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

  • Chapter
Oryza: From Molecule to Plant

Abstract

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.

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Author notes

  1. Olivier Panaud

    Present address: GEPC,Laboratoire d’évolution et systématique végétale, Université Paris XI, Bat. 362, 91405, Orsay, Cedex, France

  2. Yong Gu Cho

    Present address: Division of Cytogenetics, Department of Bio-resources, Agricultural Science and Technology Institute, RDA, Suweon, 441-707, Korea

  3. Takashige Ishii

    Present address: Laboratory of Plant Breeding, Faculty of Agriculture, Kobe University, Nada-ku, Kobe, 657, Japan

Authors and Affiliations

  1. Plant Breeding Department, Cornell University, Ithaca, NY, 14853-1901, USA

    Susan R. McCouch, Xiuli Chen, Olivier Panaud, Svetlana Temnykh, Yunbi Xu, Yong Gu Cho, Takashige Ishii & Matthew Blair

  2. Plant Breeding, Genetics, and Biochemistry Division, International Rice Research Institute, Box 933, Manila, 1099, Philippines

    Ning Huang

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  1. Susan R. McCouch
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  2. Xiuli Chen
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Takuji Sasaki Graham Moore

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McCouch, S.R. et al. (1997). Microsatellite marker development, mapping and applications in rice genetics and breeding. In: Sasaki, T., Moore, G. (eds) Oryza: From Molecule to Plant. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-5794-0_9

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  • DOI: https://doi.org/10.1007/978-94-011-5794-0_9

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