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Microsatellite Markers

For your convenience, we have listed below some useful hyperlinks to references and downloadable information about rice microsatellite (SSR) markers.

  1. SSRIT - The Simple Sequence Repeat Identification Tool identifies perfect simple sequence repeats (SSRs) in any given sequence(s). If you find this tool useful, we kindly request that you cite Temnykh et al. (2001).

  2. Panel of 50 standard SSR markers used by the Generation Challenge Program for rice diversity analysis.

  3. Table of SSR Primers from McCouch et al. (2002)
    The table is extremely large. Please be patient while it loads.

  4. Supplementary tables from IRGSP (2005) publication:

  5. All Gramene SSRs (19,480) in

  6. References and downloadable information:

    International Rice Genome Sequencing Project (2005) The map-based of the rice genome. Nature 436:793-800. Reprint from Nature Gramene ref
    McCouch et al. (2002) Development and Mapping of 2240 New SSR Markers for Rice (Oryza sativa L.). DNA Res 9:199-207. Reprints, supplemental tables and figures. Consolidates data from 2240 new RM markers developed by the International Rice Microsatellite Initiative (IRMI) as well as 500 previously-described RM markers. Gramene ref
    Coburn et al. (2002) Design and application of microsatellite marker panels for semiautomated genotyping of rice (Oryza sativa L.). Crop Sci 42:2092 Reprint and fluorescent panel information Gramene ref
    Chen et al. (2002) Sequence divergence of rice microsatellites in Oryza and other plant species. Mol Gen Genomics (2002) 268: 331-343 Reprint Gramene ref
    Temnykh et al. (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441. Reprint, genotype data, map positions, and high-resolution map images for the Rice Cornell SSR 2001 map. Gramene ref
    Temnykh et al. (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697. Reprint describes older version of the Cornell SSR map. Gramene ref
    Cho et al. (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.) Theor Appl Genet 100:713. Reprint and polymorphism data Gramene ref
    Chen et al. (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.) Theor Appl Genet 95:553. Reprint Gramene ref
    Akagi et al (1996) Microsatellite DNA markers for rice chromosomes. Theor Appl Genet 93:1071 Abstract Gramene ref
    Panaud et al. (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252:597. Reprint Gramene ref
    Panaud et al. (1995) Frequency of microsatellite sequences in rice (Oryza sativa L.). Genome 38:1170 Request reprint from McCouch lab Gramene ref
    Wu and Tanksley (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241:225. Request reprint from Tanksley lab Gramene ref
    Wu and Tanksley (1993) Genetic and physical mapping of telomeres and microsatellites of rice. Plant Mol Biol 22:861. Request reprint from Tanksley lab Gramene ref