Exogenous metabolite application is a potential strategy for expanding the use of direct rice seeding with the aim of reducing seeding costs.

Rice is a staple food for over half of the global population, necessitates efficient and cost-effective production methods to ensure food security. However, direct seeding of rice often encounters challenges due to adverse environmental conditions, resulting in increased seeding costs. In this study, we analyzed the germination and physiological data of sixty-six rice varieties under cold and submergence conditions. Our results demonstrate that selecting rice varieties with superior germination capacity in these adverse conditions can improve germination rates by 39.43%. Transcriptomic and metabolomic analyses of two contrasting varieties revealed potential regulatory mechanisms involving hormonal pathways and the glycerophospholipid metabolism pathway. Furthermore, we found that the exogenous application of specific metabolites provides a cost-effective seed enhancement strategy for varieties with poor germination capacity. These findings suggest that combining suitable variety selection with seed enhancement treatments can significantly reduce seeding costs in rice production. This research offers valuable insights for developing resilient rice varieties and cost-effective seeding strategies, potentially contributing to improved rice cultivation practices and enhanced global food security.