Computational and Experimental Analysis of Microsatellites in Rice (Oryza Sativa L.): Frequency, Length Variation, Transposon Associations, and Genetic Marker Potential

Genome Res. 2001 Aug;11(8):1441-52. doi: 10.1101/gr.184001.

Abstract

A total of 57.8 Mb of publicly available rice (Oryza sativa L.) DNA sequence was searched to determine the frequency and distribution of different simple sequence repeats (SSRs) in the genome. SSR loci were categorized into two groups based on the length of the repeat motif. Class I, or hypervariable markers, consisted of SSRs > or =20 bp, and Class II, or potentially variable markers, consisted of SSRs > or =12 bp <20 bp. The occurrence of Class I SSRs in end-sequences of EcoRI- and HindIII-digested BAC clones was one SSR per 40 Kb, whereas in continuous genomic sequence (represented by 27 fully sequenced BAC and PAC clones), the frequency was one SSR every 16 kb. Class II SSRs were estimated to occur every 3.7 kb in BAC ends and every 1.9 kb in fully sequenced BAC and PAC clones. GC-rich trinucleotide repeats (TNRs) were most abundant in protein-coding portions of ESTs and in fully sequenced BACs and PACs, whereas AT-rich TNRs showed no such preference, and di- and tetranucleotide repeats were most frequently found in noncoding, intergenic regions of the rice genome. Microsatellites with poly(AT)n repeats represented the most abundant and polymorphic class of SSRs but were frequently associated with the Micropon family of miniature inverted-repeat transposable elements (MITEs) and were difficult to amplify. A set of 200 Class I SSR markers was developed and integrated into the existing microsatellite map of rice, providing immediate links between the genetic, physical, and sequence-based maps. This contribution brings the number of microsatellite markers that have been rigorously evaluated for amplification, map position, and allelic diversity in Oryza spp. to a total of 500.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • DNA Transposable Elements / genetics*
  • Evolution, Molecular
  • GC Rich Sequence / genetics
  • Gene Frequency / genetics*
  • Genetic Markers / genetics*
  • Genetic Variation / genetics*
  • Microsatellite Repeats / genetics*
  • Molecular Sequence Data
  • Oryza / genetics*
  • Physical Chromosome Mapping / methods
  • Protein Structure, Tertiary / genetics
  • Sequence Analysis, DNA / methods
  • Trinucleotide Repeats / genetics

Substances

  • DNA Transposable Elements
  • Genetic Markers

Associated data

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