eQTL analysis for the same population in different status

Question

[jlshi.nudt]

Since the dynamic characteristics of transcriptome, different expression levels for the same population can be obtained in different status, such as before and after breakfast or taking an exercise.

The question is: how to evaluate the different eQTL at differtn status for the same population?

Do those different eQTL results reflect different biologica mechanisms? how to get useful insights from those results?

Thank you.

Answer 1

[LChart]

What you're referring to - the impact of the environment on genetic effects of a trait, is typically referred to as a "Gene-by-Environment" effect (or GxE). Practically speaking, this involves a change of model specification from expression ~ genotype + covariates to expression ~ genotype + condition + genotype*condition + covariates and examining the coefficient on the cross-term.

However, genetic effects in different environments need to be understood in the context of phenotypic differences across environments - if the phenotype has a different variance in the two conditions, then the same absolute genetic effect is a stronger relative genetic effect. I would say the frameworks for thinking about this are still under development; but a fantastic experimental paper that clearly elucidates several principles can be found here: https://www.nature.com/articles/s41467-020-19131-y

[jlshi.nudt]

thank you. That's help a lot.