Journal articles on the topic 'RFLP'
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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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Young, Nevin Dale. "Restriction Fragment Length Polymorphisms (RFLPS) and Crop Improvement." Experimental Agriculture 28, no. 4 (October 1992): 385–98. http://dx.doi.org/10.1017/s0014479700020093.
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SUMMARYRestriction fragment length polymorphisms (RFLPs) are genetic markers based on cloned molecules of DNA. Using RFLPs, scientists can construct high density genetic linkage maps and locate economically important genes. Once a gene for a valuable trait has been mapped with RFLPs, desirable genotypes can be selected using RFLPs rather than scoring for the trait itself. This is important when a trait is recessive, difficult to score, or obscured by other characters. RFLPs are particularly valuable in mapping genes controlling complex polygenic characters, including those fundamental to crop improvement. The first RFLP maps were developed in crop species primarily important in temperate countries. Now RFLP maps for major tropical and sub-tropical crop species are also being developed.
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Meagher, R. B., M. D. McLean, and J. Arnold. "Recombination within a subclass of restriction fragment length polymorphisms may help link classical and molecular genetics." Genetics 120, no. 3 (November 1, 1988): 809–18. http://dx.doi.org/10.1093/genetics/120.3.809.
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Abstract Restriction fragment length polymorphisms (RFLPs) are being used to construct complete linkage maps for many eukaryotic genomes. These RFLP maps can be used to predict the inheritance of important phenotypic loci and will assist in the molecular cloning of linked gene(s) which affect phenotypes of scientific, medical and agronomic importance. However, genetic linkage implies very little about the actual physical distances between loci. An assay is described which uses genetic recombinants to measure physical distance from a DNA probe to linked phenotypic loci. We have defined the subset of all RFLPs which have polymorphic restriction sites at both ends as class II RFLPs. The frequency of class II RFLPs is computed as a function of sequence divergence and total RFLP frequency for highly divergent genomes. Useful frequencies exist between organisms which differ by more than 7% in DNA sequence. Recombination within class II RFLPs will produce fragments of novel sizes which can be assayed by pulsed field electrophoresis to estimate physical distance in kilobase pairs between linked RFLP and phenotypic loci. This proposed assay should have particular applications to crop plants where highly divergent and polymorphic species are often genetically compatible and thus, where class II RFLPs will be most frequent.
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Gedil, Melaku Ayele, Crispin Wye, Simon Berry, Bart Segers, Johan Peleman, Richard Jones, Alberto Leon, Mary B. Slabaugh, and Steven J. Knapp. "An integrated restriction fragment length polymorphism - amplified fragment length polymorphism linkage map for cultivated sunflower." Genome 44, no. 2 (April 1, 2001): 213–21. http://dx.doi.org/10.1139/g00-111.
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Restriction fragment length polymorphism (RFLP) maps have been constructed for cultivated sunflower (Helianthus annuus L.) using three independent sets of RFLP probes. The aim of this research was to integrate RFLP markers from two sets with RFLP markers for resistance gene candidate (RGC) and amplified fragment length polymorphism (AFLP) markers. Genomic DNA samples of HA370 and HA372, the parents of the F2 population used to build the map, were screened for AFLPs using 42 primer combinations and RFLPs using 136 cDNA probes (RFLP analyses were performed on DNA digested with EcoRI, HindIII, EcoRV, or DraI). The AFLP primers produced 446 polymorphic and 1101 monomorphic bands between HA370 and HA372. The integrated map was built by genotyping 296 AFLP and 104 RFLP markers on 180 HA370 × HA372 F2 progeny (the AFLP marker assays were performed using 18 primer combinations). The HA370 × HA372 map comprised 17 linkage groups, presumably corresponding to the 17 haploid chromosomes of sunflower, had a mean density of 3.3 cM, and was 1326 cM long. Six RGC RFLP loci were polymorphic and mapped to three linkage groups (LG8, LG13, and LG15). AFLP markers were densely clustered on several linkage groups, and presumably reside in centromeric regions where recombination is reduced and the ratio of genetic to physical distance is low. Strategies for targeting markers to euchromatic DNA need to be tested in sunflower. The HA370 × HA372 map integrated 14 of 17 linkage groups from two independent RFLP maps. Three linkage groups were devoid of RFLP markers from one of the two maps.Key words: amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), Helianthus, sunflower, genetic map.
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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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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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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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Landry, Benoit S., Nathalie Hubert, René Crete, Morgan S. Chang, Steven E. Lincoln, and Takeomi Etoh. "A genetic map for Brassica oleracea based on RFLP markers detected with expressed DNA sequences and mapping of resistance genes to race 2 of Plasmodiophora brassicae (Woronin)." Genome 35, no. 3 (June 1, 1992): 409–20. http://dx.doi.org/10.1139/g92-061.
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F2 segregation analyses of DNA restriction fragment length polymorphisms (RFLPs) detected between a cabbage line (No. 86-16-5) resistant to race 2 of Plasmodiophora brassicae (Woronin), the fungus responsible for clubroot disease, and a rapid cycling line (CrGC No. 85) was used to construct a detailed genetic map of Brassica oleracea. RFLP markers were random and seedling-specific cDNA clones. The 201 loci so far mapped in B. oleracea covered 1112 cM. They are assembled into nine major linkage groups and four small linkage groups. Twelve loci were found unlinked to any other markers. Twenty-one loci were detected with the 18 seedling-specific cDNAs. Two dominant QTLs for resistance to race 2 of the clubroot disease causal agent were also identified. Leaf morphology and biennial flowering appeared to segregate as single Mendelian traits, but only leaf morphology could be linked to other markers. This RFLP study in B. oleracea is providing additional information on genome organization and complements current RFLP mapping effort in B. napus.Key words: genetic mapping, Brassica oleracea, Plasmodiophora brassicae, breeding, clubroot resistance, DNA markers, RFLP.
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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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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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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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Echt, C. S., K. K. Kidwell, S. J. Knapp, T. C. Osborn, and T. J. McCoy. "Linkage mapping in diploid alfalfa (Medicago sativa)." Genome 37, no. 1 (February 1, 1994): 61–71. http://dx.doi.org/10.1139/g94-008.
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A genome map of cultivated alfalfa was constructed using segregating restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNAs (RAPDs) in a diploid backcross population generated from noninbred parents. Among the 153 loci scored in 87 progeny, four segregation ratios were observed for codominant and dominant markers: 1:1, 1:2:1, 1:1:1:1, and 3:1. Deviations from expected Mendelian ratios (p < 0.05) were observed for 34% of the loci studied. A genome map was assembled from two separate linkage maps, each constructed from a subset of the segregation data. One linkage map was constructed from 46 RFLP and 40 RAPD markers segregating 1:1 from the F1 parent of the backcross and the other linkage map was constructed from 33 RFLP and 28 RAPD markers segregating 1:1 from the recurrent parent. Sixteen loci with alleles segregating 1:1 from both parents were used as locus bridges to align individual linkage groups between the two maps. The combined use of RFLPs and RAPDs was an effective method for developing an alfalfa genome map.Key words: genome mapping, RAPD, RFLP, locus bridges.
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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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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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Kuspa, A., and W. F. Loomis. "REMI-RFLP mapping in the Dictyostelium genome." Genetics 138, no. 3 (November 1, 1994): 665–74. http://dx.doi.org/10.1093/genetics/138.3.665.
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Abstract A set of 147 Dictyostelium discoideum strains was constructed by random integration of a vector containing rare restriction sites. The strains were generated by transformation using restriction enzyme-mediated integration (REMI) which results in the integration of linear DNA fragments into randomly distributed genomic restriction sites. Restriction fragment length polymorphism (RFLP) was generated in a single genomic site in each strain. These REMI-RFLP strains were used to confirm gene linkages previously supported by two other physical mapping techniques: yeast artificial chromosome (YAC) contig construction, and megabase-scale restriction mapping. New linkages were uncovered when two or more hybridization probes identified the same RFLP fragments. Probes for 100 genes have marked 53% of the RFLPs, representing greater than 22 Mb of the 40 Mb Dictyostelium genome. Alignment of these and other large fragments along each chromosome should lead to a complete physical map of the Dictyostelium genome.
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Landry, Benoit S., Nathalie Hubert, Takeomi Etoh, John J. Harada, and Stephen E. Lincoln. "A genetic map for Brassica napus based on restriction fragment length polymorphisms detected with expressed DNA sequences." Genome 34, no. 4 (August 1, 1991): 543–52. http://dx.doi.org/10.1139/g91-084.
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F2 segregation analyses of DNA restriction fragment length polymorphisms (RFLPs) detected between two cultivars of canola ('Westar' × Topas') was used to construct a detailed genetic map of Brassica napus. RFLP markers were from a seedling-specific cDNA library. They were either randomly selected or previously characterized as seedling-specific cDNA clones. The 120 loci so far mapped in B. napus covered 1413 recombination units. They are assembled into 19 linkage groups. Seventeen loci were found unlinked to any other markers. Few polymorphisms were detected with the seedling-specific cDNAs and only seven loci could be mapped in this cross. Duplication of RFLP loci was extensive and reflects the amphidiploid nature of this species. However, several rearrangements of the linear order of duplicated loci could be seen. This RFLP study in B. napus provides important information on genome organization of functional DNA sequences and complements our current RFLP mapping effort in Brassica oleracea. The genetic markers of this map are currently being used in several breeding applications, such as tagging important agronomic traits and fingerprinting breeding lines and cultivars of canola, a major oilseed crop.Key words: genetic mapping, Brassica napus, breeding, restriction fragment length polymorphisms.
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Galgaro, Leticia, Catalina Romero Lopes, Marcos Gimenes, José FM Valls, and Gary Kochert. "Genetic variation between several species of sections Extranervosae, Caulorrhizae, Heteranthae, and Triseminatae (genus Arachis) estimated by DNA polymorphism." Genome 41, no. 3 (June 1, 1998): 445–54. http://dx.doi.org/10.1139/g98-004.
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Genetic variation within and among accessions of the genusArachis representing sections Extranervosae, Caulorrhizae, Heteranthae, and Triseminatae was evaluated using RFLP and RAPD markers. RAPD markers revealed a higher level of genetic diversity than did RFLP markers, both within and among the species evaluated. Phenograms based on various band-matching algorithms revealed three major clusters of similarity among the sections evaluated. The first group included the species from section Extranervosae, the second group consisted of sections Triseminatae, Caulorrhizae, and Heteranthae, and the third group consisted of one accession of Arachis hypogaea, which had been included as a representative of section Arachis. The phenogramsobtained from the RAPD and RFLP data were similar but not identical. Arachis pietrarellii, assayed only by RAPD, showed a high degree of genetic similarity with Arachis villosulicarpa. This observation supported the hypothesis that these two species are closely related. It was also shown that accession V 7786, previously considered to be Arachis sp. aff.pietrarellii, and assayed using both RFLPs and RAPDs, was possibly a new species from section Extranervosae, but very distinct from A. pietrarellii.Keywords: Arachis, RFLP, RAPD, genetic similarity, genetic distance.
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Griffiths, H. M., W. A. Sinclair, E. Boudon-Padieu, X. Daire, I. M. Lee, A. Sfalanga, and A. Bertaccini. "Phytoplasmas Associated with Elm Yellows: Molecular Variability and Differentiation from Related Organisms." Plant Disease 83, no. 12 (December 1999): 1101–4. http://dx.doi.org/10.1094/pdis.1999.83.12.1101.
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Restriction fragment length polymorphism (RFLP) analyses were performed on polymerase chain reaction (PCR) amplimers of phytoplasmal DNA from eight samples obtained from Ulmus spp. (elms) affected by elm yellows (EY) in Italy and the United States, from Catharanthus roseus infected with strain EY1, and from five other plant species infected with phytoplasmas of the EY group sensu lato (group 16SrV). RFLP profiles obtained with restriction enzyme TaqI from ribosomal DNA amplified with primer pair P1/P7 differentiated elm-associated phytoplasmas from strains originally detected in Apocynum cannabinum, Prunus spp., Rubus fruticosus, Vitis vinifera, and Ziziphus jujuba. RFLP profiles obtained similarly with BfaI differentiated strains from A. cannabinum and V. vinifera from other phytoplasmas of group 16SrV. Elm-associated strains from within the United States had two RFLP patterns in ribosomal DNA based on presence or absence of an RsaI site in the 16S–23S spacer. Elm-associated phytoplasma strains from Italy were distinguished from those of American origin by RFLPs obtained with MseI in the same fragment of non-ribosomal DNA. Strain HD1, which was discovered in A. cannabinum associated with EY-diseased elms in New York State, was unique among the strains studied.
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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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Jordan, D. R., R. E. Casu, P. Besse, B. C. Carroll, N. Berding, and C. L. McIntyre. "Markers associated with stalk number and suckering in sugarcane colocate with tillering and rhizomatousness QTLs in sorghum." Genome 47, no. 5 (October 1, 2004): 988–93. http://dx.doi.org/10.1139/g04-040.
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Two important factors influencing sugar yield, the primary focus of sugarcane plant breeding programs, are stalk number and suckering. Molecular markers linked to both of these traits are sought to assist in the identification of high sugar yield, high stalk number, low-suckering sugarcane clones. In this preliminary mapping study, 108 progeny from a biparental cross involving two elite Australian sugarcane clones were evaluated at two sites for two years for both stalk number and suckering. A total of 258 DNA markers, including both restriction fragment length polymorphisms (RFLPs) and radio-labelled amplified fragments (RAFs), were scored and evaluated using single-factor analysis. Sixteen (7 RFLPs and 9 RAFs) and 14 (6 RFLPs and 8 RAFs) markers were identified that were significantly associated (P < 0.01) with stalk number and suckering, respectively, across both years and sites. The seven and six RFLP markers associated with stalk number and suckering, respectively, were generated by eight different RFLP probes, of which seven had been mapped in sorghum and (or) sugarcane. Of significant interest was the observation that all seven RFLP probes could be shown to be located within or near QTLs associated with tillering and rhizomatousness in sorghum. This observation highlights the usefulness of comparative mapping between sorghum and sugarcane and suggests that the identification of useful markers for stalk number and suckering in sugarcane would be facilitated by focussing on sorghum QTLs associated with related traits.Key words: comparative mapping, suckering, sugarcane, sorghum, tillering.
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Gedeon, A. K., J. C. Mulley, and A. Fratini. "AnMsp1 RFLP atD16S10." Nucleic Acids Research 17, no. 5 (1989): 2146. http://dx.doi.org/10.1093/nar/17.5.2146.
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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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Zerba, K. E., A. M. Kessling, J. Davignon, and C. F. Sing. "Genetic structure and the search for genotype-phenotype relationships: an example from disequilibrium in the Apo B gene region." Genetics 129, no. 2 (October 1, 1991): 525–33. http://dx.doi.org/10.1093/genetics/129.2.525.
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Abstract We analyzed allelic associations (disequilibria) for four restriction fragment length polymorphisms (RFLPs) in the region of the 43-kb Apo B gene in a sample of 233 unrelated individuals from Montreal, Canada, sampled for health. This total sample (T) included 160 individuals of known French Canadian (FC) ancestry. We present a rigorous application of current methodology to these samples, including estimation of type II error probabilities and correlations between markers for estimates of disequilibria. We then consider the utility of these estimates of allelic disequilibria for the interpretation of genotype-phenotype relations. Significant deviations from Hardy-Weinberg equilibrium were not predicted by proximity to other markers in disequilibrium. We found significant quadri-allelic disequilibrium for two marker pairs despite absence of significant deviations from Hardy-Weinberg equilibrium for either marker or tri-allelic disequilibrium, respectively. Altogether these results underscore the complexity of the genotypic structure of the data. A combination of nonevolutionary factors, including sampling for health, small sample size and data exclusion due to methodological constraints of not successfully typing all members of the sample for every RFLP, is a likely explanation for this complexity. These types of factors are common to many RFLP studies. Patterns of composite di-allelic disequilibrium indicated that some RFLP allele pairs may have a longer shared evolutionary history than others and that disequilibrium is not predicted by distance between RFLPs. Type II error probabilities were generally much higher than those for type I errors. Correlations between marker pairs for disequilibria were generally not high. We show from a review of 14 published studies of association between the XbaI RFLP and variation in a total of 15 lipid traits that deviations from Hardy-Weinberg equilibrium can cause substantial differences in the estimation of variability associated with phenotypic differences among marker genotypes relative to Hardy-Weinberg conditions.
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Liou, Pan-chi, Fred G. Gmitter, and Gloria A. Moore. "MOLECULAR CHARACTERIZATION AND LINKAGE MAPPING OF THE CITRUS GENOME USING ISOZYME AND RFLP MARKERS." HortScience 25, no. 9 (September 1990): 1154c—1154. http://dx.doi.org/10.21273/hortsci.25.9.1154c.
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Citrus genetic studies and cultivar improvement have been difficult with conventional techniques. Alternative approaches are needed to enhance efficiency of such studies. Our objectives were to characterize the Citrus genome and to initiate development of a linkage map using RFLP and isozyme analysis. Methods of Citrus DNA extraction were developed to allow the isolation of chromosomal DNA of acceptable quality for recombinant' DNA manipulations. A PstI Citrus genomic library was constructed to create DNA clones for the RFLP survey. A rapid, reliable procedure was developed to facilitate screening of the library for useful clones. The methods used and strategy followed minimized contamination with organelle DNA, increased the frequency of single copy clones, and allowed rapid screening of the newly–constructed library. Linkage relationships of 49. markers, including 36 RFLP and 6 isozyme loci, were analyzed and a map comprised of 8 linkage groups was constructed. Insertions or deletions were responsible for at least 30% of the RFLPs identified. A hypothesis of transposon activity in Citrus was proposed based on our observations.
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Keller, S. M., J. M. McDermott, R. E. Pettway, M. S. Wolfe, and B. A. McDonald. "Gene Flow and Sexual Reproduction in the Wheat Glume Blotch Pathogen Phaeosphaeria nodorum (Anamorph Stagonospora nodorum)." Phytopathology® 87, no. 3 (March 1997): 353–58. http://dx.doi.org/10.1094/phyto.1997.87.3.353.
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Restriction fragment length polymorphisms (RFLPs) were used to characterize the genetic structures of three field populations of Phaeosphaeria nodorum from Texas, Oregon, and Switzerland. Data from seven nuclear RFLP loci were used to estimate gene diversity and genetic distances and to make indirect measures of gene flow between populations. Three of the seven RFLP loci differed significantly in allele frequencies across populations. On average, 96% of the total gene diversity was found within populations. There was little evidence for population subdivision, suggesting that gene flow was not restricted among populations. Based on an average population differentiation of 0.04, we estimated that the exchange of 11 migrants among populations per generation would be needed to account for the present level of population subdivision. Genotype diversity based on DNA fingerprints was at a maximum for the Swiss population, whereas populations in Texas and Oregon had lower genotype diversities. Many multilocus haplotypes were found in each population. Ninety-five percent of RFLP allele pairs were in gametic equilibrium. The data were consistent with random mating within each population.
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Smead, Deborah L., Robert L. Nussbaum, and Jennifer M. Puck. "RFLPs in human X-linked PGK1: a new probe for the PstI RFLP demonstrates strong linkage disequilibrium with the Bgll RFLP." Nucleic Acids Research 17, no. 18 (1989): 7551. http://dx.doi.org/10.1093/nar/17.18.7551.
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Patterson, N. A., and M. Kapoor. "Detection of additional restriction fragment length polymorphisms among the weakly virulent (nonaggressive) and highly virulent (aggressive) isolates of Leptosphaeria maculans." Canadian Journal of Microbiology 41, no. 12 (December 1, 1995): 1135–41. http://dx.doi.org/10.1139/m95-158.
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Isolates of Leptosphaeria maculans were analyzed for their genetic relatedness based on DNA restriction fragment length polymorphisms (RFLPs), employing as Southern hybridization probes a combination of heat shock responsive genes (hsp70 and hsp80 from Neurospora crassa), the cutinase gene of Magnaporthe grisea, and cloned genomic DNA sequences from a virulent strain. Southern hybridization analysis revealed a high frequency of DNA polymorphism. Restriction fragments generated by each enzyme-probe combination resulted in distinct banding patterns, clearly separating the isolates into two groups. The cutinase gene probe did not reveal any polymorphisms. Although the majority of the probes used displayed RFLP profiles unique to each group, a nonaggressive isolate, LmA, showed additional genetic characteristics in common with the virulent pathotype.Key words: Leptosphaeria, genomic libraries, RFLP.
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Buse, J. B., R. Rifai-Haddad, S. Lees, H. Taniguchi, D. Chaplin, E. M. Milford, J. G. Seidman, G. S. Eisenbarth, and R. A. Jackson. "Major histocompatibility complex restriction fragment length polymorphisms define three diabetogenic haplotypes in BB and BBN rats." Journal of Experimental Medicine 162, no. 2 (August 1, 1985): 444–58. http://dx.doi.org/10.1084/jem.162.2.444.
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Class I and II major histocompatibility complex (MHC) probes can be used to subdivide diabetes-prone BB rats and their BBN control strain, coderived from the same outbred colony by selection against diabetes. Class II probes (A-alpha in particular) distinguish four restriction fragment length polymorphisms (RFLP), termed 1a, 1b, 2a, and 2b, in the BBN population, only one of which (2a) is found in BB rats. The degree of class II RFLP in the population studied is RT1.B-alpha greater than or equal to RT1.B-beta greater than RT1.D-alpha greater than or equal to RT1.D-beta, suggesting that intra-class II region dynamics may be different in rats compared with mice. A class I probe (S16) absolutely distinguished BB from BBN rats, since all BB rats exhibit an RFLP pattern termed 2a0, while 2a BBN rats can be subdivided into 2a1 and 2a2 forms. Serologic evaluation has shown that 2a0, 2a1, and 2a2 rats express RT1.AuBu, 1a rats express RT1.AaDa, and 1b rats express neither RT1a nor RT1u at the loci tested. A breeding study was carried out to determine the diabetogenicity of the MHC-defined RFLP's. As expected, the BB-derived 2a0 is diabetogenic. The BBN-derived 2a1 and 2a2 RFLPs are also diabetogenic, while 1a and 1b rats do not carry MHC-linked diabetogenic genes. The MHC-linked diabetes gene acts in a functionally recessive manner, since there is a 10-fold higher incidence in homozygotes than in heterozygotes. Analysis of the RFLP patterns leads us to hypothesize that the 2a1 RFLP results from a crossover between 1a and 2a0 MHCs and that the diabetogenic MHC-linked gene is on the class II side of Qa and T1. The availability of three diabetogenic MHC haplotypes should help localize the MHC-linked diabetogenic gene of rats.
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ASHER, A. J., L. S. WALDRON, and M. L. POWER. "Rapid identification of Giardia duodenalis assemblages in NSW using terminal-restriction fragment length polymorphism." Parasitology 139, no. 8 (March 15, 2012): 1005–13. http://dx.doi.org/10.1017/s0031182012000388.
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SUMMARYHumans are infected by 2 genetic assemblages (A and B) of Giardia duodenalis, a protozoan parasite that causes gastro-intestinal disease. Sub-assemblages AI, AII, BIII and BIV are commonly identified in human cases. Detection requires amplification of G. duodenalis loci. Subsequent DNA sequencing or restriction fragment length polymorphism (RFLP) identifies sub-assemblages but is expensive (DNA sequencing) or insensitive (RFLP). This study investigated a fluorescence-based detection method, using terminal-restriction fragment length polymorphism (T-RFLP) of the glutamate dehydrogenase gene to characterize human infections. Clinical samples (n=73), positive for Giardia were collected in New South Wales, Australia, and were used to evaluate T-RFLP detection. The accuracy and sensitivity of T-RFLP detection was established by comparison to DNA sequencing and RFLP. Sub-assemblage assignment by T-RFLP identified BIV as the common subtype in N.S.W cases, whilst AI, AII and BIII were also detected. When compared to DNA sequencing and RFLP, analysis by T-RFLP was a reliable and reproducible method. Automated fluorescent detection enabled accurate sizing of restriction fragments and provided a sensitive alternative to RFLP. Discrimination of sub-assemblages by T-RFLP was comparable to DNA sequencing, but was efficient and inexpensive. The protocol described here provides a rapid and sensitive diagnostic tool for routine sample screenings in epidemiological research.
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Rupe, J. C., J. C. Correll, J. C. Guerber, C. M. Becton, E. E. Gbur, Jr., M. S. Cummings, and P. A. Yount. "Differentiation of the sudden death syndrome pathogen of soybean, Fusarium solani f.sp. glycines, from other isolates of F. solani based on cultural morphology, pathogenicity, and mitochondrial DNA restriction fragment length polymorphisms." Canadian Journal of Botany 79, no. 7 (July 1, 2001): 829–35. http://dx.doi.org/10.1139/b01-051.
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Forty-four isolates consisting of Fusarium solani (Mart.) Sacc. f.sp. glycines Roy, Fusarium solani f.sp. phaseoli (Burkholder) W.C. Snyder & H.N. Hans., and F. solani, collected from a variety of hosts and locations, were compared based on pathogenicity on soybean and mitochondrial DNA (mtDNA) restriction fragment length polymorphisms (RFLPs). The 24 isolates of F. solani f.sp. glycines caused more severe sudden death syndrome (SDS) foliar symptoms and root rot on soybean compared with all other isolates. All isolates of F. solani f.sp. glycines belonged to a single mtDNA RFLP haplotype. The other isolates of F. solani belonged to nine mtDNA RFLP haplotypes distinct from that of the SDS pathogen and did not cause significant levels of SDS. Three isolates of F. solani f.sp. phaseoli in a single mtDNA RFLP haplotype were very similar to isolates of F. solani f.sp. glycines in culture. One of these isolates consistently produced SDS-like symptoms in pathogenicity tests, although at a low frequency. Fusarium solani f.sp. glycines represent a genetically distinct subgroup within F. solani but may be related to F. solani f.sp. phaseoli.Key words: Fusarium solani f.sp. phaseoli, Glycine max, sudden death syndrome (SDS), mtDNA.
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Lakshmi, M., M. Parani, Nivedita Ram, and Ajay Parida. "Molecular phylogeny of mangroves VI. Intraspecific genetic variation in mangrove species Excoecaria agallocha L. (Euphorbiaceae)." Genome 43, no. 1 (February 1, 2000): 110–15. http://dx.doi.org/10.1139/g99-109.
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Genomic DNA from 84 individuals of Excoecaria agallocha from seven mangrove populations were analysed for random amplified polymorphic DNAs (RAPDs) using 16 random 10-mer primers. Polymorphism within populations varied from 20% to 31%. At the interpopulation level, 111/149 (74%) of RAPDs were polymorphic. Restriction fragment length polymorphism (RFLP) analysis of 21 individuals (3 individuals randomly selected from the 7 populations) using 30 probe-enzyme combinations revealed a high level of interpopulation polymorphism (62.2%) indicating interpopulation genetic divergence. The polymorphic RAPDs and RFLPs were pooled, and clustering was carried out based on mean similarity for individual populations. The dendrogram showed groupings of populations from the West and East Coasts of India into separate clusters, at 60% similarity level. Further, RAPD and RFLP analysis of male and female plants showed approximately the same level of variation in both sexes, and no sex-linked markers were found. These results demonstrate that considerable intrapopulation and interpopulation genetic variations exist in E. agallocha, and that lack of genetic variation is not the reason for the morphological uniformity observed across the range of the species. Key words: mangroves, Excoecaria agallocha, molecular markers, RAPD, RFLP, genetic variation.
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VICTOIR, K., A. L. BAÑULS, J. AREVALO, A. LLANOS-CUENTAS, R. HAMERS, S. NOËL, S. DE DONCKER, D. LE RAY, M. TIBAYRENC, and J. C. DUJARDIN. "The gp63 gene locus, a target for genetic characterization of Leishmania belonging to subgenus Viannia." Parasitology 117, no. 1 (July 1998): 1–13. http://dx.doi.org/10.1017/s0031182098002789.
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In the present study the gp63 gene locus was used as a target for genetic characterization of Leishmania parasites by 2 methods: (i) RFLP analysis with several restriction enzymes (gp63–RFLP), and (ii) intra-genic PCR amplification coupled with restriction analysis (PCR–RFLP). Both methods were applied to a large number of natural isolates belonging to 4 species of the subgenus Viannia, namely L. (V.) braziliensis, L. (V.) peruviana, L. (V.) guyanensis and L. (V.) lainsoni: reference stocks of subgenus Leishmania were included as outgroups. Multilocus isoenzyme typing (MLEE) was used as a reference. On the one hand gp63–RFLP evidenced an extensive polymorphism and revealed specific markers for subgenus, species and geographical populations: congruence with MLEE was demonstrated statistically. The particular interest of gp63–RFLP was illustrated by infra-specific polymorphism, because of the possible relationship with phenotype diversity. On the other hand intra-genic amplification was less resolutive than gp63–RFLP, but also allowed discrimination of the 2 subgenera (PCR alone) and all the species tested in the subgenus Viannia (PCR–RFLP). PCR–RFLP presents an important operational advantage as it allows genetic characterization of minute amounts of parasites, using Leishmania specific primers. The polymorphism revealed by gp63–RFLP and PCR–RFLP illustrates the very high genomic and genetic plasticity of gp63 genes.
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Tzeng, T. H., L. K. Lyngholm, C. F. Ford, and C. R. Bronson. "A restriction fragment length polymorphism map and electrophoretic karyotype of the fungal maize pathogen Cochliobolus heterostrophus." Genetics 130, no. 1 (January 1, 1992): 81–96. http://dx.doi.org/10.1093/genetics/130.1.81.
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Abstract A restriction fragment length polymorphism (RFLP) map has been constructed of the nuclear genome of the plant pathogenic ascomycete Cochliobolus heterostrophus. The segregation of 128 RFLP and 4 phenotypic markers was analyzed among 91 random progeny of a single cross; linkages were detected among 126 of the markers. The intact chromosomal DNAs of the parents and certain progeny were separated using pulsed field gel electrophoresis and hybridized with probes used to detect the RFLPs. In this way, 125 markers were assigned to specific chromosomes and linkages among 120 of the markers were confirmed. These linkages totalled 941 centimorgans (cM). Several RFLPs and a reciprocal translocation were identified tightly linked to Tox1, a locus controlling host-specific virulence. Other differences in chromosome arrangement between the parents were also detected. Fourteen gaps of at least 40 cM were identified between linkage groups on the same chromosomes; the total map length was therefore estimated to be, at a minimum, 1501 cM. Fifteen A chromosomes ranging from about 1.3 megabases (Mb) to about 3.7 Mb were identified; one of the strains also has an apparent B chromosome. This chromosome appears to be completely dispensable; in some progeny, all of 15 markers that mapped to this chromosome were absent. The total genome size was estimated to be roughly 35 Mb. Based on these estimates of map length and physical genome size, the average kb/cM ratio in this cross was calculated to be approximately 23. This low ratio of physical length to map distance should make this RFLP map a useful tool for cloning genes.
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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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Prince, James P., and Steven D. Tanksley. "Restriction fragment length polymorphisms in plant breeding and genetics." Proceedings of the Royal Society of Edinburgh. Section B. Biological Sciences 99, no. 3-4 (1992): 23–29. http://dx.doi.org/10.1017/s0269727000005479.
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SynopsisThe usefulness of restriction fragment length polymorphisms (RFLPs) in plant breeding and genetics is discussed, with particular emphasis on tagging genes, map-based cloning, the assessment of genetic variability and distances, and comparative genome mapping.The Department of Plant Breeding and Biometry has currently established tight linkages between RFLPs and more than 20 genes of economic importance. Approximately half of these genes confer resistance to major pathogens including nematodes, bacteria, fungi, and viruses. Other genes tagged are involved in various aspects of crop quality.Locating genes with respect to DNA markers on an RFLP map provides a starting point for cloning the genes by chromosome walking. This strategy is currently being pursued for three disease-resistance genes that have been placed on the tomato RFLP map; Pto (resistance to Pseudomonas syringae), Mi (resistance to root-knot nemotodes) and Tm2a (resistance to tobacco mosaic virus). Further discussion will include the construction of a yeast artificial chromosome library and the collection of additional DNA markers in the regions of interest through RAPD analysis of nearly isogenic lines.The assessment of genetic variability and fingerprinting varieties based on RFLP data will be briefly discussed.Comparative genome mapping in the family Solanaceae has allowed the relationships among tomato, potato, and pepper to be unravelled. Tomato and potato share a near perfect conservation of gene order throughout their genomes. In contrast, while pepper shares most of its single copy DNA with tomato and potato, the order of these markers is highly rearranged compared with the other two species.
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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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Råberg, Ulrika, Nils O. S. Högberg, and Carl Johan Land. "Detection and species discrimination using rDNA T-RFLP for identification of wood decay fungi." Holzforschung 59, no. 6 (November 1, 2005): 696–702. http://dx.doi.org/10.1515/hf.2005.111.
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AbstractIn the present work PCR technology was used as a tool to detect the early stages of wood decay and was compared with microscopic evaluation. The wood decay fungiPostia placentaandConiophora puteanawere detectable in interior wood samples by terminal restriction fragment length polymorphism (T-RFLP) after 2weeks of incubation with monocultures, while microscopic detection of hyphae was not possible until after 7 weeks. A potential problem when fungal communities are studied with T-RFLPs of rDNA is that intra-specific variation complicates data analysis. In this work, we show that intra-specific sequence variation in the internal transcribed spacer of the rDNA inConiophora puteanaallows T-RFLP identification of this species. This is due to intra-specific variations in fragment length, in combination with the absence of point mutations in the selected restriction sites.
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Mackay, K., J. R. Hawkins, A. Superti Furga, B. Steinmann, and R. Dalgleish. "AHaeIII RFLP in COL1A1." Nucleic Acids Research 18, no. 19 (1990): 5926. http://dx.doi.org/10.1093/nar/18.19.5926.
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Burmeister, Margit, David R. Cox, and Richard M. Myers. "Taql RFLP at D21S137." Nucleic Acids Research 19, no. 14 (1991): 4020. http://dx.doi.org/10.1093/nar/19.14.4020.
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Scuback, D. E., L. Ozelius, and X. O. Breakefield. "Banl RFLP atAK1locus (9q34)." Nucleic Acids Research 19, no. 20 (1991): 5798. http://dx.doi.org/10.1093/nar/19.20.5798-a.
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Ozelius, L., J. F. Gusella, and X. O. Breakefield. "MspI RFLP for humanMAOAgene." Nucleic Acids Research 17, no. 24 (1989): 10516. http://dx.doi.org/10.1093/nar/17.24.10516.
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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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Stalker, H. T., J. S. Dhesi, and G. Kochert. "Genetic diversity within the species Arachis duranensis Krapov. &W.C. Gregory, a possible progenitor of cultivated peanut." Genome 38, no. 6 (December 1, 1995): 1201–12. http://dx.doi.org/10.1139/g95-158.
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Eighteen accessions of a diploid wild peanut species (Arachis duranensis) were analyzed using morphological, intercrossing, cytological, and RFLP data. Abundant variation was found for morphological characters and for RFLP patterns both between and within accessions, and each accession could be uniquely identified by RFLP pattern. Several plants were found to be F1 hybrids between different accessions, indicating that intercrossing had occurred when these were planted for seed increase. Patterns of RFLP diversity were found to correspond with geographic distribution. Analysis of the number of RFLP fragments observed per accession indicates that additional field collections of this complex of taxa will yield additional genetic variability.Key words: peanut, Arachis hypogaea, Arachis spp., RFLP, variation, genetic diversity.
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Reinisch, A. J., J. M. Dong, C. L. Brubaker, D. M. Stelly, J. F. Wendel, and A. H. Paterson. "A detailed RFLP map of cotton, Gossypium hirsutum x Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome." Genetics 138, no. 3 (November 1, 1994): 829–47. http://dx.doi.org/10.1093/genetics/138.3.829.
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Abstract We employ a detailed restriction fragment length polymorphism (RFLP) map to investigate chromosome organization and evolution in cotton, a disomic polyploid. About 46.2% of nuclear DNA probes detect RFLPs distinguishing Gossypium hirsutum and Gossypium barbadense; and 705 RFLP loci are assembled into 41 linkage groups and 4675 cM. The subgenomic origin (A vs. D) of most, and chromosomal identity of 14 (of 26), linkage groups is shown. The A and D subgenomes show similar recombinational length, suggesting that repetitive DNA in the physically larger A subgenome is recombinationally inert. RFLPs are somewhat more abundant in the D subgenome. Linkage among duplicated RFLPs reveals 11 pairs of homoelogous chromosomal regions-two appear homosequential, most differ by inversions, and at least one differs by a translocation. Most homoeologies involve chromosomes from different subgenomes, putatively reflecting the n = 13 to n = 26 polyploidization event of 1.1-1.9 million years ago. Several observations suggest that another, earlier, polyploidization event spawned n = 13 cottons, at least 25 million years ago. The cotton genome contains about 400-kb DNA per cM, hence map-based gene cloning is feasible. The cotton map affords new opportunities to study chromosome evolution, and to exploit Gossypium genetic resources for improvement of the world's leading natural fiber.
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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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Pate, M., M. Moravkova, B. Krt, I. Pavlik, and M. Ocepek. "Genotyping of Mycobacterium avium subsp. avium isolates from domestic animals in Slovenia by IS901 RFLP." Veterinární Medicína 54, No. 6 (July 29, 2009): 270–79. http://dx.doi.org/10.17221/3084-vetmed.
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ABSTRACT: Apart from birds, <I>Mycobacterium avium</I> subsp. <I>avium (MAA) </I> is often isolated from granulomatous lesions in pigs and occasionally from cattle and other animals. The objectives of this study were the detection of IS<I>901</I> restriction fragment length polymorphism (RFLP) types of <I>MAA</I> isolates from different species of domestic animals between the years 1998 and 2004 and the comparison of the detected RFLP types with previously described RFLP types collected in the database of the OIE Reference Laboratory for Avian Tuberculosis (Brno, Czech Republic). Furthermore, the RFLP types of the isolates obtained from <I>MAA</I> outbreaks on one of the largest pig farms in Slovenia were also investigated. A total of 62 isolates (56 from pigs, five from poultry and one from cattle) were identified with IS<I>901</I> PCR and IS<I>901</I> RFLP typed using restriction endonucleases <I>Pvu</I>II and <I>Pst</I>I. Seven <I>Pvu</I>II RFLP and 11 <I>Pst</I>I RFLP types resulted in 12 combined <I>Pvu</I>II <I>Pst</I>I types; none of these matched the combined RFLP types described in previous studies. Our contributions to the database were two new <I>Pvu</I>II and eight new <I>Pst</I>I RFLP types. Identical RFLP types were found among isolates of animals originating from individual farms. Finding of identical RFLP types within a farm is not surprising because the animals were epidemiologically related and infected with one strain. A unique RFLP type F-A17 was detected in isolates from different pig herds and also in isolates from poultry. Detection of identical RFLP types on different farms may reflect one <I>MAA</I> source. The other combined <I>Pvu</I>II <I>Pst</I>I RFLP types were identified only once which indicates considerable variety of <I>MAA</I> RFLP types in Slovenia.
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Alizadeh, A., M. Arlat, A. Sarrafi, C. A. Boucher, and G. Barrault. "Restriction Fragment Length Polymorphism Analyses of Iranian Strains of Xanthomonas campestris from Cereals and Grasses." Plant Disease 81, no. 1 (January 1997): 31–35. http://dx.doi.org/10.1094/pdis.1997.81.1.31.
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Restriction fragment length polymorphism (RFLP) analyses of the genomic DNA of 45 Xanthomonas campestris strains from cereals and grasses in Iran, and of 17 reference strains, were performed using two probes originating from X. campestris and including hrp genes. The Iranian strains studied belonged to three clearly distinct RFLP groups related to the grouping previously established on the basis of biochemical and physiological characters and host range. RFLP group 1 encompassed all the strains pathogenic to barley but not to the other plants tested (i.e., wheat, rye, Bromus inermis, Lolium multiflorum, Agropyron elongatum, and oat). RFLP group 2 contained strains that are pathogenic to all the above mentioned plants except oat. One strain, which has the same host range as group 2, was classified as RFLP group 3. Reference strains were distributed over these three groups, independently of their geographical origin. Strains in groups 1 and 3 had highly conserved RFLP patterns. In contrast, group 2 strains were easily split into two RFLP subgroups, although they did not differ significantly for other characters. The data suggest that RFLP analysis is a useful tool to distinguish among X. campestris strains causing bacterial leaf streak of cereals.
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Nagashima, Koji, Takayoshi Hisada, Maremi Sato, and Jun Mochizuki. "Application of New Primer-Enzyme Combinations to Terminal Restriction Fragment Length Polymorphism Profiling of Bacterial Populations in Human Feces." Applied and Environmental Microbiology 69, no. 2 (February 2003): 1251–62. http://dx.doi.org/10.1128/aem.69.2.1251-1262.2003.
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ABSTRACT New primer-enzyme combinations for terminal restriction fragment length polymorphism (T-RFLP) targeting of the 16S rRNA gene were constructed by using the T-RFLP analysis program (designated TAP T-RFLP) located at the Ribosomal Database Project website, and their performance was examined empirically. By using the fluorescently labeled 516f primer (Escherichia coli positions 516 to 532) and 1510r primer (positions 1510 to 1492), the 16S rRNA gene was amplified from human fecal DNA. The resulting amplified product was digested with RsaI plus BfaI or with BslI. When the T-RFLP was carried out with fecal DNAs from eight individuals, eight predominant operational taxonomic units (OTUs) were detected with RsaI and BfaI digestion and 14 predominant OTUs were detected with BslI digestion. The distribution of the OTUs was consistent with the results of the computer simulations with TAP T-RFLP. The T-RFLP analyses of the fecal DNAs from individuals gave characteristic profiles, while the variability of the T-RFLP profiles between duplicate DNA preparations from the same samples were minimal. This new T-RFLP method made it easy to predict what kind of intestinal bacterial group corresponded to each OTU on the basis of the terminal restriction fragment length compared with the conventional T-RFLP and, moreover, made it possible to identify the bacterial species that an OTU represents by cloning and sequencing.
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Sibley, L. D., A. J. LeBlanc, E. R. Pfefferkorn, and J. C. Boothroyd. "Generation of a restriction fragment length polymorphism linkage map for Toxoplasma gondii." Genetics 132, no. 4 (December 1, 1992): 1003–15. http://dx.doi.org/10.1093/genetics/132.4.1003.
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Abstract We have constructed a genetic linkage map for the parasitic protozoan, Toxoplasma gondii, using randomly selected low copy number DNA markers that define restriction fragment length polymorphisms (RFLPs). The inheritance patterns of 64 RFLP markers and two phenotypic markers were analyzed among 19 recombinant haploid progeny selected from two parallel genetic crosses between PLK and CEP strains. In these first successful interstrain crosses, these RFLP markers segregated into 11 distinct genetic linkage groups that showed close correlation with physical linkage groups previously defined by molecular karyotype. Separate linkage maps, constructed for each of the 11 chromosomes, indicated recombination frequencies range from approximately 100 to 300 kb per centimorgan. Preliminary linkage assignments were made for the loci regulating sinefungin resistance (snf-1) on chromosome IX and adenine arabinoside (ara-1) on chromosome V by linkage to RFLP markers. Despite random segregation of separate chromosomes, the majority of chromosomes failed to demonstrate internal recombination events and in 3/19 recombinant progeny no intramolecular recombination events were detected. The relatively low rate of intrachromosomal recombination predicts that tight linkage for unknown genes can be established with a relatively small set of markers. This genetic linkage map should prove useful in mapping genes that regulate drug resistance and other biological phenotypes in this important opportunistic pathogen.
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Pappalardo, Anna Maria, Marta Giuga, Alessandra Raffa, Marco Nania, Luana Rossitto, Giada Santa Calogero, and Venera Ferrito. "COIBar-RFLP Molecular Strategy Discriminates Species and Unveils Commercial Frauds in Fishery Products." Foods 11, no. 11 (May 26, 2022): 1569. http://dx.doi.org/10.3390/foods11111569.
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The DNA analysis is the best approach to authenticate species in seafood products and to unveil frauds based on species substitution. In this study, a molecular strategy coupling Cytochrome Oxidase I (COI) DNA barcoding with the consolidated methodology of Restriction Fragment Length Polymorphisms (RFLPs), named COIBar-RFLP, was applied for searching pattern of restriction enzyme digestion, useful to discriminate seven different fish species (juveniles of Engraulis encrasicolus and Sardina pilchardus sold in Italy as “bianchetto” and Aphia minuta sold as “rossetto”; icefish Neosalanx tangkahkeii; European perch, Perca fluviatilis and the Nile Perch, Lates niloticus; striped catfish, Pangasianodon hypophthalmus). A total of 30 fresh and frozen samples were processed for DNA barcoding, analyzed against a barcode library of COI sequences retrieved from GenBank, and validated for COIBar–RFLP analysis. Cases of misdescription were detected: 3 samples labeled as “bianchetto” were substituted by N. tangkahkeii (2 samples) and A. minuta (1 sample); 3 samples labeled as “persico reale” (P. fluviatilis) were substituted by L. niloticus and P. hypophthalmus. All species were simultaneously discriminated through the restriction pattern obtained with MspI enzyme. The results highlighted that the COIBar-RFLP could be an effective tool to authenticate fish in seafood products by responding to the emerging interest in molecular identification technologies.