Deciphering transcriptomic signatures explaining the phenotypic plasticity of nonheading lettuce genotypes under artificial light conditions.

Elucidating the mechanisms and pathways involved in genotype–environment (G×E) interactions and phenotypic plasticity is critical for improving plant growth. Controlled environment agricultural systems allow growers to modulate the environment for particular genotypes. In this study, we evaluated the effects of interactions among 14 genotypes and four artificial light environments on leaf lettuce phenotypes and dissected the underlying molecular mechanism via transcriptome‐based modeling. Variations in morphological traits and phytochemical concentrations in response to artificial light treatments revealed significant G×E interactions. The appropriate genotype and artificial light combinations for maximizing phenotypic expression were determined on the basis of a joint regression analysis and the additive main effect and multiplicative interaction model for these G×E interactions. Transcriptome‐based regression modeling explained approximately 50%–90% of the G×E variations. Further analyzes indicated Red Lettuce Leaves 4 (RLL4) regulates UV‐B and blue light signaling through the effects of the HY5–MBW pathway on flavonoid biosynthesis and contributes to natural variations in the light‐responsive plasticity of lettuce traits. Our study represents an important step toward elucidating the phenotypic variations due to G×E interactions in nonheading lettuce under artificial light conditions. Summary Statement: The statistics of genotype‐environment (G×E) interactions identified the ideal lettuce genotype and artificial light combinations for each phenotype. Transcriptome‐based modeling explained the G×E variations, especially the relationship between Red Lettuce Leaves 4 allele and the regulation of flavonoid pathway. [ABSTRACT FROM AUTHOR]