The use of microsatellite markers has greatly accelerated the mapping of important traits and the characterization of genome structure in several plant and animal species. Microsatellites (also known as simple sequence repeats) are small, repetitive DNA structures, typically distributed throughout the genome, which are highly mutable and show substantial variation in size (polymorphism). To exploit microsatellites as molecular markers, they are amplified by polymerase chain reaction (PCR); gel electrophoresis or other analytical methods determine the size of the resulting DNA product. In organisms with genomes as large and complex as those of tetraploid cottons, several thousand microsatellite markers will be required for genetic mapping and genome analysis. To date, microsatellites have not been used extensively in cotton, in part because of the complex and laborintensive methods for identifying microsatellites from large genomes.

Here we address the problem of microsatellite marker discovery, and present the initial results from a low-cost, easy-to-use, efficient method for microsatellite capture. Using an optimized protocol, more than 10,000 microsatellitecontaining fragments were obtained from Gossypium hirsutum L. genomic DNA. Sequences from 588 of these DNA fragments were determined, and oligonucleotide primers for PCR amplification of 307 microsatellite markers were designed. A subset of markers was tested in a set of G. hirsutum L. and Gossypium barbadense L. varieties. Approximately 49% showed length