Microsatellite markers in rice: abundance, diversity, and applications

A well-distributed set of 500 microsatellite markers has been genetically mapped onto the rice genome. These markers link the genetic and physical maps with the genomic sequence of rice, facilitating studies that seek to determine the relationship between the structure and function of genes and genomes. To facilitate the development of new microsatellite markers using publicly available DNA sequence information, a simple sequence repeat identification tool (SSRIT) has been developed for semiautomated identification of nonredundant simple sequence repeat (SSR) loci and for primer design (available at http://www.gramene.org/microsat/). Using this script, a total of 57.8 Mb of DNA sequence from rice was searched to determine the frequency and distribution of different SSRs in the genome. Because the length of the SSR unit in any single genome has proven to be a reasonably good predictor of overall polymorphism in related genotypes, SSR loci were categorized into two groups (class I and class II) based on the length of the repeat motif. Microsatellites with poly(AT)n repeats represented the most abundant and polymorphic class of SSRs but were frequently associated with the Micropon family of miniature inverted repeat transposable elements (MITEs) and were difficult to amplify. Estimates of total microsatellite frequencies in rice suggested that there were approximately 28,340 Class I and 70,530 Class II SSRs, or about 100,000 di-, tri-, and tetra-nucleotide SSR motifs in the rice genome. The distribution of SSR sequences showed that regions of the rice genome that were richer in expressed genes also tended to be richer in SSR sequences, underscoring their usefulness as genetic markers. Applications of SSRs in variety protection, diversity analysis, gene and QTL identification, marker-assisted selection, physical mapping, and gene isolation will be discussed.