Molecular genetic maps are commonly constructed by analyzing the segregation of restriction fragment length polymorphisms (RFLPs) among the progeny of a sexual cross. Here we describe a new DNA polymorphism assay based on the amplification of random DNA segments with single primers of arbitrary nucleotide sequence. These polymorphisms, simply detected as DNA segments which amplify from one parent but not the other, are inherited in a Mendelian fashion and can be used to construct genetic maps in a variety of species. We suggest that these polymorphisms be called RAPD markers, after Random Amplified Polymorphic DNA.

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A population of Arabidopsis thaliana recombinant inbred lines was constructed and used to develop a high-density genetic linkage map containing 252 random amplified polymorphic DNA markers and 60 previously mapped restriction fragment length polymorphisms. Linkage groups were correlated to the classical genetic map by inclusion of nine phenotypic markers in the mapping cross. We also applied a technique for local mapping that allows targeting of markers to a selected genome region by pooling DNA from recombinant inbred lines based on their genotype. We conclude that random amplified polymorphic DNAs, used in coglunction with a recombinant inbred population, can facilitate the genetic and physical characterization of the Arabidopsis genome and that this method is generally applicable to other organisms for which appropriate populations either are available or can be developed.The crucifer Arabidopsis thaliana is a useful system for basic studies in plant molecular genetics due to its relatively small genome size, small amounts of dispersed repetitive DNA, and rapid generation time (1). These attributes have made Arabidopsis an attractive model system for the analysis of genome organization and the development and use of technology to clone genes known only through their genetic map position.High-density genetic maps based upon DNA markers can provide starting points for chromosome walking experiments. Markers closely linked to a mutation of interest can reduce the amounts of DNA to be cloned and help establish the direction of the chromosome walk. Restriction fragment length polymorphisms (RFLPs) have been used as markers to construct genetic maps (2) and as starting points for chromosome walking (3). To date, two different RFLP maps have been reported in Arabidopsis (4, 5).Recently another class of genetic markers [random amplified polymorphic DNAs (RAPDs)] has been described (6, 7), which relies on the observation that a single oligonucleotide primer, of arbitrary nucleotide sequence, will direct the amplification of discrete loci (for a more detailed description of this method, see ref. 8). We report here the use of RAPD markers to construct a genetic map of A. thaliana. This map has been constructed with unprecedented speed by using RAPD markers and a recombinant inbred (RI) population. For many mapping purposes RI populations are superior to F2 or backcross populations because they constitute a permanent population in which segregation is fixed (9). Additional markers scored on the same RI population are automatically integrated with the existing map, making map information cumulative (9).Near-isogenic lines have been used to target RFLP (10) or RAPD (11) markers to specific segments of a genome. However, construction of near-isogenic lines is time consuming, and unlinked portions of the donor genome remain even after several crosses to the recurrent parent (12). Pooling DNA based on phenotype has been used as a means of either identifying additional RFLP loci (13) or mapping existing RFLP loci (14) ...