A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study
Open Access
- 15 October 2010
- journal article
- research article
- Published by Springer Science and Business Media LLC in BMC Genomics
- Vol. 11 (1), 570
- https://doi.org/10.1186/1471-2164-11-570
Abstract
Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut).Keywords
This publication has 66 references indexed in Scilit:
- Population differentiation of sessile oak at the altitudinal front of migration in the French PyreneesMolecular Ecology, 2010
- BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in appleGenomics, 2009
- FrameDP: sensitive peptide detection on noisy matured sequencesBioinformatics, 2009
- Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment biasGenome Research, 2008
- The development of a bin mapping population and the selective mapping of 103 markers in the diploidFragariareference mapGenome, 2008
- Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feedingBMC Genomics, 2008
- Detecting microsatellites within genomes: significant variation among algorithmsBMC Bioinformatics, 2007
- Genic microsatellite markers in plants: features and applicationsTrends in Biotechnology, 2005
- Microsatellites are preferentially associated with nonrepetitive DNA in plant genomesNature Genetics, 2002
- An economic method for the fluorescent labeling of PCR fragmentsNature Biotechnology, 2000