Multi-omics analysis reveals insights into hypoxia-tolerant rice growth and identifies the 1-Cys peroxiredoxin B-like...

The rapid-growth ability of rice seedlings under flooded and hypoxic conditions is a crucial determinant for seedling establishment, survival and crop yield under direct-seeded rice cultivation systems. However, the molecular mechanisms underlying rice germination and seedling growth in flooded soil remains unclear. In this study, we used hypoxia-tolerant (Ht) and hypoxia-sensitive (nHt) rice varieties to analyze the response mechanisms of rice seedlings under hypoxic stress through integrated transcriptome, proteome, metabolome sequencing, and physiological analysis. The Ht variety showed higher antioxidant enzyme activity, osmoregulatory capacity, α-amylase activity, and levels of salicylic acid (SA) and indoleacetic acid (IAA). We detected 8096 differentially transcribed genes, 1886 differentially expressed proteins, and 588 differential metabolites between Ht and nHt. KEGG enrichment analysis revealed that key metabolic pathways such as phenylpropanoid biosynthesis, glutathione metabolism, and starch and sucrose metabolism are involved in the rice adaptive response to hypoxic stress. We hypothesized that Ht activates the SA synthesis pathway for rapid elongation and growth under hypoxic stress by inhibiting the phenylpropanoid biosynthetic pathway, thereby redirecting phenylalanine flux towards SA. Exogenous application of SA and IAA increased the flooding survival rate of nHt, suggesting that nHt has a deficiency in activating SA synthesis pathway under hypoxic stress. Additionally, the upregulation of glutathione S-transferase genes in the glutathione metabolism pathway may play critical roles in ROS scavenging and maintaining redox balance under hypoxic conditions. Moreover, a strong correlation was found between 28 DEGs and 4 DAMs (glucose-6-phosphate, sucrose, fumaric acid, and 2,5-dihydroxybenzoic acid) associated with starch and sucrose metabolism and tyrosine metabolism pathways, suggesting their potential pivotal roles in mediating rice response to flooding and hypoxia. These results elucidate the mechanisms underlying rice emergence and growth under flooding and hypoxic conditions.