One rice RIL population was generated and linkage map was constructed using SSR markers years ago. Meanwhile, SNPs were developed this year. How could I combine those markers to get a more intensive map for QTL mapping? SNPs were developed on physical positions, SSR markers were located using genetic distance.
The one way that comes to mind, is sequencing the SSR-amplified fragments, and align them with genomic (if available) sequences or BLAST them to establish respective physical locations. Assuming general conservation of SSR regions, you might get lucky by BLASTing these sequences on the published rice genome sequence.
Hi Linbo, what is the program you are using for grouping your linkage map? One of the most practic softwares for grouping differents markers on the same population is JoingMap (i.e. SNPs, SSR, AFLPs, etc) beacause you can joing more than thousand markers. Respecting the SSR, If you know all information of your SSRs in the map (segregation, locus distance, phase, etc) you can combine all on the map for the QTL search. If you don't know these informations it is necessary to map again the polymorphic SSRs because this information will be necessary to include on the QTL search. The same program 'Joing Map' can help you to joing all information creating nodes. Do you have already defined wich software you will use for the QTLs search? Also one interesting program is MapQTL. If any question don't hesitate for write me.
Hi Linbo,
You could rerun the join map using all the markers including new markers(SNPs) once again to incorporate the new markers in the linkage gropus and rescan for the QTL search. Raj
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