Dynamic transcriptomics and physiological insights reveal multi-tissue salt adaptation mechanisms in Amaranthus hypochondriacus across stress gradients.

Key message: Transcriptomic and physiological analyses identified key salt-responsive pathways and genes in Amaranthus hypochondriacus under 100/250 mM NaCl stress. Soil salinization critically threatens crop productivity, necessitating the exploration of salt-tolerant species. Amaranthus hypochondriacus, recognized as a salt-tolerant grain species, exhibits distinct adaptive mechanisms under moderate (100 mM NaCl) and severe (250 mM NaCl) salinity based on the integrated physiological and multi-tissue transcriptomic analyses. Under moderate salt stress, physiological and transcriptomic analyses revealed three key tolerance strategies: rapid ABA signaling activation (e.g., NCED [9-cis-epoxycarotenoid dioxygenase] upregulation within 6 h exposure to salt stress), sustained leaf ion homeostasis (unchanged leaf Na⁺/K⁺ ratio), and tenfold root proline accumulation. Severe stress triggered osmotic imbalance (89% reduced stomatal conductance), ionic toxicity (24-fold elevated leaf Na⁺/K⁺ ratio), and oxidative damage (fivefold elevated leaf relative electrical conductivity) despite upregulated glutathione biosynthesis. Notably, A. hypochondriacus uniquely maintained DNA stability via enriched DNA repair pathways (e.g., homologous recombination) and transcriptional induction of replication-related gene. The WGCNA analysis identified multiple salt tolerance-associated key candidate genes, including the proline biosynthesis genes (P5CS [pyrroline-5-carboxylate synthetase] and P5CR [pyrroline-5-carboxylate reductase]), as well as the ion transporter genes (NHX [Na⁺/K⁺ antiporter] for sequestration of Na⁺ into vacuoles and SOS1 [Salt Overly Sensitive 1] for extrusion of Na⁺ out of cells). Clustering of 1,578 transcription factors (TFs) identified six expression clusters, with root-specific ERF/MYB activation and leaf-enriched WRKY/C3H induction. This study elucidated the conserved salt tolerance strategies of grain amaranths, emphasizing its dual-phase adaptation: osmotic/ionic homeostasis under moderate stress and DNA stability maintenance under severe stress, orchestrated by lineage-specific TF networks. These findings provide critical insights for improving crop resilience in saline environments.