Genetic analysis with random amplified polymorphic DNA markers.

For many years, the principles of genetics have been applied to crop variety improvement with great success. Severa1 crop species, notably corn, wheat, and tomato, have been used as model genetic systems because of their central importance to food production. Until recently, virtually a11 progress in both breeding and model genetic systems has relied on a phenotypic assay of genotype. Because the efficiency of a selection scheme or genetic analysis based on phenotype is a function of the heritability of the trait, factors like the environment, multigenic and quantitative inheritance, or partia1 and complete dominance often confound the expression of a genetic trait. Many of the complications of a phenotypebased assay can be mitigated through direct identification of genotype with a DNA-based diagnostic assay. For this reason, DNA-based genetic markers are being integrated into several plant systems and are expected to play an important role in the future of plant breeding. The utility of DNA-based diagnostic markers is determined to a large extent by the technology that is used to reveal DNA-based polymorphisms. Currently, the technology of choice for many species is the RFLP assay. RFLP assays detect DNA polymorphisms through restriction endonuclease digestions, coupled with DNA blot hybridizations, and are, in general, time consuming and labor intensive. Over the last few years, polymerase chain reaction technology has led to the development of several nove1 genetic assays based on selective DNA amplification (Krawetz, 1989; Innis et al., 1990). One of the strengths of these new assays is that they are more amenable to automation 'than conventional techniques. They are also simple to perform and are preferable in experiments where the genotype of a large number of individuals is to be determined at a few genetic loci. Unfortunately, because of a prerequisite for DNA sequence information, these assays are limited in their application. Nearly 2 years ago, a new genetic assay was developed independently by two different laboratories (Welsh and McClelland, 1990; Williams et al., 1990). This procedure, which we have called the RAPD assay, detects nucleotide sequence polymorphisms in a DNA amplification-based assay using only a single primer of arbitrary nucleotide sequence. In this reaction, a single species of primer binds to the genomic DNA at two different sites on opposite strands of the DNA template. If these priming sites are within an amplifiable distance of each other, a discrete DNA product