After QTL analysis in QTL cartographer, we get left flanking marker position and right flanking marker position along with QTL Position in the output file. Now, my doubt is whether I have to select markers based on QTL position or based on left and right flanking marker positions.
Suppose, I got QTL positioned on 9.8 cM, and the left and right flanking marker positions are 2.5 cM and 14.6 cM. In between 2.5 cM and 14.6 cM, many markers are present. In this case, shall I take the markers just adjacent to 9.8 cM or take markers that are closest with 2.5 cM and 14.6 cM.
If necessary, I will post my data sheet for better understanding.
Thanks and regards.
what you described as flanking markers shows confidence interval, meaning with 0.95 percent confident your QTL is placed in this interval, therefore each of markers placed at this interval can be used as flanking markers but statistically it is better to select those markers located on the two sides confidence interval. in your case 2.5 cM and 14.6cM
actually i didn't get your point . but in QTL analysis you get confidence interval meaning your QTL is most likely located in this interval, obviously there are a few markers in this interval but you can not detect the exact position of gene though software gives a position based on the maximum peak which isn't reliable. therefore you have to narrow this confidence interval to get the real position of your gene. as matter of fact due to lack of exact position of QTL you are not able to find out which flanking markers are tightly linked to gene, may be gene is linked to first or last marker of your confidence interval, but at least you know which markers from hundreds markers are most likely linked to gene of interest and you can test those markers in genotypes which are well known by phenotypic assessments
I am relatively new to qtl analysis in cartographer and i have a similar question. cartographer provides a qtl position and 95% confidence interval. I have been identifying the nearest marker as the marker closest to the qtl positing on my map. I have identified flanking markers as the nearest marker just outside the ci on my map. I have been told this is an appropriate way to present CI, but in cases where marker density is low near a qtl, i end up with a much larger CI than cartographer estimates. For example, cartographer might indicate a qtl near 95 cM and CI from 88 to 102 cM. if i have no marker just outside 102 cM and the next marker is at 115 cM, this increases my estimated CI from a 14 cM distance given by cartographer to 27 cM distance using the nearest marker outside the cartographer CI approach. Pretty sure there is a way to adjust my map distances to consensus map distances but i don't know how.
i got your point, either put more markers in that interval which involves lab work,either try to do MIM by R\qtl so that with less confidence get to narrower CI. nevertheless nobody expect to reach a small CI in biparental population, even 5 CM biologically contains thousand of DNA base pairs.
I would suggest making haplotype using multiple markers in the region. The only problem is if your region is too long you will have a large number of haplotype alleles due to high recombination. Single marker-based selection will be less reliable over multiple markers.
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