Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs)

Theor Appl Genet. 2004 Aug;109(4):800-5. doi: 10.1007/s00122-004-1685-x. Epub 2004 May 14.


The increasing availability of expressed sequence tags (ESTs) in wheat ( Triticum aestivum) and related cereals provides a valuable resource of non-anonymous DNA molecular markers. We examined 170,746 wheat ESTs from the public (International Triticeae EST Cooperative) and Génoplante databases, previously clustered in contigs, for the presence of di- to hexanucleotide simple sequence repeats (SSRs). Analysis of 46,510 contigs identified 3,530 SSRs, which represented 7.5% of the total number of contigs. Only 74% of the sequences allowed primer pairs to be designed, 70% led to an amplification product, mainly of a high quality (68%), and 53% exhibited polymorphism for at least one cultivar among the eight tested. Even though dinucleotide SSRs were less represented than trinucleotide SSRs (15.5% versus 66.5%, respectively), the former showed a much higher polymorphism level (83% versus 46%). The effect of the number and type of repeats is also discussed. The development of new EST-SSRs markers will have important implications for the genetic analysis and exploitation of the genetic resources of wheat and related species and will provide a more direct estimate of functional diversity.

Publication types

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

MeSH terms

  • Breeding / methods*
  • Chromosome Mapping
  • Computational Biology
  • DNA Primers
  • Databases, Genetic
  • Expressed Sequence Tags*
  • Genotype
  • Minisatellite Repeats / genetics
  • Polymerase Chain Reaction
  • Polymorphism, Genetic*
  • Triticum / genetics*


  • DNA Primers