Complex genetic architecture underlying the plasticity of tobacco leaf width provides insight into across-environment...

Phenotypic plasticity refers to the ability of a given genotype to produce multiple phenotypes in response to changing environmental conditions. Understanding the genetic basis of phenotypic plasticity and developing predictive models for agronomic traits are crucial for future agricultural adaptation to climate change. In this study, we investigated the genetic basis of leaf width mean (LWm) and plasticity (LWp) in a tobacco multiparent advanced generation inter-cross (MAGIC) population comprising 594 individuals. In total, we identified 14 LWm-associated loci and 43 LWp-associated loci, with 12 loci shared between LWm and LWp, indicating that LWm and LWp have a partially shared but not identical genetic basis. Among these loci, qLW14 showed a clear environment-dependent effect. Sequence analysis localized this locus to a ∼3 Mb structural-variation region, and a deletion-associated haplotype was associated with significantly greater leaf width than non-deletion haplotypes in Zhucheng, whereas no significant haplotype effect was detected in Guiyang. This locus provides a representative example of how genotype-specific responses to environmental variation contribute to trait expression and phenotypic plasticity. By integrating genotype, environment, and their interactions into a GEAI model, we improved cross-environment prediction of leaf width, with prediction accuracy increasing by 7.2%-8.7% relative to the GBLUP model. Overall, this study characterizes the genetic basis of leaf width plasticity, highlights substantial environment-dependent genetic effects, and provides a basis for incorporating multi-environment information into breeding-oriented prediction.