Spatiotemporal Transcriptome Profiling Reveals Nutrient Transport Dynamics in Rice Nodes and Roots During Reproductive Development

Efficient allocation of mineral nutrients and photoassimilates is essential for grain development in rice. However, the transcriptional programs governing nutrient transport at key reproductive stages remain largely unresolved. Here, we performed a comprehensive transcriptome analysis of rice (<i>Oryza sativa</i> L.) across spatial (nodes, roots, and five other tissues) and temporal (seven reproductive stages) dimensions to elucidate the molecular basis of nutrient transport and allocation. RNA-seq profiling of node I identified stage-specific gene expression patterns, with the grain filling stage marked by strong induction of transporters involved in mineral allocation (e.g., OsYSL2, OsZIP3, OsSULTR3;3, SPDT) and carbohydrate distribution (e.g., OsSWEET13, OsSWEET14, OsMST6). Comparative analysis with the neck-panicle node (NPN) and root revealed tissue-specific regulatory networks, including nitrate (OsNRT1.1A, OsNRT2.3) and phosphate (OsPHT1;4, OsPHO1;3) transporters enriched at the grain filling stage. Root expression of Cd/As-related transporters (OsNRAMP5, OsCd1, OsLsi1, OsLsi2, OsLsi3) during grain filling highlights the contribution of belowground uptake to grain metal accumulation. Together, our study establishes a spatiotemporal atlas of nutrient transporter gene activity during rice reproductive development and identifies candidate genes regulating upward and lateral nutrient allocation. These findings provide insights into improving nutrient use efficiency and reducing toxic metal accumulation in rice grains through targeted manipulation of nodal and root transport systems.