Molecular markers
Microsatellites - mapping and diversity screening
Microsatellite (SSR) markers will initially be the marker type of choice for assessing diversity within the BnDFFS. These markers generally exhibit a high degree of polymorphism, are amenable to high throughput assays and are frequently conserved between related species. The first point means that they are particularly well suited for diversity analysis, while the last point makes them valuable for aligning genetic linkage maps generated for the various
Brassica genomes
Information about using microsatellite markers
A detailed summary of publicly available microsatellites can be found at the
Brassica Microsatellite Information Exchange developed by Charlotte Allender ( WHRI) and Graham King (Rothamsted).
- The use of mapped markers enables us to link diversity to genomic location. Ultimately this will enable us to generate graphical genotypes for each plant line. A graphical genotype is a pictorial representation of the mosaic pattern of inheritance across a genome of an individual plant line. An example of graphical genotype viewing software is GGT which was developed at the Laboratory of Plant Breeding, Wageningen University.
- For diversity screening, priority will be given to microsatellite markers that have been mapped in the TNDH reference map. However, we are also using microsatellites to increase our understanding of the relationship between different Brassica maps. This will enable us to extend the number of mapped markers available for us to use for diversity analysis.
- The strategy we are using to map microsatellite markers is as follows:
- PCR reactions on a panel of mapping population parental DNA templates are checked on an agarose gel. Where there is no amplification from any parent that marker will no longer be used.
- If a polymorphism is detected on agarose gels the rest of the population will be scored on agarose gels.
- If the PCR reactions appear monomorphic on agarose, they will be rescreened on the more expensive, but high resolution Elchrom Spreadex® gels. These gels offer near base pair resolution.
- If the assay is monomorphic on Elchrom Spreadex® gels the marker is deemed to be monomorphic for that population and hence not informative. But if it is polymorphic the marker will be converted into a fluorescent assay and screened on a capillary sequencer.
- We have carried out initial screening of microsatellite markers, and are due to carry out a more detailed analysis: see report and dataset.
This Page Was Last Edited: 28-May-2010
