Theoretical and Applied Genetics

, Volume 100, Issue 5, pp 697–712 | Cite as

Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.)

  • S. Temnykh
  • William D. Park
  • Nicola Ayres
  • Sam Cartinhour
  • N. Hauck
  • L. Lipovich
  • Y. G. Cho
  • T. Ishii
  • S. R. McCouch
Original

Abstract 

In order to enhance the resolution of an existing genetic map of rice, and to obtain a comprehensive picture of marker utility and genomic distribution of microsatellites in this important grain species, rice DNA sequences containing simple sequence repeats (SSRs) were extracted from several small-insert genomic libraries and from the database. One hundred and eighty eight new microsatellite markers were developed and evaluated for allelic diversity. The new simple sequence length polymorphisms (SSLPs) were incorporated into the existing map previously containing 124 SSR loci. The 312 microsatellite markers reported here provide whole-genome coverage with an average density of one SSLP per 6 cM. In this study, 26 SSLP markers were identified in published sequences of known genes, 65 were developed based on partial cDNA sequences available in GenBank, and 97 were isolated from genomic libraries. Microsatellite markers with different SSR motifs are relatively uniformly distributed along rice chromosomes regardless of whether they were derived from genomic clones or cDNA sequences. However, the distribution of polymorphism detected by these markers varies between different regions of the genome.

Key words Microsatellite markers Genetic map Allelic diversity Genome organization Rice (Oryza sativa L.) 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2000

Authors and Affiliations

  • S. Temnykh
    • 1
  • William D. Park
    • 2
  • Nicola Ayres
    • 2
  • Sam Cartinhour
    • 2
  • N. Hauck
    • 1
  • L. Lipovich
    • 1
  • Y. G. Cho
    • 1
  • T. Ishii
    • 1
  • S. R. McCouch
    • 1
  1. 1.Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853-1901, USA e-mail: stm4@cornell.edu Tel.: +1 607 255 0420US
  2. 2.Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USAUS

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