5
Figure 2.1 Difference of flash-flood and stagnant flooding stress in rice Hattori et al. 2011
Recently, research on flood-tolerant rice plants revealed that some rice varieties have evolved to overcome two different flood types, ‘flash flood’ and
‘deep-water flood’ by using two mechanisms. During ‘flash-flooding’ the tolerant plants that are fully submerged for a few weeks stop elongating and thus avoid
energy consumption that will be needed to restart growth when the water recedes. On the contrary, during deep-water flooding, with water depth up to several meters
for several months, the deep-water-flood tolerant rice plants promote elongation of internodes to keep the foliage above the water surface and thus allow respiration
and photosynthesis Hattori et al. 2011. Stagnant flooding is flooding stress during which water does not recede and remains in the field at depths of 50 to 60 cm for
up to several months Mallik et al. 1995. Stagnant flooding may occur after a flash flooding event, or alone.
2.2 Genetic of Stagnant Flooding Tolerance
The genetic basis for submergence-promoted internodal elongation of deep- water rice has received less attention relatively. It appears that this trait is controlled
by a number of minor and perhaps as few as two major genes Catling 1992. Suge 1987 proposed that elongation during submergence is based on the capacity of an
internode to elongate, as well as the degree of elongation, and identified one gene with incomplete dominance that determined elongation ability.
A classic study on inheritance of deep-water characteristics also was performed by Ramiah and Ramaswami 1940 who showed that internode
elongation was controlled by duplicate gene, designated as ef1 and ef2. Hamamura and Kupkanchankul 1979 reported that the ability of rice to float was partially
dominant, and further analysis showed that approximately five or six genes were control in the floating ability. Tripathi and Rao 1985 reported that early nodal
differentiation, a typical feature of deep-water rice can be explained by the presence of complementary genes. Eiguchi et al. 1993 reported that internode elongation
in deep-water rice was associated with a single recessive gene, dw3. In more recent
6 times, with the development of QTL analysis, the deep-water response has been
suggested to be a quantitative trait regulated by QTLs Nandi et al. 1997; Sripongpangkul et al. 2000; Toohinja et al. 2003; Nemoto et al. 2004; Hattori et al.
2007, 2008; Kawano et al. 2008.
In deep-water areas, the water depth increases gradually throughout the year and maintains up to more than 50 cm of deep of water for long period. In these
situations, rapid elongation ability is necessary to allow the plants to keep up with rising floodwater. Deepwater or “floating” rice varieties initiate internode
elongation early in their growth period and their internodes undergo rapid elongation. The early initiation of elongation is controlled by QTLs on
chromosomes 3 and 12 Nemoto et al. 2004, Hattori et al. 2007, Kawano et al. 2008, and the rate of internode elongation is controlled by QTLs on chromosomes
1 and 12 Hattori et al. 2007; Hattori et al. 2008; Kawano et al. 2008.
The chromosome 12 QTL is the major determinant of the rapid elongation response of deep-water varieties. Adaptation to long-term deep flooding is
primarily achieved by stem i.e. internode elongation, as mediated by two SNORKEL genes. SNORKEL1 SK1 and SNORKEL2 SK2 both are ethylene-
responsive factor ERF transcriptional regulators that control internode elongation. The genes are very similar in sequence to the SUB1 genes. However, SUB1 has the
opposite effect of the SNORKEL genes and inhibits elongation of leaves and internodes when induced during submergence Hattori et al. 2009.
2.3 Physiological Mechanism of Stagnant Flooding Tolerance
Under stagnant flooding condition, most of plants produce low yield because of reduction of the sink capacity such as number of panicle, spikelet
fertility, and grain size Mallik et al. 2004. Effect of stagnant flooding 25-50 cm were vegetative vigour mostly poor, increasing on plant height, delaying of day to
heading, and severing from lodging Amante 1986. However, there are little information about some other characters, especially for physiological characters
such as soluble carbohydrate and starch content on stem and chlorophyll contents that related to mechanisms of adaptation of rice plants to stagnant water. Tolerance
mechanisms are controlled by various characters, therefore it is necessary to identify the secondary characters that have strong correlation with grain yield.
Many secondary characters are easier to measure than yield across representative stress environments, particularly if the character is expressed constitutively, or if it
can be measured on seedlings, or if it can be identified using genetic markers Nugraha et al. 2013.
2.4 Characteristic of IRRI 119 and IR 42
One variety developed previously at IRRI, IRRI 119 released in the Philippines as PSB Rc68. IRRI 119 is derived of IR 43581-57-3-3-6IR 26940-20-
3-3-3-1 KHAO DAWK MALI 105. IRRI 119 was developed for the rainfed lowlands. It carries the SUB1 gene but is moderately tall.
SUB1 does not confer any tolerance to submergence immediately after seeding or stagnant flooding tolerance Mackill et.al 2010; Singh et al. 2011. The
plants cultivars with SUB1 gene are sensitive to stagnant flooding if the water levels increased too rapidly because most of the canopy of plant is under water, and the
