Recent Molecular Aspects and Integrated Omics Strategies for Understanding the Abiotic Stress Tolerance of Rice

Abstract

Rice is an important staple food crop for over half of the world's population. However, abiotic stresses seriously threaten rice yield improvement and sustainable production. Breeding and planting rice varieties with high environmental stress tolerance are the most cost-effective, safe, healthy, and environmentally friendly strategies. In-depth research on the molecular mechanism of rice plants in response to different stresses can provide an important theoretical basis for breeding rice varieties with higher stress resistance. This review presents the molecular mechanisms and the effects of various abiotic stresses on rice growth and development and explains the signal perception mode and transduction pathways. Meanwhile, the regulatory mechanisms of critical transcription factors in regulating gene expression and important downstream factors in coordinating stress tolerance are outlined. Finally, the utilization of omics approaches to retrieve hub genes and an outlook on future research are prospected, focusing on the regulatory mechanisms of multi-signaling network modules and sustainable rice production.

Keywords: abiotic stress; breeding; candidate genes; omics; rice.

Figure 1

Mechanism of cold, heat, and drought stress sensing and tolerance in rice. (A) Cold stress mechanism and response. Cold stress signals are perceived by COLD1 and CIPK, and different genes related to phytohormones and osmoprotectants are regulated. The upregulation of ABA-responsive genes leads to ABA accumulation and cold tolerance. (B) Heat stress sensing and response. Heat stress signals are perceived by different heat shock transcription factors and proteins. Different genes associated with ROS, lipid metabolism, Ca²⁺ homeostasis, and phytohormones are regulated. Several ROS and cell homeostasis genes are activated to trigger the heat stress response. (C) Pathway of drought sensing and tolerance. The root system is crucial for drought tolerance, and DRO1 is upregulated under drought stress, leading to deeper roots and improved drought tolerance. Other genes associated with phytohormones, stomatal balance, water-use efficiency, osmotic adjustment, and root and shoot biomass are crucial for drought tolerance.

Figure 2

Salt stress, osmotic stress, and submergence stress tolerance mechanisms in rice. (A) Salt stress sensing and response. Different proteins play a role in antioxidant and osmoprotectant accumulation, ROS and Na⁺ homeostasis, MDA accumulation, and electrolyte leakage and are required to trigger the tolerance mechanism. Some WRKY TFs suppress the expression of OsNAC1 and DREB1B, resulting in salt susceptibility. (B) Osmotic stress tolerance mechanism overview in rice. The genes involving ABA, proline, and polysaccharides biosynthesis are mentioned. Further, genes involved in ROS scavenging, preventing electrolyte leakage, and balancing the intracellular Ca²⁺ concentration are also highlighted. (C) Submergence tolerance response and regulatory mechanism. Rice follows the quiescent strategy to adapt and escape periodic flash flooding. SUB1A is the key regulator for submergence tolerance. It triggers the transcriptional regulation of SLR1 and other ERF response factors. In floating rice, ethylene accumulation under deep-water conditions stabilizes the ethylene signaling factor OsEIL1. OsEIL1 increases gene expression by binding to the promoter of SD1. After that, the accumulated gibberellin increases the expression of ACE1; meanwhile, the expression of DEC1, a factor inhibiting internode elongation, is reduced. On the other hand, OsEIL1 also binds to the promoter regions of SNORKEL1 and SNORKEL2, triggering the expression of other downstream genes.