It's my first time identifyng QTLs by GBS in rice, and the results I've obtained by the analyses I don't understand them too much, because there are many QTLs that comprising half a chromosome, I mean, they are too large. And there are too identified QTLs that overlap each other.
For example, in chromosome 1, the first QTL identified is in the interval of the positions 26447862 and 36092039. And another QTL identified in the chromosome 1 is located in the position 26019392 to 27766901. How could I interpret those results? Can I assume that both are correct? Or the first one is not a good detection of the QTL because is too large?. The LOD I have obtained is of 21.31 for the first and 6.27 for the second, then I understand that both are good result.
Could anybody give me any tip for those cases.
Both of those QTL sound reasonable to me. With my GBS dataset that was filled with low coverage SNPs and a small population size had QTL as large as 20 Mb. I believe why you are getting two QTL is because of the algorithm to calculate QTL found two regions linked to each other that are responsible for your trait of interest. That is a major advantage of using ICI Mapping in the first place. Normal QTL mapping cannot distinguish linked QTL. Article QTL IciMapping: Integrated software for genetic linkage map ...
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