Transcriptomic Identification of Nitric Oxide–Responsive Genes Associated with Hypoxia Tolerance in Rice

Abstract A significant obstacle to rice production is flooding-induced hypoxia, but little is known about the molecular mechanisms underlying tolerance that are mediated by nitric oxide (NO). In both aerobic and hypoxic conditions with and without L-naphthaleneacetic acid (L-NAA), an inhibitor of NO signalling, we contrasted a hypoxia-tolerant rice germplasm (Rangdhakekua bao RKB) with a hypoxia-sensitive variety (IR-64). Under hypoxia, phenotypic evaluation revealed that RKB maintained noticeably more coleoptile elongation than IR-64, whereas L-NAA significantly slowed growth in both genotypes. Through transcriptomic analysis, 2503 differentially expressed genes (DEGs) under hypoxia were found, including 921 genes specific to hypoxia, 162 of which overlapped with genes that respond to L-NAA. Enrichment in photosynthesis redox homeostasis hormone metabolism and stress response pathways was found through functional categorization treatment with L-NAA significantly downregulated genes linked to photosynthesis. Although further research is necessary to confirm their functional roles, these findings point to candidate NO-responsive genes that may be involved in hypoxia tolerance. The identified gene set provides a useful tool for directing upcoming studies and breeding plans meant to increase rice's resistance to flooding.