The abundance and scattered distribution of simple-sequence repeats (SSR) in eukaryotic genomes prompted us to explore the use of SSR-based oligonucleotide primers in single primer amplification reactions. In a pilot experiment, 23 primers were used across a panel of evolutionarily diverse eukaryotic genomes, including grapes, lettuce, tomato, pine, maize, salmon, chicken, Holstein cows and humans. The primers were 16-20 bases in length and represented SSRs of di-, tri-, tetra-, and pentanucleotide repeats. The results showed that tetranucleotide repeat primers were most effective in amplifying polymorphic patterns. Of 11 such primers tested, 70% produced polymorphic patterns from the DNA of one or more species. Primers representing a combination of two tetranucleotide repeats, or compound microsatellites, were equally effective. The polymorphisms contained in such fingerprints were able to identify individuals of vertebrate species as well as lines or varieties of plants. Inheritance of the polymorphic bands was studied in a maize recombinant inbred population, DE811 x B73. Thirty-two polymorphic bands, derived from two amplification patterns, were mapped as dominant markers on an existing RFLP map of the same population. The bands were distributed across nine of the ten chromosomes.

No abstract

DNA amplification reactions using long, non-random, single oligonucleotide primers with thermostable DNA polymerase and avian genomic DNA generate unique, reproducible multiband patterns of DNA fragments. These DNA fragments are produced from amplification reactions using single primers of at least twentyfive bases in length which were derived from the chicken α A -globin gene. The patterns of amplified DNA fragments were polymorphic among individual chickens. Within families, polymorphic band patterns were found to be heritable, as the DNA fragments of progeny were present in at least one of the parents. In a conventional polymerase chain reaction containing a pair of primers, the relative concentrations of the primers can be manipulated to produce either a discrete two primer product or a multiband pattern identical to the single primer products. In addition, the number of bands in the multiband pattern increases as the stringency of the annealing step of the DNA amplification is decreased. The products are believed to result from recognition of a family of related sequences in the genome. This single primer amplification method has general application in the establishment of molecular relatedness, discovery of new genetic markers, resolution of questions of paternity, identification of individual organisms, and measurement of biodiversity within and among populations.