Rice plants (Oryza sativa) accumulate photo-assimilates in the form of non-structural carbohydrates (NSCs) in their stems prior to heading. These can later be mobilized to supplement photosynthate production during grain-filling. There has been longstanding enthusiasm by rice physiologists in optimizing stem NSC as a strategy for rice improvement. Despite this interest, documented since the 1970s and 80s, very little about the genetic controls regulating NSC accumulation, remobilization, and re- accumulation is known. In this dissertation, we first lay the groundwork for large-scale diversity studies on rice stem NSC. We assess the relationship of stem NSC components with 21 agronomic traits in large-scale, tropical yield trials using 33 breeder-nominated lines, establish an appropriate experimental design for future genetic studies using a Bayesian framework to sample sub-datasets from highly- replicated greenhouse data using 36 genetically diverse genotypes, and use 434 phenotypically divergent rice stem samples to develop two partial least squares (PLS) models using near infrared (NIR) spectra for accurate, rapid prediction of rice stem starch, sucrose, and total non-structural carbohydrates. Secondly, we reveal the genetic architecture that underlies stem NSC dynamics in tropical japonica rice using a GWAS approach on two panels complemented by a Near-Isogenic Line library evaluation. Finally, we present preliminary results for a study on the effects of CO2, temperature, and CO2 x temperature interaction effects on structural and non-structural carbohydrate constituents in a New Plant Type accession of rice.