Plant Molecular Biology

, Volume 35, Issue 1–2, pp 89–99 | Cite as

Microsatellite marker development, mapping and applications in rice genetics and breeding

  • Susan R. McCouch
  • Xiuli Chen
  • Olivier Panaud
  • Svetlana Temnykh
  • Yunbi Xu
  • Yong Gu Cho
  • Ning Huang
  • Takashige Ishii
  • Matthew Blair


Microsatellites are simple, tandemly repeated di- to tetra-nucleotide sequence motifs flanked by unique sequences. They are valuable as genetic markers because they are co-dominant, detect high levels of allelic diversity, and are easily and economically assayed by the polymerase chain reaction (PCR). Results from screening a rice genomic library suggest that there are an estimated 5700-10 000 microsatellites in rice, with the relative frequency of different repeats decreasing with increasing size of the motif. A map consisting of 120 microsatellite markers demonstrates that they are well distributed throughout the 12 chromosomes of rice. Five multiple copy primer sequences have been identified that could be mapped to independent chromosomal locations. The current level of genome coverage provided by these simple sequence length polymorphisms (SSLPs) in rice is sufficient to be useful for genotype identification, gene and quantitative trait locus (QTL) analysis, screening of large insert libraries, and marker-assisted selection in breeding. 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 RFLP and AFLP maps, increasing the power and resolution of genome analysis in rice.

allelic diversity microsatellite marker molecular mapping polymerase chain reaction (PCR) simple sequence length polymorphism (SSLP) simple sequence repeat (SSR) 


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Copyright information

© Kluwer Academic Publishers 1997

Authors and Affiliations

  • Susan R. McCouch
    • 1
  • Xiuli Chen
    • 1
  • Olivier Panaud
    • 1
  • Svetlana Temnykh
    • 1
  • Yunbi Xu
    • 1
  • Yong Gu Cho
    • 1
  • Ning Huang
    • 2
  • Takashige Ishii
    • 1
  • Matthew Blair
    • 1
  1. 1.Plant Breeding DepartmentCornell UniversityIthacaUSA
  2. 2.Plant Breeding, Genetics, and Biochemistry DivisionInternational Rice Research InstituteManilaPhilippines

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