RAPD

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

Sequence-tagged-site-facilitated PCR for barley genome mapping

Abstract: Speed, efficiency, and safety considerations have led many genome mapping projects to evaluate polymerase chain reaction (PCR) sequence amplification as an alternative to Southern blot analysis However, the availability of informative primer sequences can be a limiting factor in PCR-based mapping An alternative to random amplified polymorphism detection (RAPD) is the sequence-tagged-site (STS) approach If informative primer sequences could be derived from known sequences, then current maps, which are based on both known function and anonymous clones, might be easily converted to maps utilizing PCR technology In this paper, four pairs of primer sequences were obtained from published sequences, and four pairs were obtained by sequencing portions of DNA clones from genomic clones derived from a random genomic library used in the North American Barley Genome Mapping Project (NABGMP) These primers were used to screen for polymorphisms in the progeny of a winter x spring and a spring x spring barley cross Two types of polymorphisms were distinguished using these primer sets: (1) insertion/deletion events that could be read directly from agarose gels, and (2) point mutation events The latter were identified using polyacrylamide-gel electrophoresis of PCR products following digestion with restriction endonucleases (four-base cutters) To determine whether the PCR-based polymorphisms were allelic to polymorphisms identified by the clones from which the primer sequences derived, chromosomal assignments and (when possible) co-segregation analysis was performed

Genomic mapping in Pinus pinaster (maritime pine) using RAPD and protein markers

Abstract: A detailed genomic map was constructed for one F1 individual of maritime pine, using randomly amplified polymorphic DNA (RAPD) and protein markers scored on megagametophytes of germinated seeds. Proteins allowed the localization of exclusively coding DNA in the large genome of this Pinus species, mapped with RAPD markers that essentially fall within repetitive (i.e. mostly noncoding) DNA. Dot blots experiments of 53 RAPD fragments showed that 89 per cent amplified from highly repetitive chromosomal regions. The map comprised 463 loci, including 436 RAPDs amplified from 142 10-mer oligonucleotide primers and 27 protein loci. Twelve major and one minor linkage groups were identified using a LOD score ⩽ 5 and a recombination fraction Θ ≤ 0.30. A framework map was ordered with an interval support ≥4, covering 1860 cM which provided almost complete coverage of the maritime pine genome. The average distance between two framework markers was 8.3 cM; only one interval was larger than 30 cM. Protein loci were well distributed throughout the map. Their potential use as anchor points to join RAPD-based maps is discussed. Finally, the genomic maps of Arabidopsis and maritime pine were compared. Linkage groups were shown to have similar total map lengths on a chromosomal basis, despite a 57-fold difference in DNA content.

Genetic variation detected with RAPD markers among upland and lowland rice cultivars (Oryza sativa L.).

Abstract: Genetic variation of nine upland and four lowland rice cultivars (Oryza sativa L.) was investigated at the DNA level using the randomly amplified polymorphic DNA (RAPD) method via the polymerase chain reaction (PCR). Forty-two random primers were used to amplify DNA segments and 260 PCR products were obtained. The results of agarosegel electrophoretic analysis of these PCR products indicated that 208 (80%) were polymorphic. All 42 primers used in this experiment were amplified and typically generated one-to-four major bands. Only two primers showed no polymorphisms. In general, a higher level of polymorphism was found between japonica and indica subspecies while fewer polymorphisms were found between upland and lowland cultivars within the indica subspecies. A dendrogram that shows the genetic distances of 13 rice cultivars was constructed based on their DNA polymorphisms. Classification of rice cultivars based on the results from the RAPD analysis was identical to the previous classification based on isozyme analysis. This study demonstrated that RAPD analysis is a useful tool in determining the genetic relationships among rice cultivars.

Extensive clonality in the endangered shrub Haloragodendron lucasii (Haloragaceae) revealed by allozymes and RAPDs

Abstract: The occurrence of clonality in threatened plants can have important implications for their conservation. In this study, allozymes and RAPDs were used to determine the extent of clonality in the endangered shrub Haloragodendron lucasii (Haloragaceae), which is known from only four sites within an 8 km range. Allozyme markers identified only six multilocus genotypes among the 53 ramets sampled across the four sites, although a total of 54 different genotypes were possible with the three polymorphic allozyme loci detected. The polymorphic bands detected in the RAPD analysis were capable of producing 246 genotypes, but again only six multilocus genotypes were delineated. The allozyme and RAPD data were congruent at three of the four sites. At the fourth site two genotypes were detected by each marker; however, once combined, three multilocus genotypes were observed. The probabilities that the observed number of replicates of each combined allozyme and RAPD genotype could be generated by sexual reproduction were less than 10–18, leaving little doubt that clonality is the explanation for the observed patterns of genotypes. The genetic conclusions are supported by root excavations which show potential for vegetative reproduction and the observation of no sexual reproduction in the species. The recognition of extensive clonality in H. lucasii has had immediate implications for the conservation management of the species and resulted in changes to the management priorities for the species. Thus it is clear that appropriate genetic studies can play an important role in the management of threatened species.