Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs).
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.
Nicot
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N
UMR INRA-UBP Amélioration et Santé des Plantes, 234 Avenue du Brézet, Domaine de Crouël, 63039 Clermont-Ferrand Cedex 2, France.
Chiquet
V
V
Gandon
B
B
Amilhat
L
L
Legeai
F
F
Leroy
P
P
Bernard
M
M
Sourdille
P
P
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*
D017931:DNA Primers