# Molecular and Physiological Mechanisms Underlying Submerged Germination in Rice

## TL;DR

This paper reviews how rice seeds adapt to flooding during germination, focusing on molecular and physiological mechanisms that could help breed flood-tolerant rice varieties.

## Contribution

The paper provides a comprehensive review of the physiological and molecular mechanisms underlying submerged germination in rice, highlighting key genes and emerging technologies for breeding flood-tolerant varieties.

## Key findings

- Flood-tolerant rice varieties maintain energy and cellular balance through enhanced amylase activity and fermentation efficiency.
- Key genes like SUB1A, OsTPP7, and OsGF14h are involved in hypoxia perception and metabolic reprogramming during submerged germination.
- Plant hormones such as ethylene and gibberellin play critical roles in regulating submerged germination processes.

## Abstract

Seed dormancy and germination are crucial traits that enable rice to adapt to adverse conditions and maintain its reproductive capacity. Flood (submergence) is a major abiotic stress that inhibits rice seed germination, reducing submerged germination efficiency and seedling uniformity. This review summarizes the molecular and physiological mechanisms of submerged germination in rice, including morphological adaptation, low-oxygen perception, phytohormone interaction, and key genes relevant to breeding flood-tolerant varieties. Emerging technologies, such as whole-genome selection and gene editing technologies, are poised to accelerate the cultivation of rice varieties with enhanced flood tolerance. These advances would provide a theoretical basis and genetic resources to boost crop productivity under hypoxia stress.

Submergence during germination (SG) is a major constraint during sowing, severely limiting the promotion and application of direct-seeded rice. Recent studies have revealed the adaptive mechanisms by which rice responds to SG. At the physiological level, flood-tolerant varieties effectively maintain energy supply and cellular homeostasis by enhancing amylase activity, improving glycolysis and ethanolic fermentation efficiency, promoting embryo sheath elongation, and activating antioxidant enzyme systems; at the molecular level, multiple key genes and signalling pathways have been identified, including SUB1A, OsTPP7, OsGF14h, etc., participating in hypoxia perception, metabolic reprogramming, and hormone signal integration to regulate SG under flooding. In addition, the interactions among plant hormones, such as ethylene, gibberellin, abscisic acid, and cytokinin, also play key roles in the SG process. Future research should prioritize breeding strategies that pyramid multiple genes by integrating gene editing, whole-genome selection, and high-throughput phenotyping to improve seed germination under flood stress.