Comparative Transcriptome and Hormonal Analysis Reveals the Mechanisms of Salt Tolerance in Rice

Abstract

Salt stress is a major constraint to seed germination and early seedling growth in rice, affecting crop establishment and productivity. To understand the mechanisms underlying salt tolerance, we investigated two rice varieties with contrasting responses as follows: salt-tolerant sea rice 86 (SR86) and salt-sensitive P559. Germination assays under increasing NaCl concentrations (50-300 mM) revealed that 100 mM NaCl induced clear phenotypic divergence. SR86 maintained bud growth and showed enhanced root elongation under moderate salinity, while P559 exhibited significant growth inhibition. Transcriptomic profiling of buds and roots under 100 mM NaCl identified over 3724 differentially expressed genes (DEGs), with SR86 showing greater transcriptional plasticity, particularly in roots. Gene ontology enrichment revealed tissue- and genotype-specific responses. Buds showed enrichment in photosynthesis-related and redox-regulating pathways, while roots emphasized ion transport, hormonal signaling, and oxidative stress regulation. SR86 specifically activated genes related to photosystem function, DNA repair, and transmembrane ion transport, while P559 showed activation of oxidative stress-related and abscisic acid (ABA)-regulated pathways. Hormonal profiling supported transcriptomic findings as follows: both varieties showed increased gibberellin 3 (GA3) and gibberellin 4 (GA4) levels under salt stress. SR86 showed elevated auxin (IAA) and reduced jasmonic acid (JA), whereas P559 maintained stable IAA and JA levels. Ethylene precursor and salicylic acid levels declined in both varieties. ABA levels rose slightly but not significantly. These findings suggest that SR86's superior salt tolerance results from rapid growth, robust transcriptional reprogramming, and coordinated hormonal responses. This study offers key insights into early-stage salt stress adaptation and identifies molecular targets for improving stress resilience in rice.

Keywords: hormonal regulation; rice; salt stress; salt-tolerance mechanisms; seed germination; transcriptome analysis.

Figure 1

The influence of salt stress (4-day exposure) on seed germination. (A): Phenotype of germination of SR86 and P559 seeds under different concentrations of NaCl; (B): Bud length of SR86; (C): Bud length of P559; (D): Root length of SR86; (E): Root length of P559. Note: ●, ■, ▲, ▼, ◆, ○ and □ represent data under different concentrations of NaCl; ns and ** indicate no significant difference and significant difference (p < 0.01) compared to the control.

Figure 2

Effects of salt stress on bud and root length. (A) Bud length of SR86 and P559; (B) Root length of SR86 and P559 under control and 100 mmol/L NaCl. Different letters in the data columns indicate significant differences (p < 0.05) according to Duncan’s test.

Figure 3

The number of differentially expressed genes (DEGs) and the GO analysis of DEGs at germination. (A): Pearson correlation analysis of DEGs; (B): The number of DEGs between four groups, i.e., SR86CKB vs. SR86SSB (SR86B), SR86CKR vs. SR86SSR (SR86R), P55986CKB vs. P559SSB (P559B), P559CKR vs. P559SSR (P559R); (C): GO enrichment of DEGs at SR86B group; (D): GO enrichment of DEGs at P559B group; (E): GO enrichment of DEGs at SR86R group; (F): GO enrichment of DEGs at P559R group.

Figure 4

Venn diagrams of DEGs between two groups and GO enrichment analysis of DEGs. (A): Venn diagram indicating the numbers of common and specific DEGs in buds between SR86 and P559; (B): Venn diagram indicating the numbers of common and specific DEGs in rootss between SR86 and P559; (C): GO enrichment analysis of comment DEGs in buds between SR86 and P559; (D) GO enrichment analysis of comment DEGs in roots between SR86 and P559.

Figure 5

The effect of the endogenous hormone under salt stress. Note: Different letters in the data columns indicate significant differences (p < 0.05) according to Duncan’s test.