Comparative Transcriptomic Analysis of Starch Biosynthesis and Carbon Partitioning Gene Networks Under Simulated and Actual Spaceflight Conditions

Long-duration human space exploration missions to the Moon, Mars, and beyond will require bioregenerative life support systems (BLSS) capable of producing food crops in situ. Understanding how spaceflight conditions affect plant carbon metabolism and starch biosynthesis is critical for developing high-yielding crop varieties optimized for the space environment. This dissertation presents a comparative transcriptomic analysis investigating the molecular responses of starch biosynthesis and carbon partitioning gene networks to spaceflight and simulated microgravity conditions across multiple plant species relevant to BLSS applications. Analysis of 11 NASA GeneLab spaceflight datasets encompassing Arabidopsis thaliana, Oryza sativa (rice), and Triticum aestivum (wheat) revealed consistent patterns of transcriptional reprogramming affecting carbon metabolism. Starch biosynthesis genes, including those encoding ADP-glucose pyrophosphorylase (AGPase), starch synthases (SS), and starch branching enzymes (SBE), exhibited coordinated downregulation across species, with mean log₂ fold changes ranging from -0.95 to -1.13. Concurrently, sugar transporters from the SWEET and SUT families showed significant upregulation, indicating enhanced capacity for carbon export and a shift in partitioning away from storage. Stress-responsive transcription factors from the bZIP, NAC, and WRKY families were consistently activated, providing mechanistic insight into the regulatory cascade connecting stress perception to metabolic reprogramming. Weighted gene co-expression network analysis identified hub genes—SS4, SPS3F, and APS2 in Arabidopsis; OsAGPL1, SS2, and OsSUS2 in rice—that represent central regulatory nodes and promising targets for genetic improvement strategies. These findings demonstrate that spaceflight induces a conserved transcriptional response that redirects carbon from storage to stress response, with direct implications for achieving optimal harvest index in space-grown crops. The identification of specific hub genes and regulatory mechanisms provides actionable targets for developing spaceflight-adapted crop varieties through precision breeding and genetic engineering approaches.