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Background and Aims Elucidating how plant species respond to variable light conditions is important to understand the ecological adaptation to heterogeneous natural habitats. Plant performance and its underlying gene regulatory network have been well documented in sun-grown plants. However, the phenotypic and molecular responses of shade-grown plants under variable light conditions have remained largely unclear. Methods We assessed the differences in phenotypic performance between Panax ginseng (shade-grown) and Arabidopsis thaliana (sun-grown) under sunlight, shade and deep-shade conditions. To further address the molecular bases underpinning the phenotypic responses, we compared time-course transcriptomic expression profiling and candidate gene structures between the two species. Key Results Our results show that, compared with arabidopsis, ginseng plants not only possess a lower degree of phenotypic plasticity among the three light conditions, but also exhibit higher photosynthetic efficiency under shade and deep-shade conditions. Further comparisons of the gene expression and structure reveal that differential transcriptional regulation together with increased copy number of photosynthesis-related genes (e.g. electron transfer and carbon fixation) may improve the photosynthetic efficiency of ginseng plants under the two shade conditions. In contrast, the inactivation of phytochrome-interacting factors (i.e. absent and no upregulation of the PIF genes) are potentially associated with the observed low degree of phenotypic plasticity of ginseng plants under variable light conditions. Conclusions Our study provides new insights into how shade-grown plants respond to variable light conditions. Candidate genes related to shade adaptation in ginseng provide valuable genetic resources for future molecular breeding of high-density planting crops.

Elucidating how the plant species respond to variable light conditions is essential to understand the ecological adaptation to heterogeneous environments. Plant performance and gene regulatory network underpinning the adaptation have been well-documented in sun-grown species. In this study, we surveyed phenotypic and transcriptomic features of four shade-grown and one sun-grown woody species of the family Araliaceae under distinct light conditions. Our phenotypic comparisons demonstrate that the four shade-grown species possess lower light saturation point and higher assimilation ability of the net photosynthetic rate compared to the sun-grown species. In particular, the four shade-grown species maintain similar photosynthesis efficiency in both highlight and lowlight conditions. However, a significantly decreased photosynthesis rate was observed under lowlight condition of the sun-grown species compared to highlight condition. In addition, our leaf anatomical analyses reveal that while all the five species show different anatomical structures under distinct light conditions, the shade-grown species possess lower degree of phenotypic plasticity relative the sun-grown species. Further comparisons of the transcriptome profiling show that all the five species exhibit gene expression divergence among different light conditions. The differentially expressed genes identified in the five species are functionally related to photosynthesis, secondary metabolites and other basic metabolisms. More importantly, differential regulation of the photosynthesis- and photomorphogenesis-related genes are potentially correlated with the phenotypic responses to distinct light conditions of the five species. Our study provides new insights on how the sun- and shade-grown woody species respond to shade and sunlight environments.

Elucidating how plant species respond to variable light conditions is important to understanding the ecological adaptation to heterogeneous natural habitats. However, the phenotypic responses and gene regulatory network of shade-loving plants under distinct light conditions have remained largely unclear. In this study, we assessed the differences in phenotypic and transcriptomic responses between Arabidopsis (sun-loving) and Panax ginseng (shade-loving) to sunlight and dim-light conditions. Our results showed that, compared to the Arabidopsis, ginseng plants not only exhibited a lower degree of phenotypic plasticity in response to distinct light conditions, but also showed higher photosynthetic efficiency under dim-light conditions. Further time-course transcriptome profiling and gene structural analyses revealed that differentially transcriptional regulation together with increased copy number of the photosynthesis-related genes (i.e., electron transfer and carbon fixation) may improve the photosynthetic efficiency of ginseng plants under dim-light conditions. In contrast, the loss-function and inactivation of phytochrome-interacting factors are potentially associated with the observed low degree of phenotypic plasticity of ginseng plants under the changing light conditions. Our study provides new insights on how shade-loving plants respond to variable light conditions. Candidate genes related to shade adaptation in ginseng provide valuable genetic resources for future molecular breeding of high-density planting crops.HighlightThe shade-loving species Panax ginseng possesses lower phenotypic plasticity under distinct light conditions and shows high photosynthesis efficiency under dim-light condition.