Abstract
In most existing methods and softwares of genome-wide association studies (GWAS) for detecting quantitative trait nucleotides (QTNs), QTN-by-environment interactions (QEIs), and QTN-by-QTN interactions (QQIs), only the allele substitution effect and its interaction-related effects are detected and estimated, conditional on method-specific polygenic background control, leading to confounding in effect estimation and insufficient polygenic background control (Li et al., 2022; Supplemental Tables 1‒3).
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