Discerning Genes to Deliver Varieties: Enhancing Vegetative- and Reproductive-Stage Flooding Tolerance in Rice

Abstract

Flooding in rice fields, especially in coastal regions and low-lying river basins, causes significant devastation to crops. Rice is highly susceptible to prolonged flooding, with a drastic decline in yields if inundation persists for more than 7 d, especially during the reproductive stage. Although the SUB1 QTL, which confers tolerance to complete submergence during the vegetative stage, has been incorporated into breeding programs, the development of alternative sources is crucial. These alternatives would broaden the genetic base, mitigate the influence of the genomic background, and extend the efficacy of SUB1 QTL to withstand longer submergence periods (up to approximately 21 d). Contemporary breeding strategies predominantly target submergence stress at the vegetative stage. However, stagnant flooding (partial submergence of vegetative parts) during the reproductive phase inflicts severe damage on the rice crop, leading to reduced yields, heightened susceptibility to pests and diseases, lodging, and inferior grain quality. The ability to tolerate stagnant flooding can be ascribed to several adaptive traits: accelerated aerenchyma formation, efficient underwater photosynthesis, reduced radial oxygen loss in submerged tissues, reinforced culms, enhanced reactive oxygen species scavenging within cells, dehydration tolerance post-flooding, and resistance to pests and diseases. A thorough investigation of the genetics underlying these traits, coupled with the integration of key alleles into elite genetic backgrounds, can significantly enhance food and income security in flood-prone rice-growing regions, particularly in coastal high-rainfall areas and low-lying river basins. This review aims to delineate an innovative breeding strategy that employs genomic, phenomic, and traditional breeding methodologies to develop rice varieties resilient to various dimensions of flooding stress at both the vegetative and reproductive stages.