMARYThe genetic diversity of dinitrogen-fixing bacteria associated with rice (Oryza sativa) was assessed by a polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) approach on thenifHgene amplified directly from DNA extracted from washed rice roots and rhizospheric soil. Restriction digestion with the enzymesMnlI andHaeIII was performed to characterize 54 clonednifHPCR products. RFLP profiles were clustered and analysed with the UPGMA program. Eight pairs of similar RFLP patterns (similarity>50%) and two pairs of homologous RFLP patterns (100% identity) were found from the washed roots and the rhizospheric soil, respectively. Three specific diazotrophic patterns were found from rhizospheric soil and rice roots. The analyses have revealed the presence of differentnifHtypes, which appear to be significant components of the diazotrophic community in paddy fields, indicating that some of the diazotrophs may colonize the inside and the surface of the rice roots.
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Silva, Jorge A. G. da, Mark E. Sorrells, William L. Burnquist, and Steven D. Tanksley. "RFLP linkage map and genome analysis of Saccharum spontaneum." Genome 36, no. 4 (August 1, 1993): 782–91. http://dx.doi.org/10.1139/g93-103.

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An RFLP linkage map of the wild sugarcane species Saccharum spontaneum L. (2n = 8x = 40–128) was constructed, comprising 216 loci, detected by 116 DNA probes, and distributed over 44 linkage groups. At a density of at least one marker every 25-cM interval, the coverage of the genome was estimated as 86%. For the generation of RFLP markers, probes were surveyed from seven DNA libraries: three sugarcane cDNA, one oat cDNA, one rice cDNA, and one barley cDNA, as well as one sugarcane genomic. Sixty-two maize genomic clones that were previously mapped on maize were used to initiate a comparative map between the sugarcane, sorghum, and maize genomes. Based on the RFLP segregation data, we conclude that this species is an autopolyploid, with an estimated genome size of 2107 cM.Key words: sugarcane, polyploid, RFLP, map, genome.
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Jackson, Colin J., Richard C. Barton, and E. Glyn V. Evans. "Species Identification and Strain Differentiation of Dermatophyte Fungi by Analysis of Ribosomal-DNA Intergenic Spacer Regions." Journal of Clinical Microbiology 37, no. 4 (1999): 931–36. http://dx.doi.org/10.1128/jcm.37.4.931-936.1999.

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Restriction fragment length polymorphisms (RFLPs) identified in the ribosomal-DNA (rDNA) repeat were used for molecular strain differentiation of the dermatophyte fungus Trichophyton rubrum. The polymorphisms were detected by hybridization ofEcoRI-digested T. rubrum genomic DNAs with a probe amplified from the small-subunit (18S) rDNA and adjacent internal transcribed spacer (ITS) regions. The rDNA RFLPs mapped to the nontranscribed spacer (NTS) region of the rDNA repeat and appeared similar to those caused by short repetitive sequences in the intergenic spacers of other fungi. Fourteen individual RFLP patterns (DNA types A to N) were recognized among 50 random clinical isolates ofT. rubrum. A majority of strains (19 of 50 [38%]) were characterized by one RFLP pattern (DNA type A), and four types (DNA types A to D) accounted for 78% (39 of 50) of all strains. The remaining types (DNA types E to N) were represented by one or two isolates only. A rapid and simple method was also developed for molecular species identification of dermatophyte fungi. The contiguous ITS and 5.8S rDNA regions were amplified from 17 common dermatophyte species by using the universal primers ITS 1 and ITS 4. Digestion of the amplified ITS products with the restriction endonucleaseMvaI produced unique and easily identifiable fragment patterns for a majority of species. However, some closely related taxon pairs, such as T. rubrum-T. soudanense andT. quinkeanum-T. schoenlenii could not be distinguished. We conclude that RFLP analysis of the NTS and ITS intergenic regions of the rDNA repeat is a valuable technique both for molecular strain differentiation of T. rubrum and for species identification of common dermatophyte fungi.
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Maki, Shinya, Keiji Oyama, Takao Kurahashi, Tamao Nakahira, Toyoki Kawabata, and Takashi Yamada. "RFLP analysis for cultivar identification of persimmons." Scientia Horticulturae 91, no. 3-4 (December 2001): 407–12. http://dx.doi.org/10.1016/s0304-4238(01)00254-0.

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30

Permutt, M. A., and S. C. Elbein. "Insulin Gene in Diabetes Analysis Through RFLP." Diabetes Care 13, no. 3 (March 1, 1990): 364–74. http://dx.doi.org/10.2337/diacare.13.3.364.

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31

Noreen, H. J., M. L. Davidson, M. B. Stewart, and M. Segall. "RFLP analysis fo HLA class II phenotyping." Human Immunology 23, no. 2 (January 1988): 128. http://dx.doi.org/10.1016/0198-8859(88)90218-2.

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Noreen, Harriet J., Maurine L. Davidson, Mary B. Stewart, and Miriam Segall. "HLA class II typing by RFLP analysis." Clinical Immunology Newsletter 10, no. 5 (May 1990): 73–77. http://dx.doi.org/10.1016/0197-1859(90)90021-y.

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Oshaghi, Mohammad Ali, Ali Reza Chavshin, and Hassan Vatandoost. "Analysis of mosquito bloodmeals using RFLP markers." Experimental Parasitology 114, no. 4 (December 2006): 259–64. http://dx.doi.org/10.1016/j.exppara.2006.04.001.

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34

Nocelli, E., T. Giovannini, M. Bioni, and R. Alicchio. "RFLP- and RAPD-based genetic relationships of seven diploid species of Avena with the A genome." Genome 42, no. 5 (October 1, 1999): 950–59. http://dx.doi.org/10.1139/g99-029.

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Relatively few molecular analyses are available for diploid oat species, which constitute the majority of the wild species of Avena and, therefore, the principal natural reservoir of variability. The present work reports an RAPD- (random amplified polymorphic DNA) and RFLP-(restriction fragment length polymorphism) based study of the intra- and interspecific variability of seven diploid A-genome oat species. Both types of markers resulted in valid tools for identifying polymorphisms both within and between species. The two statistical analyses, UPGMA (unweighted pair group method, arithmetic mean) and PCoA (principal coordinate analysis), computed on the basis of genetic similarities estimated from RAPDs and RFLPs, showed that the different accessions grouped according to species, but the similarity coefficients were consistently higher in the RFLP analysis. Furthermore, slight differences were observed in the intra- and interspecific relationships found with the two types of markers. This may support the hypothesis that the polymorphisms revealed by the two types of markers may associate with regions of the genome having different evolutionary rates. The relationships among species are not identical to those deduced from previous karyotypic and morphological studies, thus suggesting a partially different evolutionary pathway in oat speciation.Key words: RAPD and RFLP markers, genetic similarity, oat, diploids, polymorphism.
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35

Lueders, Tillmann, and Michael W. Friedrich. "Evaluation of PCR Amplification Bias by Terminal Restriction Fragment Length Polymorphism Analysis of Small-Subunit rRNA and mcrA Genes by Using Defined Template Mixtures of Methanogenic Pure Cultures and Soil DNA Extracts." Applied and Environmental Microbiology 69, no. 1 (January 2003): 320–26. http://dx.doi.org/10.1128/aem.69.1.320-326.2003.

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ABSTRACT Terminal restriction fragment length polymorphism (T-RFLP) analysis is a widely used method for profiling microbial community structure in different habitats by targeting small-subunit (SSU) rRNA and also functional marker genes. It is not known, however, whether relative gene frequencies of individual community members are adequately represented in post-PCR amplicon frequencies as shown by T-RFLP. In this study, precisely defined artificial template mixtures containing genomic DNA of four different methanogens in various ratios were prepared for subsequent T-RFLP analysis. PCR amplicons were generated from defined mixtures targeting not only the SSU rRNA but also the methyl-coenzyme M reductase (mcrA/mrtA) genes of methanogens. Relative amplicon frequencies of microorganisms were quantified by comparing fluorescence intensities of characteristic terminal restriction fragments. SSU ribosomal DNA (rDNA) template ratios in defined template mixtures of the four-membered community were recovered absolutely by PCR-T-RFLP analysis, which demonstrates that the T-RFLP analysis evaluated can give a quantitative view of the template pool. SSU rDNA-targeted T-RFLP analysis of a natural community was found to be highly reproducible, independent of PCR annealing temperature, and unaffected by increasing PCR cycle numbers. Ratios of mcrA-targeted T-RFLP analysis were biased, most likely by PCR selection due to the degeneracy of the primers used. Consequently, for microbial community analyses, each primer system used should be evaluated carefully for possible PCR bias. In fact, such bias can be detected by using T-RFLP analysis as a tool for the precise quantification of the PCR product pool.
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36

Givney, Rodney, Alison Vickery, Anne Holliday, Mary Pegler, and Richard Benn. "Evolution of an Endemic Methicillin-ResistantStaphylococcus aureus Population in an Australian Hospital from 1967 to 1996." Journal of Clinical Microbiology 36, no. 2 (1998): 552–56. http://dx.doi.org/10.1128/jcm.36.2.552-556.1998.

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The evolution over 30 years of a population of methicillin-resistant Staphylococcus aureus (MRSA) from a tertiary referral hospital was studied by phylogenetic analysis ofSmaI-generated restriction fragment length polymorphisms (RFLPs). The results suggest that a new clone of MRSA appeared at the hospital in the early 1980s, which, although usually retaining its ancestral phage-type, developed four different RFLP pulsotypes in the next 16 years. This finding indicates that multiple RFLP patterns in MRSA do not necessarily represent multiple clones deriving from different mec gene transfer events. Such variation within a clone may be significant in the interpretation of RFLP patterns during outbreaks and emphasizes the need to use two typing methods in studies of such populations. Since the appearance of new clones of MRSA is a relatively rare event, cross-infection control is paramount in the prevention of MRSA dissemination.
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37

Ignjatovic-Micic, Dragana, Ksenija Markovic, and Vesna Lazic-Jancic. "Application of molecular markers in bulk segragant analysis of yield in maize (Zea mays L) synthetic populations." Genetika 38, no. 1 (2006): 59–66. http://dx.doi.org/10.2298/gensr0601059i.

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Chromosome regions which carry potential QTLs for high grain yield in two synthetic maize populations - B73xMol7 and LlxMol7, were identified by bulk segregant analysis (BSA). Yield was evaluated on F2 testcross families in field trials using a Nested design. Based on yield data, p3 families with the corresponding highest and lowest testcross yields were selected for BSA. Genome analysis of F3 families was carried out with 58 RFLP markers. Allele frequency differences were detected at four RFLP loci n chromosomes 1, 2, 6 and 10 (B73xMol7), i.e. four RFLP loci on chromosomes 1, 2, 6 and 9 (LlxMo17). Only one region, at chromosome 6, was identified in both populations, but with two different RFLP markers. In B73xMol7 it was umc65 and in LlxMol7 umc2l RFLP marker. Bulk segregant analysis was shown to be a quick and informative method for identification of chromosome regions which determine high yield expression in maize, i.e. for identification of RFLP markers closely linked to potential genes involved in expression of the trait.
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IQBAL, S. J., D. S. PLAHA, G. H. LINFORTH, and R. DALGLEISH. "Hypophosphatasia: diagnostic application of linked DNA markers in the dominantly inherited adult form." Clinical Science 97, no. 1 (June 1, 1999): 73–78. http://dx.doi.org/10.1042/cs0970073.

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Hypophosphatasia is a rare disease characterized by low serum levels of tissue non-specific alkaline phosphatase (TNSALP) and a spectrum of skeletal disease varying from the severest form with death in utero to mild with no clinical abnormality in adults. Currently, the diagnosis of hypophosphatasia is made on the basis of clinical findings, radiography, low serum alkaline phosphatase levels and raised abnormal phosphorylated metabolites; there are elevations in serum pyridoxal 5′-phosphate, urinary phosphoethanolamine and inorganic pyrophosphate. In borderline cases the biochemical diagnosis remains uncertain. Prenatally, diagnosis is made using radiography and ultrasonography together with chorionic villus tissue biopsy, in which TNSALP levels are measured using an antibody-based assay. Since hypophosphatasia results from mutations in the TNSALP gene we have, for the first time in two U.K. families, undertaken restriction fragment length polymorphism (RFLP) analysis using three intragenic RFLPs for BclI and MspI at the ALPL locus. One family was informative, and a mutant-allele-specific haplotype with respect to three RFLPs was defined. In the other family the disease was shown to segregate with one allele of the BclI RFLP, but the MspI RFLPs were not informative. The disease segregated in the two families with different alleles of the BclI RFLP, suggesting that the mutations are likely to be different. We confirm that DNA analysis is likely to be the way ahead for diagnosing hypophosphatasia, and that standardized screening methods need to be developed for detecting mutations in these and other families.
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39

Morgan, JM, and MK Tan. "Chromosomal Location of a Wheat Osmoregulation Gene Using RFLP Analysis." Functional Plant Biology 23, no. 6 (1996): 803. http://dx.doi.org/10.1071/pp9960803.

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The chromosomal location of an osmoregulation gene locus (or) was examined by exploring genetic linkage to restriction fragment length polymorphism (RFLP) loci which have been mapped on group 7 chromosomes or located specifically on chromosome 7A. The osmoregulation gene had previously been located on chromosome 7A, but its specific position was unknown. Analysis of linkage with the RFLP loci suggested a probable position on the short arm approximately 13 cM towards the centromere from RFLP locus Xpsr119. The findings, which were based on a relatively small sample, are of a preliminary nature and require confirmation with a larger set of genetic stocks.
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40

Whisson, SC, BJ Howlett, ECY Liew, DJ Maclean, JM Manners, and JAG Irwin. "An Assessment of Genetic Relationships between Members of the Phytophthora megasperma Complex and Phytophthora vignae using Molecular Markers." Australian Systematic Botany 6, no. 4 (1993): 295. http://dx.doi.org/10.1071/sb9930295.

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Genetic relationships between Phytophora megasperma f. sp. glycinea (Pmg) and morphologically similar taxa, P. megasperma f. sp. medicaginis (Pmm), P. megasperma f. sp. trifolii (Pmt), P. megasperma from Douglas Fir (PmDF) and asparagus (PmAS) and Phytophthora vignae, were explored by restriction fragment length polymorphism (RFLP) analysis of nuclear DNA using random genomic multi-copy, cDNA, and ribosomal DNA probes as well as random amplified polymorphic DNA (RAPDs) and RFLP analysis of ribosomal intergenic spacer regions amplified by the polymerase chain reaction (PCR). Each method detected large differences between these taxa and P. megasperma f. sp. glycinea. P. vignae was more closely related to P. megasperma f. sp. glycinea than the other taxa on the basis of the cDNA RFLPs and RFLPs of PCR amplified rDNA intergenic spacer regions. We conclude that each of the taxa examined represent separate species. This supports the most recent reclassification based on mitochondrial RFLPs and electrophoretic protein patterns of the host-specific taxa to P. sojae (Pmg), P. trifolii (Pmt) and P. medicaginis (Pmm).
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41

LIU, Yao Guang, Naoki MORI, and Koichiro TSUNEWAKI. "Restriction fragment length polymorphism (RFLP) analysis in wheat. I. Genomic DNA library construction and RFLP analysis in common wheat." Japanese Journal of Genetics 65, no. 5 (1990): 367–80. http://dx.doi.org/10.1266/jjg.65.367.

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42

Hookey, John V., Judith F. Richardson, and Barry D. Cookson. "Molecular Typing of Staphylococcus aureus Based on PCR Restriction Fragment Length Polymorphism and DNA Sequence Analysis of the Coagulase Gene." Journal of Clinical Microbiology 36, no. 4 (1998): 1083–89. http://dx.doi.org/10.1128/jcm.36.4.1083-1089.1998.

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A typing procedure for Staphylococcus aureus was developed based on improved PCR amplification of the coagulase gene and restriction fragment length polymorphism (RFLP) analysis of the product. All coagulase-positive staphylococci produced a single PCR amplification product of either 875, 660, 603, or 547 bp. Those strains of epidemic methicillin-resistant S. aureus 16 (EMRSA-16) studied all gave a product of 547 bp. PCR products were digested withAluI and CfoI, and the fragments were separated by gel electrophoresis. Ten distinct RFLP patterns were found among 85 isolates of methicillin-resistant S. aureus (MRSA) and 10 propagating strains (PS) of methicillin-sensitive S. aureus(MSSA) examined. RFLP patterns 1, 2, and 3 were specific to strains of EMRSA-3, -15, and -16, respectively. By contrast, RFLP patterns 4 and 5 were seen with a heterogeneous collection of strains, together with drug-resistant forms of S. aureus isolated in Europe and four propagating strains used for the international phage set. RFLP pattern 6 was given by the Airedale isolate and PS 95. RFLP pattern 7 encompassed EMRSA-2 (isolate 331), PS 94, and PS 96. An isolate from Germany gave RFLP pattern 8. Eight strains of MSSA gave patterns similar to those of methicillin-resistant strains (RFLP patterns 3, 4, 5, 6, and 7), but two, PS 42E and PS 71, gave unique RFLP patterns 9 and 10, respectively. The coagulase gene PCR products for 24 isolates of MRSA and two isolates of MSSA were sequenced for both strands. The sequences were aligned, and evolutionary lineages were inferred based on pairwise distances between isolates.
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43

King, Joseph J., James M. Bradeen, and Michael J. Havey. "Variability for Restriction Fragment-length Polymorphisms (RFLPs) and Relationships among Elite Commercial Inbred and Virtual Hybrid Onion Populations." Journal of the American Society for Horticultural Science 123, no. 6 (November 1998): 1034–37. http://dx.doi.org/10.21273/jashs.123.6.1034.

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Nuclear RFLPs were used to estimate relationships among 14 elite commercial inbreds of bulb onion (Allium cepa) from Holland, Japan, and the United States. Variability for known alleles at 75 RFLP loci and 194 polymorphic fragments revealed by 69 anonymous cDNA probes and a clone of alliinase were scored to yield genetically characterized and uncharacterized data sets, respectively. The inbred onion populations possessed more than two alleles at 20 of 43 (46%) codominant RFLP loci. Relationships among the inbreds were estimated by cluster analysis of simple-matching (genetically characterized data) and Jaccard (genetically uncharacterized data) coefficients using the unweighted pair group method and agreed with known pedigrees. RFLPs confidently distinguished among elite inbreds within and between specific market classes. RFLP profiles for virtual hybrids were computer-generated by combining gametic arrays among inbreds of the same market class and analyzed as described above. Allelic and genetically uncharacterized RFLPs confidently distinguished among these hybrids, even though heterozygosity for many markers produced a majority of monomorphic fragments. We randomly sampled decreasing numbers of RFLPs from the complete data sets and calculated simple-matching and Jaccard distances, noting the numbers of probes that were unable to distinguish any two inbreds or hybrids. As few as 10 polymorphic probe-enzyme combinations distinguished among all the inbreds and samples of 20 genetically characterized or 10 genetically uncharacterized clones distinguished all the virtual hybrids. This study demonstrated that the previously reported few RFLPs observed among open-pollinated (OP) onion populations were due to the highly heterozygous nature of the OP population.
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44

Walker, Elaine S., Robert A. Preston, J. Christopher Post, Garth D. Ehrlich, John H. Kalbfleisch, and Karin L. Klingman. "Genetic Diversity among Strains of Moraxella catarrhalis: Analysis Using Multiple DNA Probes and a Single-Locus PCR-Restriction Fragment Length Polymorphism Method." Journal of Clinical Microbiology 36, no. 7 (1998): 1977–83. http://dx.doi.org/10.1128/jcm.36.7.1977-1983.1998.

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Moraxella (Branhamella)catarrhalis, a causative agent of otitis media, sinusitis, and exacerbation of bronchitis, has acquired widespread ability to produce β-lactamase and can be nosocomially transmitted. The typing methods used in epidemiological analyses of M. catarrhalisare not optimal for genetic analyses. Two methods, a multiple-locus Southern blot (SB) method and a single-locus PCR-restriction fragment length polymorphism (RFLP) method, were developed and used to assess genetic diversity and potential clinical and geographic relationships in M. catarrhalis. Nine randomly cloned M. catarrhalis DNA fragments were used as probes of SBs containing DNA from 54 geographically and clinically diverse strains. For comparison, a PCR-RFLP method was developed as a quick, inexpensive, and discriminating alternative. A highly variable 3.7-kb genomic region (M46) was cloned and sequenced, and 3.5 kb of the cloned DNA was targeted for PCR amplification. DNAs from the 54 strains were subjected to PCR-RFLP. SB analysis distinguished all strains that had no apparent epidemiological linkage (40 of 54), and PCR-RFLP distinguished fewer strains (21 of 54). Epidemiologically linked strains appeared genetically identical by both methods. PCR-RFLP was compared to pulsed-field gel electrophoresis (PFGE) for 8 of the 54 strains and 23 additional strains. PCR-RFLP distinguished fewer strains than PFGE typing (16 of 31 versus 20 of 31 strains), but PCR-RFLP was more useful for inferring interstrain relatedness. Separate cluster analyses of multilocus SB and single locus PCR-RFLP data showed high genetic diversity within and across geographic locations and clinical presentations. The resultant dendrograms were not entirely concordant, but both methods often gave similar strain clusters at the terminal branches. High genetic diversity, nonconcordance of cluster analyses from different genetic loci, and shared genotypes among epidemiologically linked strains support a hypothesis of high recombination relative to spread of clones. Single-locus PCR-RFLP may be suitable for short-term epidemiological studies, but the SB data demonstrate that greater strain discrimination may be obtained by sampling variation at multiple genomic sites.
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45

Guillemaut, Cécile, Véronique Edel-Hermann, Pierre Camporota, Claude Alabouvette, Marc Richard-Molard, and Christian Steinberg. "Typing of anastomosis groups ofRhizoctonia solaniby restriction analysis of ribosomal DNA." Canadian Journal of Microbiology 49, no. 9 (September 1, 2003): 556–68. http://dx.doi.org/10.1139/w03-066.

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A method based on restriction analysis of polymerase chain reaction (PCR)-amplified ribosomal DNA was developed for the rapid characterization of large populations of Rhizoctonia solani at the anastomosis group (AG) level. The restriction maps of the internal transcribed spacers (ITS) sequences were compared for 219 isolates of R. solani belonging to AG-1 to AG-12 and AG-BI, representing diverse geographic and host range origins. Four discriminant restriction enzymes (MseI, AvaII, HincII, and MunI) resolved 40 restriction fragment length polymorphism (RFLP) types among the 219 ITS sequences of R. solani. Each RFLP type could be assigned to a single AG except for two RFLP types, which were common to two AG. A fifth enzyme allowed the discrimination of AG-6 and AG-12. In addition, the combination of four enzymes allowed the discrimination of subsets within AG-1, AG-2, AG-3, and AG-4. The efficiency of the typing method was confirmed by analyzing PCR-amplified ITS sequences of 30 reference strains. Furthermore, the PCR–RFLP method was used to characterize at the AG level 307 isolates of R. solani originating from ten sugar beet fields exhibiting patches of diseased plants in France. The PCR-based procedure described in this paper provides a rapid method for AG typing in R. solani.Key words: Rhizoctonia solani, anastomosis group, PCR–RFLP, ITS, identification, sugar beet.
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46

Sharma, Deepak. "PCR-RFLP Analysis of CD18 Gene in Buffalo." Journal of Animal Health and Production 2, no. 1 (2014): 5–7. http://dx.doi.org/10.14737/journal.jahp/2014/2.1.5.7.

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47

Yamashita, Kenichiro, and Yosuke Tashiro. "RFLP Analysis of Mitochondrial DNA in Wakegi Onion." Engei Gakkai zasshi 70, no. 2 (2001): 232–34. http://dx.doi.org/10.2503/jjshs.70.232.

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48

HUANG, Wei, Li WANG, Ping YI, Xue-Lin TAN, Xue-Mei ZHANG, Zai-Jun ZHANG, Yang-Sheng LI, and Ying-Guo ZHU. "RFLP Analysis for Mitochondrial Genome of CMS-Rice." Acta Genetica Sinica 33, no. 4 (April 2006): 330–38. http://dx.doi.org/10.1016/s0379-4172(06)60058-9.

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49

Aras Hisar, Sukriye, Ercument Aksakal, Olcay Hisar, Telat Yanik, and Suhendan Mol. "Discrimination of Penaeid Shrimps with PCR-RFLP Analysis." Journal of Shellfish Research 27, no. 4 (August 2008): 917–20. http://dx.doi.org/10.2983/0730-8000(2008)27[917:dopswp]2.0.co;2.

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50

Lee, Henry C., E. M. Pagliaro, R. E. Gaensslen, K. M. Berka, T. P. Keith, G. N. Keith, and D. D. Garner. "DNA analysis in human bone tissue: RFLP typing." Journal of the Forensic Science Society 31, no. 2 (April 1991): 209–12. http://dx.doi.org/10.1016/s0015-7368(91)73141-1.

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