Multidimensional effects of low-light stress on growth and development of gmfa9 mutant in soybean

• Revealed that the gmfa9 mutant shows prolonged reproductive development and more distinct morphological changes than wild-type soybean under low-light stress. • Demonstrated fa9 mutation downregulates fatty acid synthesis-related genes and upregulates photosynthetic light reaction-associated genes, with seeds exhibiting higher protein/sugar contents but lower per-plant total seed weight across light conditions. • Identified gmfa9 as a valuable genetic resource for breeding high-quality soybean varieties with tailored seed compositions adaptable to low-light environments. The yield and quality of soybean ( Glycine max [L.] Merr.), a globally important food and cash crop, are affected by a variety of environmental factors, one of which is low-light stress. In previous work, we demonstrated that knockout of the SEIPIN homolog FA9 , whose encoded protein participates in lipid-droplet formation, reduced oil content and increased protein content in seeds. In this study, we compared the responses of gmfa9 knockout mutants ( fa9 -KO) and wild-type (WT) Dongnong 50 (DN50) soybean to low-light stress. Vegetative indices (GNDVI and CIGreen), spectral reflectance, and chlorophyll-fluorescence parameters were higher in fa9 -KO than in the WT under low light. fa9 -KO exhibited prolonged reproductive development and more pronounced morphological changes than WT soybean under low-light conditions; under all light conditions, it produced larger seeds with higher protein and sugar contents but had a lower total seed weight per plant. Transcriptome and RT-qPCR analyses demonstrated that FA9 mutation was associated with the downregulation of multiple genes involved in fatty acid synthesis and photosynthetic light reactions. These findings suggest that FA9 is an important genetic resource for breeding high-quality soybean varieties adapted to low-light environments.