Functional characterization of transporter genes in rice node at single-cell resolution through multi-omics...

The rice node is a critical hub for the distribution of mineral nutrients, mediated by transporters. Manganese (Mn) is an essential micronutrient for plant growth. However, the precise cell types and the cell-type-enriched transporter genes in rice node, and the molecular mechanisms underlying the translocation and distribution of Mn in rice remain poorly understood.

We characterize 11 distinct cell types using multiple cluster-enriched genes in rice node I through single-nucleus RNA sequencing (snRNA-seq), systematically profile the expression patterns of putative 1,144 transporter genes within 11 cell types, and identify six candidate transporter genes linked to the tissue-specific deposition of six elements through combining spatial ionomics in node, respectively. Furthermore, we functionally characterize OsMTP7 that is highly expressed in phloem cells in node, as well as in root stele cells and anther. OsMTP7 is localized to plasma membrane in rice and shows efflux activity for Mn. OsMTP7 knockout inhibites Mn uptake and xylem-mediated Mn translocation in root and Mn distribution in node, leading to decreased Mn concentration in various organs and root xylem sap, resulting in reduced biomass and yield. We reveal that OsMTP7 knockout alters expression of genes for multiple biological processes in spikelets using bulk RNA-seq, resulting in increased oxidative stress in anther and low fertility.

Our study reveals the precise cell types and the cell-type-enriched transporter genes in node, identifies candidate transporters for elements deposition in node, and demonstrates a novel and critical Mn efflux transporter mediating Mn uptake, translocation and distribution for improving growth and yield in rice.