We did GBS on a segregating population, developed Linkage Map and identified QTLs for different traits. We also developed a marker with 85% predication accuracy.
Now, reviewer is asking to to evaluate the influence of allelic difference of this marker on the trait in segregating population. Can you please let me know, how can I do it. Suggesting any tutorial, literature will also be helpful.
Thank you
Hi Mohammad,
If I understand your question correctly, the reviewer is asking how much of the variation could be explained by having different alleles at the marker locus that you identified.
One way to estimate it is that you can plot your data into two groups (assuming there are two alleles at the locus; see attached example). The x-axis is the allelic state at the locus, and the y-axis is the phenotype value. You can then do a regression of the data points, and the R^2 of this regression is the maximum phenotypic variation that can be explained by having different alleles at this locus.
Hope it helps. Good luck!
All best,
Sheng
Thank you Dr. Sheng Sun. I got your point. That was very helpful. Best wishes.
Mohammad Rashed Hossain , can you please share your material details (which generation?) and methods followed (collecting DNA etc). We are planning GBS in cotton and need some directions.
Dear Rajesh S Patil, we did ddRAD-seq for Strawberry from segregating F1 population. DNA was extracted using qiagen kit. Once the paper is published, I can share it with you. Thank you
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