A Major QTL Confers Rapid Internode Elongation in Response to Water Rise in Deepwater Rice

To avoid drowning under flooded conditions, deepwater rice responds to rising water level by rapid internode elongation. Quantitative trait locus (QTL) analysis, using a deepwater rice cultivar (Oryza sativa) and a wild rice species (O. rufipogon) with deepwater characteristics, revealed the presence of major QTLs (qTIL12, qNEI12 and qLEI12) in a common chromosomal region that regulates internode elongation. Genetic analysis revealed that a QTL inherited in a dominant manner, was located on the long arm of chromosome 12. A nearly isogenic line (NIL), produced by backcross introduction of a chromosome fragment carrying this major QTL into non-deepwater rice, exhibited a dramatic internode elongation in response to water rise. This indicates that the difference between deepwater rice and non-deepwater rice is associated with the presence of the QTL, and that this sequence is sufficient to confer deepwater characteristics. Although deepwater rice and non-deepwater rice share a common machinery for internode elongation; non-deepwater rice cannot activate the machinery in response to flooding, unlike deepwater rice which harbors this major QTL.