Discovery and characterisation of gene by environment and epistatic genetic effects in a vertebrate model

Welz, B.; Pierotti, S.; Fitzgerald, T. W.; Thumberger, T.; Suzuki, R.; Watson, P.; Fuss, J.; Cordeiro da Trindade, T.; Defranoux, F.; Ferreira, M.; Naruse, K.; Gierten, J.; Loosli, F.; Wittbrodt, J.; Birney, E.

doi:10.1101/2025.04.24.650462

bioRxiv · 10.1101/2025.04.24.650462

Discovery and characterisation of gene by environment and epistatic genetic effects in a vertebrate model

Welz, B.·Pierotti, S.·Fitzgerald, T. W.·Thumberger, T.·Suzuki, R.·Watson, P.·Fuss, J.·Cordeiro da Trindade, T.·Defranoux, F.·Ferreira, M.·Naruse, K.·Gierten, J.·Loosli, F.·Wittbrodt, J.·Birney, E.

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Abstract

Phenotypic variation arises from the interplay between genetic and environmental factors. However, disentangling these interactions for complex traits remains challenging in observational cohorts such as human biobanks. Instead, model organisms where genetic (G) and environmental (E) variation can be controlled offer a valuable complement to human studies in the analysis of higher-order genetic effects such as GxE interactions, dominance, and epistasis. Here, we utilized 76 medaka strains of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel, to compare heart rate plasticity across temperatures. An F2 segregation analysis identified 16 quantitative trait loci (QTLs), with many exhibiting dominance, GxE, GxG, and GxGxE interactions. We experimentally validated four candidate genes using gene editing, revealing their temperature-sensitive impact on heart function. Finally, we devised simulations to assess how GWAS discovery power is influenced by the choice of statistical models, showing that the apparent additivity in human GWAS is to be expected given study design and sample sizes of current studies. This work demonstrates the value of controlled model organism studies for dissecting the genetics of complex traits and provides guidance on the design of genetic association studies.

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Welz, B., Pierotti, S., Fitzgerald, T. W., Thumberger, T., Suzuki, R., Watson, P., Fuss, J., Cordeiro da Trindade, T., Defranoux, F., Ferreira, M., Naruse, K., Gierten, J., Loosli, F., Wittbrodt, J., Birney, E.. 2025-04-26. Discovery and characterisation of gene by environment and epistatic genetic effects in a vertebrate model. https://doi.org/10.1101/2025.04.24.650462

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