Pangenomic Architecture of Harvest Index Determinants in Bioregenerative Life Support Systems Staple Crops

As humanity prepares for long-duration missions to the Moon and Mars, the development of Bioregenerative Life Support Systems (BLSS) capable of sustaining crews through in situ food production has emerged as a critical technological imperative. The prohibitive cost of launching consumables from Earth—estimated at 20, 000 per kilogram for Mars missions—necessitates closed-loop systems that regenerate essential resources including food, water, and oxygen. Central to BLSS optimization is harvest index (HI) —the ratio of edible yield to total biomass—which directly determines the efficiency with which limited spacecraft resources are converted into consumable food. Despite the fundamental importance of HI for space agriculture, no systematic cross-species analysis has characterized the pangenomic architecture of HI determinants across BLSS candidate crops. This dissertation addressed this critical gap through a comprehensive pangenomic investigation of HI-controlling genes in four staple species prioritized for space agriculture: rice (Oryza sativa), wheat (Triticum aestivum), potato (Solanum tuberosum), and soybean (Glycine max). Employing a four-phase computational comparative genomics approach, this study constructed a systematic gene inventory, conducted ortholog analysis across species, characterized structural variants through integration of genome-wide association study (GWAS) and quantitative trait locus (QTL) data, and examined evolutionary patterns underlying HI regulation. Results identified 30 HI-associated genes organized into five functional categories: dwarfing/gibberellin signaling, grain/tuber development, flowering and maturity, branching and tillering, and nutrient partitioning. Ortholog analysis revealed remarkable conservation of HI-regulatory pathways, with gibberellin signaling demonstrating 100% conservation across all four species—a finding reflecting the enduring legacy of Green Revolution selection for semi-dwarf architecture. Integration of 20 GWAS hits and 25 QTLs validated the gene catalog while illuminating the genomic architecture of HI variation in these economically vital crops. This research contributes a unified pangenomic framework for HI analysis applicable to both space and terrestrial agriculture, and identifies priority molecular targets for NASA crop development programs, thereby advancing the foundational science necessary for sustainable human presence beyond Earth and enhanced food security on our home planet. Keywords: pangenomics, harvest index, bioregenerative life support systems, space agriculture, structural variants, gibberellin signaling, crop improvement