An omnigenic interactome model to chart the genetic architecture of individual plants

Abstract

Complex traits are controlled by many unknown genes, making it difficult to elucidate a global picture of the genotype-phenotype map. Here, we develop a statistical mechanics model to contextualize all possible genes into informative, dynamic, omnidirectional, and personalized idopNetworks. This model, derived from the combination of functional mapping and evolutionary game theory, can visualize and trace how genes act and interact with each other to shape the genetic architecture of complex traits. The model can estimate changes in the genotypic value of one gene due to the influence of other genes, specifically on individual subjects, surpassing traditional quantitative genetic studies that can only capture the marginal effect of a gene at the population level. We reconstruct growth idopNetworks from a genome-wide mapping data in a woody plant, mei, identifying unique genetic interaction architecture that distinguishes between fast-growing trees and slow-growing trees. We perform computer simulation to validate the statistical power of the model. IdopNetworks can disentangle the genetic control mechanisms of complex traits and provide guidance on how to alter phenotypic values of specific individuals by promoting or inhibiting the expression of interactive genes.

Acknowledgements

This work is supported by the National Natural Science Foundation of China (No.32572116), the Fundamental Research Funds for the Central Universities (QNTD202503), and the Interdisciplinary Project at the Shanghai Institute for Mathematics and Interdisciplinary Sciences (SIMIS-ID-2024-WN).

Author contributions

C.F., J.C., A.D., and D.Y. developed the model and performed data analysis and computer simulation. G.W. and L.S. conducted mapping experiments and analyzed the data. R.W. conceived the idea and drafted the manuscript. L.S. supervised the project and drafted the manuscript.

Data availability

The data and code are available at https://github.com/ChangjianFa/BIMSA_IdopNetwork.

Conflicts of interest statement

All authors claim no conflict of interest.

Supplementary material

Supplementary material is available at Horticulture Research online.

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