Theoretical and Applied Genetics

, Volume 100, Issue 5, pp 713–722

Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.)

Authors

  • Y. G. Cho
    • Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853–1901, USA
  • T. Ishii
    • Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853–1901, USA
  • S. Temnykh
    • Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853–1901, USA
  • X. Chen
    • Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853–1901, USA
  • L. Lipovich
    • Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853–1901, USA
  • S. R. McCouch
    • Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853–1901, USA
  • W. D. Park
    • Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA
  • N. Ayres
    • Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA
  • S. Cartinhour
    • Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA
Original

DOI: 10.1007/s001220051343

Cite this article as:
Cho, Y., Ishii, T., Temnykh, S. et al. Theor Appl Genet (2000) 100: 713. doi:10.1007/s001220051343

Abstract 

The growing number of rice microsatellite markers warrants a comprehensive comparison of allelic variability between the markers developed using different methods, with various sequence repeat motifs, and from coding and non-coding portions of the genome. We have performed such a comparison over a set of 323 microsatellite markers; 194 were derived from genomic library screening and 129 were derived from the analysis of rice-expressed sequence tags (ESTs) available in public DNA databases. We have evaluated the frequency of polymorphism between parental pairs of six inter- subspecific crosses and one inter-specific cross widely used for mapping in rice. Microsatellites derived from genomic libraries detected a higher level of polymorphism than those derived from ESTs contained in the GenBank database (83.8% versus 54.0%). Similarly, the other measures of genetic variability [the number of alleles per locus, polymorphism information content (PIC), and allele size ranges] were all higher in genomic library-derived microsatellites than in their EST-database counterparts. The highest overall degree of genetic diversity was seen in GA-containing microsatellites of genomic library origin, while the most conserved markers contained CCG- or CAG-trinucleotide motifs and were developed from GenBank sequences. Preferential location of specific motifs in coding versus non-coding regions of known genes was related to observed levels of microsatellite diversity. A strong positive correlation was observed between the maximum length of a microsatellite motif and the standard deviation of the molecular-weight of amplified fragments. The reliability of molecular weight standard deviation (SDmw) as an indicator of genetic variability of microsatellite loci is discussed.

Key words Allelic diversitySimple sequence repeat (SSR)Microsatellite markerRice (Oryza sativa L.)

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© Springer-Verlag Berlin Heidelberg 2000