Besides being a metabolic fuel, carbohydrates play important roles in plant growth and development, in stress responses, and as signal molecules. We exploited natural variation in Arabidopsis (Arabidopsis thaliana) to decipher the genetic architecture determining carbohydrate content. A quantitative trait locus (QTL) approach in the Bay-0 3 Shahdara progeny grown in two contrasting nitrogen environments led to the identification of 39 QTLs for starch, glucose, fructose, and sucrose contents representing at least 14 distinct polymorphic loci. A major QTL for fructose content (FR3.4) and a QTL for starch content (ST3.4) were confirmed in heterogeneous inbred families. Several genes associated with carbon (C) metabolism colocalize with the identified QTL. QTLs for senescence-related traits, and for flowering time, water status, and nitrogen-related traits, previously detected with the same genetic material, colocalize with C-related QTLs. These colocalizations reflect the complex interactions of C metabolism with other physiological processes. QTL fine-mapping and cloning could thus lead soon to the identification of genes potentially involved in the control of different connected physiological processes.Sugars and starch are important plant products used for human diet and as raw material in industry (Roeper, 2002). The level and quality of carbohydrates depends on the species, the organ, growth conditions, and many other parameters, but globally reflects the balance between photosynthesis and growth. In addition, total plant biomass and, therefore, yield in the case of many crops largely depend on photosynthetic carbon (C) fixation and carbohydrate metabolism.During photosynthesis, CO 2 is fixed in the chloroplast into triose-phosphates, which are mainly used to regenerate ribulose-1,5-bisphosphate. Only the surplus is exported in the cytosol in counter exchange with inorganic orthophosphate (Edwards and Walker, 1983). In the cytosol triose-phosphates are converted to end products, including Suc, by releasing phosphate. Suc is the main transport form of C, which is translocated via the phloem to the sink organs. Suc phosphate synthase and Suc synthase (Susy) catalyze the formation of Suc in the cytosol, either with the substrates Fru-6-P and UDP-Glc or from Fru and UDPGlc, respectively. Susy, a reversible enzyme, is more important for Suc degradation than for Suc synthesis. The catalytic reaction of Suc phosphate synthase results in Suc-6-P, and Suc synthesis is completed by the action of Suc-6-P phosphatase.In the chloroplast, some of the photosynthate is directly converted to starch, which represents a transient storage, and is remobilized during the night to maintain leaf metabolism and Suc export to sink organs (Geiger and Servaites, 1994). ADP-Glc pyrophosphorylase catalyzes the first committed step of starch synthesis, producing ADP-Glc, the substrate for soluble and granule-bound starch synthases. The first product, amylose, is then further processed by starch branching enzymes I and II (Dennis and Blakele...