title: 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.
authors.affiliation: UMR INRA-UBP Amélioration et Santé des Plantes, 234 Avenue du Brézet, Domaine de Crouël, 63039 Clermont-Ferrand Cedex 2, France.
authors.forename: N
authors.initials: N
authors.lastname: Nicot
authors.forename: V
authors.initials: V
authors.lastname: Chiquet
authors.forename: B
authors.initials: B
authors.lastname: Gandon
authors.forename: L
authors.initials: L
authors.lastname: Amilhat
authors.forename: F
authors.initials: F
authors.lastname: Legeai
authors.forename: P
authors.initials: P
authors.lastname: Leroy
authors.forename: M
authors.initials: M
authors.lastname: Bernard
authors.forename: P
authors.initials: P
authors.lastname: Sourdille
mesh_terms: D001947:Breeding / Q000379:methods*; D002874:Chromosome Mapping; D019295:Computational Biology; D017931:DNA Primers; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005838:Genotype; D018598:Minisatellite Repeats / Q000235:genetics; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D014908:Triticum / Q000235:genetics*
chemical_list: D017931:DNA Primers