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Theoretical and Applied Genetics

, Volume 109, Issue 4, pp 800–805 | Cite as

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
Original Paper

Abstract

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.

Keywords

Simple Sequence Repeat Marker Deletion Line Genomic SSRs Wheat ESTs Dinucleotide Motif 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

The authors gratefully acknowledge B. Charef for excellent technical assistance and G. Gay and A. Loussert for growing the plants. S. Reader and B. Gill are acknowledged for furnishing the aneuploid and deletion lines. This work was supported by Génoplante, the French joint program in plant genomics. All of the experiments described herein comply with the current laws of France.

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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • N. Nicot
    • 1
    • 4
  • V. Chiquet
    • 2
  • B. Gandon
    • 2
  • L. Amilhat
    • 1
  • F. Legeai
    • 3
  • P. Leroy
    • 1
  • M. Bernard
    • 1
  • P. Sourdille
    • 1
  1. 1.UMR INRA-UBP Amélioration et Santé des PlantesClermont-Ferrand Cedex 2France
  2. 2.ZAC “Les Portes de Riom”Limagrain GeneticsRiom CedexFrance
  3. 3.InfobiogenEvryFrance
  4. 4.Cellule de Recherche en Environnement et BiotechnologiesCentre de Recherche Public, Gabriel LippmannLuxembourg CityLuxembourg

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