The use of marker aided selection (MAS) was key to the development of submergence-tolerant rice, a potentially revolutionary rice variety able to withstand submergence in water for a number of weeks. Rice in Asia is typically grown in standing water, but deep flooding for more than a couple of days is detrimental to crop growth and viability. Deep flooding affects more than 25% of global rice-producing land, a proportion expected to rise as a result of global warming. Flash flooding can submerge rice plants, often at the seedling stage, for several weeks.
Deepwater rice is known for its ability to elongate its internodes. These have hollow structures and function as snorkels to allow gas exchange with the atmosphere to prevent drowning. In 2009, a pair of genes responsible was identified by a team at the Nagoya University in Japan. They were named SNORKEL1 and SNORKEL2. Under deep-water conditions, ethylene – a plant hormone – accumulates in the plant and induces expression of the two genes. Their products then trigger remarkable internode elongation through growth hormones, causing the rice plant to grow by up to eight metres in the presence of rising water levels.
Another gene Sub1A with a similar function has also been discovered by the International Rice Research Institute (IRRI) in the Philippines. The resulting rice was named Scuba rice. It responds to ethylene by limiting the elongation of the internodes. This conserves carbohydrates so permitting regrowth when the flood recedes. The rice becomes dormant during the flooding then continues growing once floodwaters recede.
There is potential to utilise both sets of genes so that high-yielding rice varieties can withstand both flooding that is deep and quick, where submergence genes are appropriate, and floodwaters that climb in a progressive and prolonged fashion, for which snorkel genes are better suited.
MAS-based breeding is already underway. Markers for the Sub1 locus have now been used to integrate Sub1A from IRRI deep-water rice into a widely grown Indian variety, Swarna. The resulting crosses when grown in the field in the Philippines exhibited submergence tolerance, but the yields, plant height, harvest index and grain quality remained the same. New submergence-tolerant varieties are now being produced in this way in Laos, Bangladesh and India, and in Thailand where a submergence-tolerant jasmine rice is being bred. In one farmer’s fields during IRRIs Indian field trials, 95% to 98% of the scuba rice plants recovered while only 10% to 12% of the traditional varieties survived. Within 1 year of its release, scuba rice was adopted by more than 100,000 Indian farmers. As of 2012, 3 million farmers were using the new variety, Swarna-Sub1.