Climate Resilient Rice: Progress and Perspectives in Submergence Tolerance

Abstract

Rice cultivation in rainfed lowland regions faces mounting challenges due to climate-driven flooding stress, which severely threatens crop productivity. Farmers in flood-prone areas are often reluctant to adopt improved rice varieties due to their limited tolerance to submergence stress. Consequently, breeding rice for submergence tolerance has become a critical goal across Asia. Rice possess natural adaptation to wet environments, such as aerenchyma formation, which facilitate oxygen transport under waterlogged conditions. However, prolonged or complete submergence still disrupts physiological processes, limiting growth and yield. The discovery and fine-mapping of the Sub1 QTL in the flood-tolerant landrace FR13A was a breakthrough in rice breeding. This enabled marker-assisted introgression of Sub1 into popular high-yielding varieties, enhancing their resilience to flash flooding. Such genetic advancements are vital for stabilizing rice production in rainfed lowland areas prone to climate-induced submergence. Recent advances in molecular breeding and genomics have significantly accelerated the development of rice varieties with combined stress tolerance. The successful introgression of the Sub1 locus using SSR markers has led to the release of widely adopted submergence-tolerant cultivars such as Swarna-Sub1, BR11-Sub1, and IR64-Sub1 across South and Southeast Asia. This review synthesizes recent progress in understanding the morphological, biochemical, physiological and molecular mechanisms that govern submergence tolerance in rice. Diverse adaptive strategies employed by rice plants to withstand flooding stress is dicussed and a comprehensive overview of the genetic basis underlying these responses is provided. The review also discusses current breeding strategies aimed at developing submergence-tolerant cultivars, identifies critical gaps in existing approaches, and proposes targeted solutions to enhance breeding efficiency.