MICROSATELLITE MARKER DEVELOPMENT, MAPPING AND APPLICATIONS IN RICE GENETICS AND BREEDING

Microsatellites are simple, tandemly repeated di-to tetra-nucleotide s equence motifs flanked by unique sequences. They an valuable as geneti c markers because they are co-dominant, detect high levels of allelic diversity, and are easily and economically assayed by the polymerase c hain reaction (PCR). Results from screening a rice genomic library sug gest that there are an estimated 5700-10 000 microsatellites in rice, with the relative frequency of different repeats decreasing with incre asing size of the motif. A map consisting of 120 microsatellite marker s demonstrates that they are well distributed throughout the 12 chromo somes of rice. Five multiple copy primer sequences have been identifie d that could be mapped to independent chromosomal locations. The curre nt level of genome coverage provided by these simple sequence length p olymorphisms (SSLPs) in rice is sufficient to be useful for genotype i dentification, gene and quantitative trait locus (QTL) analysis, scree ning of large insert libraries, and marker-assisted selection in breed ing. Studies of allelic diversity have documented up to 25 alleles at a single locus in cultivated rice germplasm and provide evidence that amplification in wild relatives of Oryza sativa is generally reliable. The availability of increasing numbers of mapped SSLP markers can be expected to complement existing RELP and AFLP maps, increasing the pow er and resolution of genome analysis in rice.