Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs) - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles TAG Theoretical and Applied Genetics Year : 2004

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

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.

Dates and versions

hal-02682409 , version 1 (01-06-2020)

Identifiers

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N. Nicot, V. Chiquet, B. Gandon, Laurence Amilhat, F. Legeai, et al.. Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). TAG Theoretical and Applied Genetics, 2004, 109 (4), pp.800-805. ⟨10.1007/s00122-004-1685-x⟩. ⟨hal-02682409⟩
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