Plant & Animal Genome VI Conference

W90

DIVERSITY OF MICROSATELLITES DERIVED FROM GENOMIC LIBRARIES AND cDNA SEQUENCES IN RICE (ORYZA SATIVA L.)

1. Department of Plant Breeding, Cornell University, Ithaca, NY 14853-1901, USA
2. National Institute of Agricultural Science and Technology, Suwon 441-707, Korea
3. Plant Breeding, Faculty of Agriculture, Kobe University, Nada-ku, Kobe 657, Japan
4. Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA

Three hundred six microsatellite markers developed for rice (Oryza sativa) were compared for number of alleles per locus, polymorphism information content (PIC value) and size range of alleles based on a panel of 14 rice varieties (13 Oryza sativa cultivars and one O. longistaminata accession). Of the 306 markers, 171 were developed from sequenced genomic clones (genomic microsatellites) and 135 were developed from cDNA sequences extracted from public databases (cDNA microsatellites). The rice varieties used in this study represented seven mapping populations developed in rice research programs in the US, China, Japan, Korea and the Philippines. Genomic microsatellites detected polymorphism more frequently among these varieties (83.8%) than did cDNA microsatellites (54.0%), with an average value of 71.1% overall. The number of alleles per locus was 5.13 for genomic microsatellites and 2.78 for cDNA microsatellies. This corresponded to an average PIC value of 0.68 for genomic microsatellites and 0.39 for cDNA microsatellites. Among the cDNA microsatellites, 29 represented completely sequenced genes. Of these, 14 (48%) contained microsatellites in the 5' or 3' untranslated regions and 5 (17%) contained microsatellite motifs in introns. Ten trinucleotide microsatellites were found in amino acid-rich regions of open reading frames (ORFs) of these genes, and these tri-nucleotide motifs coded for 5 different amino acids. On average, the number of simple sequence repeat units was lower for markers originating from cDNAs than from genomic clones. The highest number of alleles and the longest tracts of repeating units were detected in clones isolated from a Tsp509-digested library. The fact that the flanking regions of the majority of these highly polymorphic genomic microsatellites were rich in A and T nucleotides suggests that microsatellite variation accumulates at a higher rate in AT-rich regions of the rice genome than in the more conserved GC-rich coding regions. Information about primer sequence, repeat motif, map position and allelic diversity of these microsatellite markers, including images of silver-stained polyacrylamide gel electrophoresis patterns, are available over the RiceGenes database (http://probe.nalusda.gov:8300).