I used a new Prunus mume genome for QTL mapping.
In this step, I regulated the values in minDP and maf
But the grouping result is always over 8 groups.
Then, I choose 8 of these groups for drawing genetic maps.
One group create over three genetic maps.
Could anyone give me some suggestions for this problem?
It could be that you don't have enough markers and as a result you get gaps. Due to these gaps, one chromosome could be broken to 2 or 3 linkage groups.
Hi. Yes, Mohamed El-Soda got his point. Classical linkage mapping depends on the recombination frequency between markers in a bi-parental family. The greater distance between markers allow higher chance of recombination. Typically, the markers are not linked when the recombination frequency is more than 0.5. Hence, it is depending on where the markers located in the genome, besides of the number of markers tested. For example, recombination frequency at both telomeric regions decrease towards the centromere. You probably could try out a few things. 1. Try to lower the LOD threshold when running the mapping analysis, so that linkage groups can be reduced close to 8. However, you need to be careful by monitoring the marker distribution throughout each linkage group. 2. Consider to expand your mapping population to capture minor recombination frequency between markers. This is to dense up the map and help in bridging the linkage fragments. Average mapping interval with 5-10 cM should be a good start. Actually, we do not necessary need to get the perfect number of linkage groups, if your objective is just to locate some QTLs. Hope this will help.
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