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

N. Nicot, V. Chiquet, B. Gandon, L. Amilhat, F. Legeai, P. Leroy, M. Bernard*, P. Sourdille

*Corresponding author for this work

Research output: Contribution to journalArticleResearchpeer-review

164 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)800-805
Number of pages6
JournalTheoretical And Applied Genetics
Issue number4
Publication statusPublished - Aug 2004
Externally publishedYes


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