Living organisms must acquire new biological functions to adapt to changing and hostile environments. Deepwater rice has evolved and adapted to flooding by acquiring the ability to significantly elongate its internodes, which have hollow structures and function as snorkels to allow gas exchange with the atmosphere, and thus prevent drowning. Many physiological studies have shown that the phytohormones ethylene, gibberellin and abscisic acid are involved in this response, but the gene(s) responsible for this trait has not been identified. Here we show the molecular mechanism of deepwater response through the identification of the genes SNORKEL1 and SNORKEL2, which trigger deepwater response by encoding ethylene response factors involved in ethylene signalling. Under deepwater conditions, ethylene accumulates in the plant and induces expression of these two genes. The products of SNORKEL1 and SNORKEL2 then trigger remarkable internode elongation via gibberellin. We also demonstrate that the introduction of three quantitative trait loci from deepwater rice into non-deepwater rice enabled the latter to become deepwater rice. This discovery will contribute to rice breeding in lowland areas that are frequently flooded during the rainy season.

Deepwater rice (floating rice) can survive under flooded conditions because of their floating ability. We conducted genetic analysis to elucidate the genetic control of floating ability by using an F 2 and BC 3 F 2 populations derived from a cross between deepwater and non-deepwater rice varieties. Internode elongation is the most important trait responsible for this adaptation, and is characterized by two factors: timing of the initiation of elongation and the rate of elongation. The position of the lowest elongated internode (LEI) and the rate of internode elongation (RIE) were used to measure floating ability. Two QTLs for LEI were detected on chromosomes 3 (qLEI3) and 12 (qLEI12). For RIE, two QTLs were detected on chromosomes 1 (qRIE1) and 12 (qRIE12). We confirmed the genetic effects and map positions of qLEI3, qLEI12 and qRIE12 by using BC 3 F 2 populations. Characterization of near-isogenic lines of qLEI3, qLEI12 and qRIE12 revealed that the LEI and RIE are at least partly controlled by different genetic pathways. Observation of near-isogenic lines suggested that the introgressed segment of qLEI12 and qRIE12 of chromosome 12 affected the deepwaterresponsive elongation.

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