Molecular Soil Biology 2025, Vol.16, No.6, 287-296 http://bioscipublisher.com/index.php/msb 293 6.2 Molecular mechanisms underlying root adaptation to salinity stress The germination and seedling growth experiments of the salt-tolerant variety "Sea Rice 86" (SR86) and the sensitive variety P559 under 100 mM NaCl conditions showed that SR86 maintained bud growth and enhanced root elongation at moderate salt levels, while the root system of P559 was significantly inhibited. The number of differentially expressed genes (DEGs) in SR86 in the roots was much higher than that in P559 (1829 vs. 480); SR86 was enriched in transmembrane ion transport, hormone signaling, and oxidative stress regulation pathways, while P559 mainly activated ABA-related and oxidative stress pathways (Jin et al., 2025). Both genotypes showed an increase in GA3 and GA4 under salt stress, but IAA in the roots of SR86 was significantly increased and JA was decreased, while IAA and JA in the roots of P559 remained basically unchanged. The expression of vacuolar protein transport-related gene OsVPS16 was significantly inhibited under salt stress, and the T-DNA insertion mutant vps16 hardly expressed this gene. In the presence of 150 mM NaCl, vps16 exhibited longer main roots, higher survival rates, and lower Na+/K+ ratios compared to the wild type DJ. The determination of Na+ and K+ contents in the roots indicated that vps16 plants reduced Na+ transport to the stems and leaves while maintaining higher K+ levels, accompanied by a decrease in MDA content and an increase in SOD and POD activities (Liu et al., 2025). Under salt stress, there were 1236 DEGs common between vps16 and DJ, with functional enrichment in serine/threonine protein kinase activity, Ca2+ signaling, and MAPK signaling pathways. Key upregulated factors included OsSRK1, OsCDPK21, and OsNAC45, etc. Under continuous salt treatment, both salt-tolerant CSR28 and sensitive IR28 significantly accumulated osmotic regulatory substances (various amino acids and sugars), while most organic acids decreased, but the accumulation of osmotic regulators in CSR28 was greater (Lelekami et al., 2025a). The activities of proline, inositol, CAT, and SOD were highly correlated with their encoding genes OsP5CS2, OsIMP, OsNCA1a, and OsSOD-Fe, while H2O2 content was correlated with the expression of GLO (ethylmalonyl-CoA oxidase) (Lelekami et al., 2025b). Under salt stress, a total of 249 lipid components were differentially accumulated in the roots, with phospholipids (PA, PC, PS) and sphingolipids (Cer, CerP, Hex1Cer, SPH) significantly increasing, while triglycerides decreased (Xue et al., 2024). 6.3 Gene–environment interactions shaping stress-adaptive root architecture Cell cycle genes in the meristematic zone reduce DNA synthesis to inhibit growth under conditions of excess water (flooding or paddy fields), but maintain or enhance it under drought/water deficit conditions. In the root cortex and pericycle tissues, genes related to auxin signaling, circadian clock, and small RNA regulation are highly sensitive to extreme changes in water availability, regulating lateral root initiation and cortical aerenchyma formation (Reynoso et al., 2022). Local varieties containing different OsWRKY53 alleles showed differential Na+ efflux and xylem retrieval capabilities in salt field trials, thereby affecting root-stem Na+ distribution and plant growth (Yu et al., 2023). Under salt stress, the expression curve of OsWRKY53 shows a time- and dose-dependent negative correlation with OsMKK10.2 and OsHKT1;5, and root Na⁺ flux measurements directly correlate this transcriptional difference with the measured Na+ efflux rate. 7 Conclusions and Future Perspectives The PSTOL1 locus enhances yield under low phosphorus conditions by promoting early root growth and phosphorus uptake, highlighting the close coupling between root development and nutrient efficiency. The multi-omics studies on drought and salt stress revealed the molecular response network consisting of root tip zone-specific transcriptional responses, epigenetic mark remodeling such as 5mC/5hmC, and reconfiguration of membrane lipids and cell wall components. Most candidate genes have been analyzed under nutrient solution or single stress conditions. Long-term data is still lacking regarding their comprehensive effects on water/ion flux at the root-soil interface, soil structure (aggregates, porosity), rhizosphere redox state, and microbial communities under realistic field conditions with multiple stresses (drought × high temperature × nutrient deficiency × salt/secondary hardpan). In the future, rice root molecular biology, combined with CRISPR/Cas, precise insertion, and multi-gene editing technologies, will be used to superimpose deep roots, shallow roots, aeration, root hair/root diameter, and specific
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