Preprint challenges reaction norm GWAS methods for detecting phenotypic plasticity

A preprint posted to bioRxiv on 28 July 2026 presents a mathematical critique of CERIS-JGRA, a variant of reaction norm genome-wide association mapping that substitutes a climate-derived environmental index for the environmental mean used in standard Finlay–Wilkinson regression. The preprint's central argument is that this design choice prevents the method from achieving its stated aim of dissecting the genetics of phenotypic plasticity independently of mean performance.

The authors demonstrate algebraically that any index correlated with environmental means decomposes into a component proportional to those means plus an orthogonal residual. Because sensitivity independent of mean performance is by definition orthogonal to the mean, its contribution to the association slope can only reach the analysis through the residual component — whose loading on informative variation is bounded above by the square root of one minus the squared correlation between index and mean. In high-correlation index designs, this ceiling substantially constrains what the method can detect.

The critique is relevant to quantitative genetics researchers and plant and animal breeders who use genotype-by-environment interaction mapping to dissect adaptive plasticity in complex traits. The work does not introduce a new method but clarifies when existing approaches recover genuine plasticity signals versus confounded mean-performance effects. The preprint has not yet undergone peer review.

Note: this is a preprint. The analysis and conclusions have not been independently peer reviewed and should be interpreted accordingly.