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Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs).
1UMR INRA-UBP Amélioration et Santé des Plantes, 234 Avenue du Brézet, Domaine de Crouël, 63039 Clermont-Ferrand Cedex 2, France.
Summary
Wheat expressed sequence tags (ESTs) yield valuable simple sequence repeat (SSR) markers. Dinucleotide SSRs, though less common, show higher polymorphism, aiding wheat genetic analysis and resource exploitation.
Area of Science:
- Plant genetics
- Molecular biology
- Bioinformatics
Background:
- Expressed sequence tags (ESTs) are increasingly available for wheat (Triticum aestivum) and related cereals.
- ESTs serve as a valuable resource for developing non-anonymous DNA molecular markers.
Purpose of the Study:
- To identify and characterize simple sequence repeats (SSRs) within wheat ESTs.
- To evaluate the potential of EST-derived SSRs (EST-SSRs) as molecular markers for wheat.
Main Methods:
- Analysis of 170,746 wheat ESTs from public databases.
- Clustering of ESTs into contigs and identification of di- to hexanucleotide SSRs.
- Primer design, amplification, and polymorphism screening across eight wheat cultivars.
Main Results:
- 3,530 SSRs were identified in 46,510 contigs (7.5%).
- Successful primer design, amplification, and high-quality products were achieved for 74%, 70%, and 68% of SSR-containing sequences, respectively.
- 53% of EST-SSRs exhibited polymorphism; dinucleotide SSRs (15.5% of total) showed higher polymorphism (83%) than trinucleotide SSRs (66.5%, 46%).
Conclusions:
- EST-SSRs are a valuable resource for wheat genetic analysis.
- The development of EST-SSR markers has significant implications for exploiting wheat genetic resources and estimating functional diversity.
- SSR type and repeat number influence marker utility and polymorphism levels.