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

Rice, a staple food for over half the world's population, requires efficient and cost-effective production to ensure food security. Direct seeding (DSR) offers a potential solution by reducing labor and costs compared to transplanting. However, DSR is vulnerable to environmental stresses like cold temperatures and submergence, particularly prevalent with increasing climate change variability. These stresses can significantly impact seed germination, a critical stage in rice production, leading to lower yields and increased production costs. This study aims to address these challenges by investigating the genetic and metabolic mechanisms underlying rice seed germination under stress conditions and exploring cost-effective strategies to enhance germination rates in DSR systems. The successful implementation of improved DSR techniques will contribute significantly to global food security by increasing rice production efficiency and lowering overall production costs, making rice cultivation more sustainable and accessible.

A literature review on enhancing rice germination rates, using keywords like "enhance rice germination rate," "gene expression regulation in plants," "genetically modified plants," and "signal transduction," revealed two primary approaches: crop breeding and seed enhancement techniques. Crop breeding leverages genetic diversity and modern technologies like transgenic breeding and genome editing to develop varieties with superior germination capacity under stress. Seed enhancement techniques, such as exogenous hormone application and seed coating, aim to improve germination rates in existing varieties. This study builds upon these existing approaches by integrating both strategies, exploring the underlying molecular mechanisms and assessing the cost-effectiveness of a combined approach.

Sixty-six rice varieties were screened for germination performance under four conditions: normal temperature and non-submergence (T1S1, control), normal temperature and submergence (T1S2), cold temperature and non-submergence (T2S1), and cold temperature and submergence (T2S2). Germination rates, morphological, and physiological-biochemical indicators were assessed to calculate a D-value representing overall stress tolerance. Two contrasting varieties, "Jingliangyou 1468" (RR, resistant) and "Basimadi 385" (SR, sensitive), were selected for in-depth transcriptomic and metabolomic analyses using RNA sequencing and LC-MS/MS, respectively. Differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) were identified and analyzed for pathway enrichment using GO analysis. Ten key metabolites predominantly enriched in the glycerophospholipid metabolism pathway were selected for validation experiments. These metabolites were exogenously applied to both RR and SR under the four conditions at various concentrations (0-100 µmol/L). Seed germination rates, germination index, and seedling dry weight were measured after a 5-day stress period and a 5-day recovery period. A cost-effectiveness analysis compared the cost of applying metabolites to improve germination in sensitive varieties with the cost savings achieved by increased germination rates.

The screening of 66 rice varieties revealed significant variation in stress tolerance under cold and submergence conditions. Selecting superior varieties improved germination rates by 39.43%. Transcriptomic analysis of RR and SR under various stress conditions identified 37 common DEGs, primarily associated with the NAC and WRKY transcription factor families and pathways related to signal transduction and hormone-mediated signaling. The expression of NAC and WRKY genes was significantly higher in RR compared to SR. qRT-PCR validation confirmed the RNA-Seq results. Metabolic profiling identified 918 biochemical compounds, with 10 common DEMs consistently expressed in both RR and SR across all conditions. These common DEMs were primarily enriched in the glycerophospholipid metabolism pathway. Exogenous application of six metabolites from this pathway (Eth, Cho, PEth, PCho, PC, PE) significantly enhanced germination rates, particularly in the sensitive SR variety. The cost-effectiveness analysis demonstrated that applying these metabolites is a more economical strategy compared to solely relying on selecting high-quality varieties.

This study demonstrates the significant impact of both genetic selection and exogenous metabolite application on enhancing rice germination under stress. The identification of key genes (NAC and WRKY families) and metabolic pathways (glycerophospholipid metabolism) provides valuable insights into the molecular mechanisms underlying rice's response to cold and submergence. The successful exogenous application of specific metabolites, particularly Eth, Cho, PEth, and PCho, offers a cost-effective strategy to improve the performance of sensitive rice varieties in DSR systems. The findings highlight the synergistic potential of combining genetic improvement with targeted seed enhancement treatments to overcome the challenges of DSR and enhance rice productivity.

This research successfully demonstrates a combined strategy for improving direct-seeded rice cultivation by integrating superior variety selection with exogenous metabolite application. The cost-effectiveness of the metabolite application, coupled with the significant improvement in germination rates, especially in sensitive varieties, positions this approach as a viable solution to enhance DSR efficiency and contribute to improved global food security. Future research should focus on field trials to validate these findings under real-world conditions and explore the long-term effects of metabolite application on yield and other agronomic traits. Further investigation into the precise roles of the identified genes and metabolic pathways is also warranted.

The study's findings are primarily based on controlled indoor experiments using selected rice varieties. The results may not fully reflect the complexity of field conditions where various biotic and abiotic factors can influence rice growth and yield. The shorter growth period of direct-seeded rice compared to transplanted rice may lead to greater susceptibility to diseases and pests in later growth stages. Additionally, the study focused on rice varieties commonly grown in Southern China; the generalizability of these findings to other regions and rice varieties needs further investigation.