Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat
Top Cited Papers
- 24 September 2003
- journal article
- research article
- Published by Springer Science and Business Media LLC in Molecular Genetics and Genomics
- Vol. 270 (4), 315-323
- https://doi.org/10.1007/s00438-003-0921-4
Abstract
Nearly 900 SSRs (simple sequence repeats) were identified among 15,000 ESTs (expressed sequence tags) belonging to bread wheat ( Triticum aestivum L.). The SSRs were defined by their minimum length, which ranged from 14 to 21 bp. The maximum length ranged from 24 to 87 bp depending upon the length of the repeat unit itself (1–7 bp). The average density of SSRs was one SSR per 9.2 kb of EST sequence screened. The trinucleotide repeats were the most abundant SSRs detected. As a representative sample, 78 primer pairs were designed, which were also used to screen the dbEST entries for Hordeum vulgare and Triticum tauschii (donor of the D-genome of cultivated wheat) using a cut-off E (expectation) value of 0.01. On the basis of in silico analysis, up to 55.12% of the primer pairs exhibited transferability from Triticum to Hordeum, indicating that the sequences flanking the SSRs are not only conserved within a single genus but also between related genera in Poaceae. Primer pairs for the 78 SSRs were synthesized and used successfully for the study of (1) their transferability to 18 related wild species and five cereal species (barley, oat, rye, rice and maize); and (2) polymorphism between the parents of four mapping populations available with us. A subset of 20 EST-SSR primers was also used to assess genetic diversity in a collection of 52 elite exotic wheat genotypes. This was done with a view to compare their utility relative to other molecular markers (gSSRs, AFLPs, and SAMPL) previously used by us for the same purpose with the same set of 52 bread wheat genotypes. Although only a low level of polymorphism was detected, relative to that observed with genomic SSRs, the study suggested that EST-SSRs can be successfully used for a variety of purposes, and may actually prove superior to SSR markers extracted from genomic libraries for diversity estimation and transferability.Keywords
This publication has 31 references indexed in Scilit:
- Genomic analysis of cultivated barley (Hordeum vulgare) using sequence-tagged molecular markers. Estimates of divergence based on RFLP and PCR markers derived from stress-responsive genes, and simple-sequence repeats (SSRs)Molecular Genetics and Genomics, 2002
- Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheatTheoretical and Applied Genetics, 2002
- Microsatellites are preferentially associated with nonrepetitive DNA in plant genomesNature Genetics, 2002
- Initial sequencing and analysis of the human genomeNature, 2001
- Plant genotyping by analysis of single nucleotide polymorphisms.Published by CABI Publishing ,2001
- Analysis of SSRs derived from grape ESTsTheoretical and Applied Genetics, 2000
- Developing expressed sequence tags (ESTs) from polymorphic transcript-derived fragments (TDFs) in cassava (Manihot esculentaCrantz)Genome, 2000
- Developing expressed sequence tags (ESTs) from polymorphic transcript-derived fragments (TDFs) in cassava (Manihot esculenta Crantz)Genome, 2000
- Basic Local Alignment Search ToolJournal of Molecular Biology, 1990
- Basic local alignment search toolJournal of Molecular Biology, 1990