Identification and characterization of low-sulfur-inducible genes and pathways in roots of upland and lowland rice grown under hydroponic and soil conditions

Sulfur is an essential nutrient for all living organisms, but inorganic sulfur, typically in the form of sulfate (SO42-), can be taken up only by photosynthetic organisms and certain bacteria. Low-sulfur (LS) conditions are becoming increasingly widespread across diverse agricultural regions, constraining crop productivity. While the molecular mechanisms of LS responses have been well characterized in Arabidopsis, they remain incompletely understood in rice, particularly in upland varieties. To address this gap, we focused on the root-the initial site of sulfate uptake from the soil-and established genome and transcriptome analysis platforms for the upland rice variety DJ123 to investigate LS responses in DJ123 and the lowland variety Nipponbare (NB). Transcriptomic analyses of roots under hydroponic and soil conditions identified a core set of LS-inducible genes and promoters shared between the two varieties. Genome-wide promoter analysis revealed conserved cis-acting elements, and transient expression assays demonstrated that Ethylene-insensitive 3-like 4 (EIL4) acts as a key transcriptional activator. Functional analysis of transgenic rice plants showed that Sulfate transporter 1;1 (SULTR1;1), a representative LS-inducible gene, promotes root elongation under LS conditions. These findings provide new insights into sulfur-responsive regulation in roots and the molecular basis of rice adaptation to sulfur-limited environments.