Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice

Abstract

Most Oryza sativa cultivars die within a week of complete submergence--a major constraint to rice production in south and southeast Asia that causes annual losses of over US 1 billion dollars and affects disproportionately the poorest farmers in the world. A few cultivars, such as the O. sativa ssp. indica cultivar FR13A, are highly tolerant and survive up to two weeks of complete submergence owing to a major quantitative trait locus designated Submergence 1 (Sub1) near the centromere of chromosome 9 (refs 3, 4, 5-6). Here we describe the identification of a cluster of three genes at the Sub1 locus, encoding putative ethylene response factors. Two of these genes, Sub1B and Sub1C, are invariably present in the Sub1 region of all rice accessions analysed. In contrast, the presence of Sub1A is variable. A survey identified two alleles within those indica varieties that possess this gene: a tolerance-specific allele named Sub1A-1 and an intolerance-specific allele named Sub1A-2. Overexpression of Sub1A-1 in a submergence-intolerant O. sativa ssp. japonica conferred enhanced tolerance to the plants, downregulation of Sub1C and upregulation of Alcohol dehydrogenase 1 (Adh1), indicating that Sub1A-1 is a primary determinant of submergence tolerance. The FR13A Sub1 locus was introgressed into a widely grown Asian rice cultivar using marker-assisted selection. The new variety maintains the high yield and other agronomic properties of the recurrent parent and is tolerant to submergence. Cultivation of this variety is expected to provide protection against damaging floods and increase crop security for farmers.

Elucidating Rice Cell Metabolism under Flooding and Drought Stresses Using Flux-Based Modeling and Analysis

“…However, the growing population and adverse climatic changes pose huge challenges to sustaining the growing demand for rice. Moreover, of several abiotic stresses, flooding stress tremendously limits rice productivity (Xu et al, 2006), particularly in the rain-fed lowlands of Southeast Asia. In general, when plants are waterlogged by flooding, they experience a lower oxygen availability (hypoxia) or a total absence of oxygen (anoxia), thus severely impairing energy generation through reduced/eliminated mitochondrial respiration.…”

Genomic breeding for food, environment and livelihoods

“…Although economic considerations have contributed to lack of interest in 'generalist' crops, these crops would also be difficult to breed from existing crop varieties given the likely loss of such traits during previous breeding efforts (Tanksley and McCouch 1997). Moreover, resilience traits are multi-genic, flood-tolerant rice being a notable exception (Septiningsih et al 2009;Bailey-Serres et al 2010;Xu et al 2006). Thus, similar breeding considerations apply as described above for nutritional quality breeding: genomic breeding will also play a growing role in breeding for crop resilience.…”

Nitrogen metabolism in plants under low oxygen stress

“…Two contrasted strategies: the 'quiescence' and the 'escape' strategy were very well dissected in lowland and deepwater rice lines. The first strategy observed also in species like Rumex palustris naturally adapted to face rapid and complete submergence for few weeks, is triggered by an ERF of the sub-group VII, SUB1A (submergence tolerance) (Xu et al 2006). Only few cultivars highly tolerant and able to survive up to 2 weeks of complete submergence express SUB1A.…”