I found two QTLs on the same LG at different interval. The one which have the higher LOD (7.03) explained (21.6%) , where as the other QTL with LOD score 6.21 explained (26.5%). How do you explain this relationship?
See link below (pages 11-13) to get some idea
https://www.uni-hohenheim.de/fileadmin/einrichtungen/plant-breeding/software/plabqtl_manual.pdf
R2 is determined by two factors, ie., genetic variance (Vg) and phenotypic variance (Vp). Vg can further be determined by the effect of QTL as well as the allele frequency. Hence, if one QTL has larger additive (or dominant) effect, it always has a higher R2. LOD score reflects the reliability of specific QTL. It has no direct relationship with QTL effect. In other words, R2 and LOD has no direct relationship between them.
Dear B.B. Getahun
I agree with Mr. Zhai, and in addition,
1. Usually higher LOD score results in higher R2, but no direct relationships between them. Further, LOD score shows the strength of prediction of the presence of a QTL on that particular location.
2. Did you find these QTLs for different traits or same trait? If different they might be paralog of each other, because their effects are not so much different and on the same LG.
Thanks
i have a important comment for you, some time software gives two QTL which in reality is one QTL even though there is a large distance like 10 cm btween two QTL , it occurred for me in QTL cart by CIM methode nevethelss when i did MIM the result showed one QTL.
Actually, LOD measures the strength of linkage in traits, higher the LOD(>3) more would be the linkages in traits. However, R2 predicted the variations in phenotypes explained by genotypic value predicted by dna markers. Moreover, in some cases, higher the R2 more will be the LOD if the effect usually controlled by additive or dominant gene action.
Actually, LOD measures the strength of linkage in traits, higher the LOD(>3) more would be the linkages in traits with markers. However, R2 predicted the variations in phenotypes explained by genotypic value predicted by dna markers. In some cases, higher the R2, more will be the LOD if the effect usually controlled by additive or dominant gene action rather by epiestatic effect
I got LOD = 2.9 (significant) but R2 = 0. Can anyone help to explain why for me? Thanks a lot!
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