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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: Three different DNA mapping techniques were used on identical soybean germplasm to compare their ability to identify markers in the development of a genetic linkage map, and AFLP is concluded to be the most useful.
Abstract: Three different DNA mapping techniques—RFLP, RAPD and AFLP—were used on identical soybean germplasm to compare their ability to identify markers in the development of a genetic linkage map. Polymorphisms present in fourteen different soybean cultivars were demonstrated using all three techniques. AFLP, a novel PCR-based technique, was able to identify multiple polymorphic bands in a denaturing gel using 60 of 64 primer pairs tested. AFLP relies on primers designed in part on sequences for endonuclease restriction sites and on three selective nucleotides. The 60 diagnostic primer pairs tested for AFLP analysis each distinguished on average six polymorphic bands. Using specific primers designed for soybean fromEco RI andMse I restriction site sequences and three selective nucleotides, as many as 12 polymorphic bands per primer could be obtained with AFLP techniques. Only 35% of the RAPD reactions identified a polymorphic band using the same soybean cultivars, and in those positive reactions, typically only one or two polymorphic bands per gel were found. Identification of polymorphic bands using RFLP techniques was the most cumbersome, because Southern blotting and probe hybridization were required. Over 50% of the soybean RFLP probes examined failed to distinguish even a single polymorphic band, and the RFLP probes that did distinguish polymorphic bands seldom identified more than one polymorphic band. We conclude that, among the three techniques tested, AFLP is the most useful.
129 citations
TL;DR: One hundred and ten markers were analysed for linkage in 218 F2 plants derived from two divergent cultivars of Cucumis melo, spanning 14 linkage groups covering 1390 cM of the melon genome.
Abstract: One hundred and ten markers were analysed for linkage in 218 F2 plants derived from two divergent cultivars (‘Vedrantais’ and ‘Songwhan Charmi’) of Cucumis melo (L.). Thirty-four RFLPs, 64 RAPDs, one isozyme, four disease resistance markers and one morphological marker were used to construct a genetic map spanning 14 linkage groups covering 1390 cM of the melon genome. RAPD and RFLP markers detected similar polymorphism levels. RFLPs were largely due to base substitutions rather than insertion/deletions. Twelve percent of markers showed distorted segregation. Phenotypic markers consisted of two resistance genes against Fusarium wilt (Fom-1 and Fom-2), one gene (nsv) controlling the resistance to melon necrotic spot virus, one gene (Vat) conferring resistance to Aphis gossypii, and a recessive gene for carpel numbers (3 vs 5 carpels: p).
128 citations
TL;DR: Dendrograms which took into account all fragments produced, either by RFLP or RAPD, reflected better the relationships between cultivars than did dendrogram based on only one type of marker, reflecting the importance of the number of markers used in determining the genetic relationships between genotypes.
Abstract: The genetic similarities of eight closely related rye cultivars were estimated using two molecular marking techniques: restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD). Cultivars were evaluated for variation by 11 random cDNA and genomic clones used in combination with four restriction enzymes and 40 decamer primers. A total of 53 polymorphic RFLP fragments and 94 polymorphic RAPD fragments were observed. Based on the presence/absence of fragments, two genetic similarity matrices were calculated which were then used in cluster analysis. Differences between pair of cultivars were observed in RFLP and RAPD dendrograms. RFLP analysis produced estimates of genetic relationships more in accordance with the partially known pedigree of the cultivars than did RAPD analysis. The use of bulk samples of DNA in these analyses affected the sensitivity of RAPD assays more strongly. Dendrograms which took into account all fragments produced, either by RFLP or RAPD, reflected better the relationships between cultivars than did dendrograms based on only one type of marker. This reflects the importance of the number of markers used in determining the genetic relationships between genotypes.
128 citations
TL;DR: RAPD markers generated by mixtures of two different primers were developed for octoploid × Tritordeum and eight of them were converted into dominant SCAR markers by direct sequencing of the RAPD products, avoiding the costly and time-consuming cloning step.
Abstract: RAPD markers generated by mixtures of two different primers were developed for octoploid × Tritordeum (amphiploid Hordeum chilense × Triticum aestivum) and its parents Addition lines were used to identify 21 specific RAPD markers for the H chilense chromosomes detectable in a wheat background Ten RAPD bands were selected and eight of them were converted into dominant SCAR markers by direct sequencing of the RAPD products, avoiding the costly and time-consuming cloning step The methodology overcomes some of the pitfalls associated with the election of the right clones when developing SCARs from RAPD markers The SCARs generated have maintained both the chromosome specificity and the possibility of detection in a wheat background This strategy provides a rapid method for the characterization of RAPD markers and for the development of PCR-based markers for both the characterization of the introgression of H chilense in bread and durum wheat, as well as the efficient and reliable screening of tritordeum lines
128 citations
TL;DR: The magnitude of the phenotypic variation explained by the joint action of the segregating quantitative trait alleles indicated that genetic factors of large effect were involved in the control of the studied characters.
Abstract: The objective of this study was to use random amplified polymorphic DNA (RAPD) to determine the genetic location and effects of genomic regions controlling wood density, stem growth and stem form in two species of Eucalyptus. Two hundred F1 trees generated from an interspecific cross E. urophylla×E. grandis between two elite trees were used. Genetic maps were constructed for each parent with markers segregating in the 1:1 ratio in FS progeny. A total of 86 and 92 markers distributed among 11 linkage groups covered 1295 cM and 1312 cM for the E. urophylla and E. grandis parent, respectively. Traits were measured three times up to selection age (38 months). The magnitude of the phenotypic variation explained by the joint action of the segregating quantitative trait alleles indicated that genetic factors of large effect were involved in the control of the studied characters. Several regions controlling part of the variation for the studied traits were identified by interval mapping. Some regions of the genome exerted effects on more than one trait, providing a genetic explanation for at least some of the correlation between the traits. On the basis of an age-by-age analysis, a partial stability of QTL expression was observed with 68% of the QTL being expressed at two ages and 32% being age-specific. No QTL were significant for all three ages. Taking advantage of repeated measurements on the same material across different ages, we investigated with a maximum statistical power, the effect of marker genotype on traits, with age and QTL×age interaction effects being removed. A two-way analysis of variance made it possible to detect significant marker-trait associations over the period studied. Most of them had already been detected in the annual analysis. This result is very encouraging for the application of marker information to the early selection of hybrid trees to be vegetatively propagated for the production of clonal varieties.
128 citations