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arXiv · 2604.03337

Significance and Stability Analysis of Genotype-Environment Interaction using GxEStat

Meng'en Qin·Zhe Li·Hui Huang·Xihong Liu
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Abstract

Genotype-environment (GxE) interactions can influence the performance of genotypes across diverse environments, limiting the reliability of genotype evaluation and selection in breeding programs. In-depth analysis of GxE interactions is therefore essential for understanding how genetic advantages or defects are expressed under varying environmental conditions and for identifying superior and stable genotypes. This study presents an integrated computational framework for GxE analysis that combines significance and stability evaluation within a unified analytical workflow. The framework incorporates the mixed effect modeling to quantify the significance of environment, genotype, and GxE effects, together with multiple stability analysis approaches for characterizing genotype adaptability, environmental representativeness, and performance consistency across environments. To support reproducible statistical analysis, we develop GxEStat, an interactive R platform that automates model construction, parameter estimation, statistical inference, and graphical visualization. GxEStat substantially improves analytical efficiency, reproducibility, and accessibility for multi-environment trial analysis. Applications to real breeding datasets demonstrate the effectiveness of the proposed framework for practical breeding research. Codes are available at https://github.com/mason-ching/GxEStat.

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Meng'en Qin, Zhe Li, Hui Huang, Xihong Liu. 2026-04-03. Significance and Stability Analysis of Genotype-Environment Interaction using GxEStat. https://arxiv.org/abs/2604.03337

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