Rethinking phenotypic evaluation in plant genetic resources: Environmental mismatch as a hidden source of bias

Abstract The evaluation of plant genetic resources underpins crop improvement and adaptation. However, current phenotypic screening approaches, whether conducted in controlled environments or limited-location field trials, often expose diverse germplasm to standardized growing conditions that do not reflect their ecological origins. This leads to systematic bias in trait evaluation, particularly for adaptive traits shaped by local environments. Genotypes may be incorrectly rated as inferior when assessed outside their optimal growing conditions, leading to underutilization of valuable genetic diversity. Here, we argue that environmental mismatch represents a fundamental limitation in plant genetic resource screening. Drawing on evidence from genotype by environment interactions, phenotyping research and ecological genomics, we highlight how current practices can misrepresent adaptive potential. We propose a shift towards environment-aware phenotyping frameworks that incorporate ecological context, genomics, multi-environment testing and reaction-norm approaches. Addressing this issue is critical for unlocking the full value of plant genetic resources in the face of changing agro-ecological conditions and practices.