Rising demand for food and bioenergy makes it imperative to breed for increased crop yield. Vegetative plant growth could be driven by resource acquisition or developmental programs. Metabolite profiling in 94 Arabidopsis accessions revealed that biomass correlates negatively with many metabolites, especially starch. Starch accumulates in the light and is degraded at night to provide a sustained supply of carbon for growth. Multivariate analysis revealed that starch is an integrator of the overall metabolic response. We hypothesized that this reflects variation in a regulatory network that balances growth with the carbon supply. Transcript profiling in 21 accessions revealed coordinated changes of transcripts of more than 70 carbon-regulated genes and identified 2 genes (myo-inositol-1-phosphate synthase, a Kelch-domain protein) whose transcripts correlate with biomass. The impact of allelic variation at these 2 loci was shown by association mapping, identifying them as candidate lead genes with the potential to increase biomass production.Arabidopsis ͉ association mapping ͉ biomass ͉ metabolites ͉ predictive P lants use light energy to convert CO 2 into carbohydrates.Although we might expect plant growth to be driven by the availability of carbohydrates and other central metabolites, recent studies point to a more complex interaction. Numerous free air CO 2 elevation studies show that higher rates of photosynthesis do not lead to a commensurate increase in biomass and yield (1). Studies of natural genetic diversity reveal a negative correlation between the levels of metabolites and biomass or yield (2-4). Although biomass was only very weakly correlated with individual metabolites in an Arabidopsis recombinant inbred line (RIL) population, a highly significant prediction was obtained when multivariate analysis was used on the entire metabolite profile (3). These results indicate that much of the genetic variation for biomass production affects the balance between resource availability and developmental programs, which determine how rapidly these resources are used for growth.Plants are exposed to a changeable environment and need to cope with continual changes in carbon (C) availability. One striking example is the daily alternation between a positive C balance in the light and a negative C balance in the dark. Growth nevertheless continues at night (5). This continued growth is possible because some newly fixed C accumulates as starch in the light and is remobilized at night to support respiration and growth. Starch is almost completely exhausted by the end of the night. If a change in the conditions (e.g., longer nights) leads to a temporary period of C starvation, the C budget is rebalanced (6-11) by increasing the rate of starch synthesis, decreasing the rate of starch breakdown, and decreasing the rate of growth (10,11). Starchless mutants illustrate the importance of this buffer; they cannot grow in a light/dark cycle because they become C-starved every night, leading to an inhibition of growth that is no...

SUMMARYA platform using reverse-phase liquid chromatography coupled to tandem mass spectrometry was developed to measure 28 metabolites from photosynthetic metabolism. It was validated by comparison with authentic standards, with a requirement for distinct and clearly separated peaks, high sensitivity and repeatability in Arabidopsis rosette extracts. The recovery of authentic standards added to the plant material before extraction was 80-120%, demonstrating the reliability of the extraction and analytic procedures. Some metabolites could not be reliably measured, and were extracted and determined by other methods. Measurements of 37 metabolites in Arabidopsis rosettes after 15 min of illumination at different CO 2 concentrations showed that most Calvin cycle intermediates remain unaltered, or decrease only slightly (<30%), at compensation point CO 2 , whereas dedicated metabolites in end-product synthesis pathways decrease strongly. The inhibition of end-product synthesis allows high levels of metabolites to be retained in the Calvin cycle to support a rapid cycle with photorespiration.

Analysis of labeling kinetics, pool sizes, and concentration gradients of metabolites reveals the operation of multiple decarboxylation pathways and rapid movement of carbon between the Calvin–Benson cycle and the CO2-concentrating shuttles in maize.

Natural genetic diversity provides a powerful resource to investigate how networks respond to multiple simultaneous changes. In this work, we profile maximum catalytic activities of 37 enzymes from central metabolism and generate a matrix to investigate species-wide connectivity between metabolites, enzymes, and biomass. Most enzyme activities change in a highly coordinated manner, especially those in the Calvin-Benson cycle. Metabolites show coordinated changes in defined sectors of metabolism. Little connectivity was observed between maximum enzyme activities and metabolites, even after applying multivariate analysis methods. Measurements of posttranscriptional regulation will be required to relate these two functional levels. Individual enzyme activities correlate only weakly with biomass. However, when they are used to estimate protein abundances, and the latter are summed and expressed as a fraction of total protein, a significant positive correlation to biomass is observed. The correlation is additive to that obtained between starch and biomass. Thus, biomass is predicted by two independent integrative metabolic biomarkers: preferential investment in photosynthetic machinery and optimization of carbon use.

Interspecific divergence in metabolite profiles in C3 and C4 species points to differing evolutionary trajectories of the Calvin–Benson cycle in different seed plant lineages