Submergence Tolerant Rice: SUB1’s Journey from Landrace to Modern Cultivar

Abstract

Rice landraces tolerant of up to 2 weeks of complete submergence were collected from farmers' fields in the 1950s. Success in fine mapping of SUBMERGENCE 1 (SUB1), a robust quantitative trait locus from the submergence tolerant FR13A landrace, has enabled marker-assisted breeding of high-yielding rice capable of enduring transient complete submergence. At the molecular level, SUB1 is a variable polygenic locus encoding two or three ethylene responsive factor (ERF) DNA binding proteins. All Oryza sativa accessions encode SUB1B and SUB1C at this locus. An additional ERF, SUB1A, is present at SUB1 in FR13A and other tolerant accessions. The induction of SUB1A expression by ethylene during submergence disrupts the elongation escape strategy typical of lowland and deepwater rice, by limiting ethylene-induced gibberellic acid-promoted elongation. Microarray and metabolite studies confirm that SUB1A orchestrates its effects on metabolism and growth in a submergence-dependent manner. Due to the conditional activity of SUB1A, new "Sub1" mega-varieties effectively provide submergence tolerance without apparent ill effect on development, productivity, or grain quality.

Waterproofing Crops: Effective Flooding Survival Strategies

“…Leaf gas films cling to the surface of leaves of many semiaquatic species . Bailey-Serres et al, 2010). There are also landraces that can be dry seeded directly into shallow paddies (less than 10 cm depth) that can become established despite limited oxygen availability (Angaji et al, 2010;Ismail et al, 2012).…”

Genomic breeding for food, environment and livelihoods

“…Many 'resilience' traits are being bred into crops: drought-resistant cereals which can survive water shortage, harsh heat, and light, and proceed to yield a crop, are very important for the future of Australian farming (Chaves et al 2003). Flood-tolerant rice varieties are another example (Bailey-Serres et al 2010).…”

“…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.…”

Induction and Repression of Gene Expression Mediating Ethylene Biosynthesis and Sodium/Proton Exchange in Rice Seedlings Under Submergence Stress

“…A volume of study supports the 'quiescent strategy' as a principal mechanism of submergence tolerance, and it has been well established that the ethyleneresponse-factor-like genes located at the SUB1 locus plays a key role (2,8,9,10,39). Meanwhile, the "elongation escape or avoidance strategy" has been considered as another mechanism for adaptation to submergence stress, whereby rice plants can escape from or avoid the stress to keep normal metabolic pathways (12).…”