Theoretical and Applied Genetics

, Volume 105, Issue 2–3, pp 449–457 | Cite as

Fluorescent-labeled microsatellite panels useful for detecting allelic diversity in cultivated rice (Oryza sativa L.)

  • Matthew W. Blair
  • Veena Hedetale
  • Susan R. McCouch

Abstract.

Four multiplex panels of fluorescent-labeled rice microsatellite markers were designed to survey allelic diversity at a total of 27 simple sequence repeat loci. Automated fragment detection, size calling and binning were used to identify the microsatellite alleles. The panels were tested on 72 accessions representing the diversity of ecotypes and isozyme groups in cultivated rice (Oryza sativa L.). Genetic diversity was evaluated by estimating the distribution and range of allele sizes, as well as the polymorphism information content (PIC), for each microsatellite locus. The multiplex panels were shown to be useful for fingerprinting and for clustering rice varieties, and genetic associations determined in this analysis agreed well with previous isozyme- and RFLP-based studies of these genotypes. Because of the wide cross-section of germplasm represented, we expect that the allele size-ranges reported here are close to the maximum for cultivated rice. In the future, panels of microsatellites from each rice chromosome will be made to facilitate the mapping of segregating populations and the identification of genes and QTLs underlying traits of interest.

Rice (Oryza sativa L.) Fluorescent-labeled microsatellites Allelic diversity Multiplex panels 

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Copyright information

© Springer-Verlag 2002

Authors and Affiliations

  • Matthew W. Blair
    • 1
  • Veena Hedetale
    • 1
  • Susan R. McCouch
    • 1
  1. 1.Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA
  2. 2.Present address: CIAT, International Center for Tropical Agriculture, A. A. 6713, Cali, Columbia, S.A.
  3. 3.Present address: CPGL Monsanto Enterprises Ltd. Private, #60, II Floor, 8th Main, 18th Cross Opposite Post Office, Bangalore 560 5509, India

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