Plant & Animal Genome VI Conference

P53

A MICROSATELLITE MAP FOR RICE: RECENT PROGRESS AND PERSPECTIVES

1. Department of Plant Breeding, Cornell University, Ithaca, NY 14853-1901, USA
2. Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77853, USA
3. National Institute of Agicultural Science and Technology, Suwon 441-707, Korea

A framework map based solely on microsatellite markers has been constructed for the rice genome. The map provides good coverage for all twelve chromosomes and consists of about 300 SSLP loci, including more than 150 newly developed markers. As a continuation of the previous work microsatellite containing sequences were isolated from a Tsp-digested small-insert genomic library, but at this time different di- and tri-nucleotide motifs (GT, CAT, CTT) were targeted in addition to the most common GA motif. About 25 nonredundant microsatellite markers have been characterized for each GT, CAT and CTT motif. Another set of SSLP markers has been developed based on SSR-containing sequences extracted from the GenBank database. Twenty nine out of 135 sequences used for primer design corresponded to known genes, with the rest of the sequences presenting randomly sequenced cDNA clones. For this collection of SSR markers only 60% of the 135 primer pairs produced highly informative polymorphic markers, while the rest presented monomorphic or highly conserved sequences (see poster about SSLP diversity analysis by Cho et al.) and were not incorporated into the existing framework map. Basically, new polymorphic markers were mapped onto the population of doubled haploid lines derived from the intersubspecific cross between IR64 (indica) and Azucena (japonica). A number of additional SSLPs were integrated into the framework map based on mapping in three other populations and aligning them in relation to common anchor markers. Our success in generating microsatellite markers containing different motifs and from different sources of DNA sequences and building a representative map with good genome coverage provides evidence that this approach can be effective for further saturation of the microsatellite map of the rice genome as well as for construction of microsatellite maps in other species.