The Effects of Elevated Atmospheric CO2 on Root and Shoot Gene Expression and Metabolite Profiles of Solanum lycopersicum and Solanum pennellii

Elevated CO₂ predicted for the latter half of this century will increase photosynthetic carbon assimilation of C₃ plants, stimulating biomass. Increased root biomass is predicted to improve plant access to water and nutrient resources in the future. However, we do not know the molecular mechanisms and developmental changes that underlie enhanced root biomass in elevated CO₂. We used domesticated tomato (Solanum lycopersicum, cv ‘M82’) and a wild species (Solanum pennellii, ‘LA0716’) as models. We measured the effect of elevated CO₂ on the transcriptome and metabolome of root and shoot tissue, root cellular anatomy and physiological responses over developmental time. Genes that were differentially expressed in response to elevated CO₂ in M82 and S. pennellii shoots showed significant enrichment for GO categories related to translation and biosynthesis of ribosome components. Genes that were differentially expressed in response to elevated CO₂ in S. pennellii roots were enriched for GO categories including epigenetic regulation of gene expression and chromatin binding. Profiling of primary metabolites also showed significant variation between CO₂ treatments, species, root and shoot tissue, and dates. Elevated CO₂ significantly increased photosynthesis and root and shoot biomass in both species, and biomass responses tended to be greater in S. pennellii. Elevated CO₂ also affected root vascular anatomy, with stronger responses in S. pennellii compared to M82. These results shed light on the molecular mechanisms of whole plant responses to climate change, and demonstrate interspecies variation in root responses to elevated CO₂.