Submergence Tolerance Mechanisms in Rice Crop Systems

Rice is uniquely capable of germinating and growing under flooded conditions that would be lethal to most crops. Submergence tolerance encompasses a suite of physiological, genetic and biochemical strategies that allow rice seedlings and established plants to withstand complete or partial flooding. Two primary adaptive responses have been identified: quiescence and escape. Quiescence involves growth suppression to conserve non-structural carbohydrate reserves and minimise energy expenditure, whereas escape relies on rapid elongation of the coleoptile and stem to restore contact with air. Central to these processes is the fine-tuned regulation of phytohormones—principally ethylene, abscisic acid and gibberellin—which coordinate growth, carbohydrate metabolism and antioxidant defences under oxygen deficit. The discovery of major quantitative trait loci such as SUB1 and allelic variants that govern coleoptile elongation has facilitated marker-assisted breeding of submergence-tolerant cultivars. Advances in molecular genetics, metabolite profiling and field screening have yielded new targets for improving direct-seeding systems in flood-prone regions, with a view to enhancing yield stability under climate-driven variability in water regimes.

Research from Nature Portfolio

Recent studies have uncovered the role of a rice UDP-glucosyltransferase in modulating coleoptile length under complete submergence. Natural variation in the gene encoding this enzyme was shown to govern the glycosylation and inactivation of abscisic acid and jasmonic acid, resulting in accelerated coleoptile elongation during anaerobic germination. Molecular analyses revealed that this enzyme mediates interactions between jasmonate-ZIM-domain repressors and ABA-insensitive factors, integrating hormone signalling to promote shoot emergence. Introgression of the favourable haplotype into indica backgrounds significantly enhanced submergence tolerance, offering a concrete target for breeding direct-seeded rice cultivars adapted to flooded soils.

Submergence Tolerance Mechanisms in Rice Crop Systems publication trend

The graph below shows the total number of articles in submergence tolerance mechanisms in rice crop systems across all publications each year (not limited to Nature Index journals).

Technical terms

Submergence tolerance: The capacity of a plant to survive and recover from periods of complete or partial flooding.

Coleoptile elongation: Rapid extension of the protective sheath around the emerging shoot, enabling access to oxygen above floodwater.

Phytohormone: A naturally occurring plant hormone that regulates growth, development and stress responses.

Glycosylation: The enzymatic attachment of sugar moieties to hormones or metabolites, altering their activity or stability.

Doubled-haploid lines: Genetically uniform lines produced by doubling the chromosome complement of haploid cells, used for rapid trait fixation.

Osmoregulation: The control of solute concentrations and water potential within cells to maintain turgor under stress.

Antioxidant capacity: The ability of a plant to scavenge reactive oxygen species and protect cellular components during stress.

References

1. UDP-glucosyltransferase OsUGT75A promotes submergence tolerance during rice seed germination. Nature Communications (2023).
2. Systematic selection to adaptive doubled haploid rice lines under different environments of submergence screening methods. Journal of Agriculture and Food Research (2023).
3. Chitosan Oligosaccharides Mitigate Flooding Stress Damage in Rice by Affecting Antioxidants, Osmoregulation, and Hormones. Antioxidants (2024).