From seed to lab to farm: the story of Submergence tolerant rice

Environmental stresses, particularly water availability and disease, are the largest factors determining plant yields and quality. Each year millions of small farmers in the poorest areas of the world lose their entire crops to submergence. Approximately one fourth of the global rice crop is grown in rainfed, lowland plots that are prone to seasonal flooding. These seasonal flash floods are extremely unpredictable and may occur at any growth stage of the rice crop. While rice is the only cereal crop that can withstand submergence at all, most rice varieties will die if fully submerged for more than three days. When the plant is covered with water, its oxygen and carbon dioxide supplies are reduced, which interferes with photosynthesis and respiration. Because the submerged plants lack the air and sunlight they need to function, growth is inhibited and the plants will die if they remain underwater for more than four days. In collaboration with Dave Mackill, my laboratory isolated the Submergence tolerance 1 (Sub1) QTL through a map-based cloning approach (Xu et al., 2006). This work revealed a complex locus of three genes carrying three genes that encode putative transcriptional regulators of the AP2 class. Through transgenic analysis my laboratory demonstrated that the overexpression of Sub1a is sufficient to confer submergence tolerance to intolerant varieties. Our collaborators at the International Rice Research Institute have introduced this gene into agronomically important varieties using marker assisted selection (precision breeding). The resulting rice plants are not only tolerant of submergence but also produce high yields and retain other beneficial crop qualities. Cultivation of these new varieties is now underway in the Philippines, Bangladesh and India. In 2011, over 1 million farmers have planted Sub1 rice. Cultivation of the new variety is expected to increase food security for 70 million of the world's poorest people. My laboratory has also collaborated with Julia Bailey Serres to elucidate the complex molecular networks involved in regulation of submergence tolerance (Fukao et al., 2006). As part of this goal, our laboratory completed a transcriptomics analysis using a rice oligonucleotide array to identify genes and pathways regulated by the Sub1 QTL (Jung et al., 2010). The Bailey Serres lab has recently demonstrated that Sub1 also controls tolerance to drought in rice (Fukao et al., 2011). My laboratory has also developed a rice stress response interactome (Seo et al., 2011) to identify other genes involved in Sub1-mediated stress tolerance and recently constructed RiceNet, the first experimentally validated genome-scale gene network for a monocotyledonous species (Lee et al., PNAS in press). Many different datasets, derived from five different organisms including plants, animals, yeast, and humans, were evaluated, and 24 of the most useful were integrated into a statistical framework that allowed for the prediction of functional linkages between pairs of genes.  We showed that RiceNet can accurately predict gene function in rice as well as another major monocotyledonous crop species, maize. RiceNet thus enables the identification of genes regulating important crop traits, facilitating engineering of pathways critical to crop productivity.