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RAPD

About: RAPD is a research topic. Over the lifetime, 15960 publications have been published within this topic receiving 360391 citations.


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TL;DR: The results suggest extensive gene flow among populations, but higher GST and lower Nm values relative to other outcrossing, woody species with endozoochorous dispersal, also suggest a process of isolation by distance.
Abstract: We examined the patterns of random amplified polymorphic DNA (RAPD) variation among seven Prunus mahaleb (Rosaceae) populations extending over ∪ ∪ ∪ 100 km 2 to examine local differentiation in relation to spatial isolation due to both geographical distance and differences in elevation. No less than 51.4% of the RAPD loci were polymorphic, but very few were fixed and among-population variation accounted for 16.46% of variation in RAPD patterns. Mean gene diversity was 0.1441, with mean Nei’s genetic diversity for individual populations ranging between 0.089 and 0.149. Mean G ST value across loci was 0.1935 (range, 0.0162‐0.4685), giving an average estimate for Nm of 1.191. These results suggest extensive gene flow among populations, but higher G ST and lower Nm values relative to other outcrossing, woody species with endozoochorous dispersal, also suggest a process of isolation by distance. The combined effect of both geographical and elevation distances and nonoverlapping flowering and fruiting phenophases on the G ST matrix was partially significant, revealing only marginal isolation of the P. mahaleb populations. The matrix correlation between estimated Nm values among populations and the geographical + elevation distance matrices ( r = ‐0.4623, P = 0.07), suggests a marginal trend for more isolated populations to exchange less immigrants. Long-distance seed dispersal by efficient medium-sized frugivorous birds and mammals is most likely associated to the high levels of within-population genetic diversity. However, vicariance factors and demographic bottlenecks (high postdispersal seed and seedling mortality) explain comparatively high levels of local differentiation.

103 citations

Journal ArticleDOI
TL;DR: Microsatellites are tandem repeats of short sequence motifs that occur ubiquitously in eukaryotic genomes and are an extraordinarily high level of variation among taxa, mainly expressed as a variable copy number of tandem repeats.
Abstract: Summary Microsatellites are tandem repeats of short sequence motifs that occur ubiquitously in eukaryotic genomes. A key feature of this class of repetitive DNA is an extraordinarily high level of variation among taxa, mainly expressed as a variable copy number of tandem repeats. A multitude of techniques were described that exploit microsatellite variability as molecular markers. Basically, these approaches can be classified into four different experimental strategies. (1) Oligonucleotides complementary to microsatellites are used as hybridization probes for multilocus RFLP fingerprinting. (2) Microsatellite-complementary oligonucleotides serve as PCR primers, either alone or in combination with arbitrary primers, to amplify certain regions of genomic DNA. (3) (Non)radioactively labelled microsatellite motifs are hybridized to electrophoretically resolved RAPD fragments, resulting in new and unexpected banding patterns on the autoradiograms. (4) Length variation of individual microsatellite loci is analy...

103 citations

Journal ArticleDOI
TL;DR: The genetic fidelity of in vitro-raised gerbera clones was assessed by using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers and a similarity matrix based on Jaccard’s coefficient revealed that the pair-wise value between the mother and the in vivo-raised plantlets was 1, indicating 100% similarity.
Abstract: The genetic fidelity of in vitro-raised gerbera clones was assessed by using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Out of 35 RAPD and 32 ISSR primers screened, only 12 RAPD and 10 ISSR primers produced clear, reproducible and scorable bands. The 12 RAPD primers produced 54 distinct and scorable bands, with an average of 4.5 bands per primer. The number of scorable bands for ISSR primers varied from 3 (ISSR-14) to 9 (ISSR-07), with an average of 5.5 bands per primer. The number of bands generated per primer was greater in ISSR than RAPD. All banding profiles from micropropagated plants were monomorphic and similar to those of the mother plant. A similarity matrix based on Jaccard’s coefficient revealed that the pair-wise value between the mother and the in vitro-raised plantlets was 1, indicating 100% similarity. This confirmed the true-to-type nature of the in vitro-raised clones.

102 citations

Journal ArticleDOI
TL;DR: UPGMA cluster analysis carried out on these data separately for RAPDs and AFLPs and on the combined data reflected, to some extent, pedigree relationships and cophenetic correlations that indicate a good fit of respective clusters to genetic similarity data.
Abstract: In order to obtain an overview of the genetic diversity present within the set of pea cultivars released in Germany, 21 cultivars were analysed at the DNA level by random amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs), as well as for agronomic traits. Yield of grain cultivars ranged from 2.95 to 3.87 t/ha. Based on the screening of 60 RAPD primers and 32 Eco RI + 3/Mse I+3 AFLP primer combinations, 20 RAPD primers and 11 Eco RI + 3/MseI+ 3 primer combinations generating polymorphic and distinct fragments were chosen for estimation of genetic diversity. Twenty RAPD primers amplified a total of 314 scorable bands ranging from about 262 bp to 1996 bp. Of these, 175 fragments (55.7%) were polymorphic. Based on these data, genetic similarity (GS) was estimated between 0.80 (‘Lisa’ vs.‘Grapis’) and 0.94 (‘Bohatyr’ vs. ‘Sponsor’; mean GS = 0.88). Eleven AFLP primer combinations led to the amplification of 949 scorable fragments ranging from 43 to 805 bp and of these, 462 (48.7%) were polymorphic. Genetic similarity based on AFLPs was calculated between 0.85 (‘Lisa’ vs.‘Laser’) and 0.94 (‘Bohatyr’ vs. ‘Sponsor’, mean GS = 0.90). Correlation of genetic similarity estimated on RAPDs and AFLPs was estimated at r = 0.79** using Spearman's rank correlation coefficient and at r = 0.84 by the Mantel test, respectively. UPGMA cluster analysis carried out on these data separately for RAPDs and AFLPs and on the combined data reflected, to some extent, pedigree relationships and cophenetic correlations (r = 0.89 for RAPDs, r = 0.88 for AFLPs, and r = 0.93 RAPDs + AFLPs) indicate a good fit of respective clusters to genetic similarity data. The correlation of cluster analyses to pedigree information and the impact on parental genotype selection is discussed.

102 citations

Journal ArticleDOI
TL;DR: The RAPD technique revealed intraserotype-specific variations, undetectable by the combination of several phenotypic typing methods, among the ETEC strains analyzed, showing that RAPD typing represents a useful tool for population genetics as well as for epidemiological studies of ETEC.
Abstract: The genetic diversity of 47 enterotoxigenic Escherichia coli (ETEC) strains of serotypes O6:H16, O27:H7, O29:H21, O128ac:H12, and O153:H45, previously isolated from diarrheic patients in Brazil over a period of 15 years, was investigated by random amplification of polymorphic DNA (RAPD). Informative band arrays were obtained with three 10-mer primers with G+C contents of 50, 60, and 70%. Based on the combination of the band profiles generated by the three primers 22 RAPD types were detected, and 5 major clonal clusters, each one with at least 80% identical bands, were established. The clonal clusters corresponded to strains having the same serotype which, in most cases, also had the same virulence factors (colonization factors and toxin types) and outer membrane protein and lipopolysaccharide sodium dodecyl sulfate-polyacrylamide gel electrophoresis profiles. The results suggested a correlation between phenotypic properties and genetic relatedness of ETEC isolates of human origin and indicated that a reduced number of clonally related strains are found in areas of ETEC endemicity in Brazil. Moreover, the RAPD technique revealed intraserotype-specific variations, undetectable by the combination of several phenotypic typing methods, among the ETEC strains analyzed. These results show that RAPD typing represents a useful tool for population genetics as well as for epidemiological studies of ETEC.

102 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20241
2023149
2022309
2021152
2020195
2019246