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
7 plants cannot easily elongate out of the water due to the elongation-suppressive
effect of SUB1 Fukao et al. 2006, Xu et al. 2006, Fukao and Bailey-Serres 2008b. However, in cultivars that are taller 100 cm a sufficient part of the canopy
remains above the water level to allow the plants to grow well. Partial elongation ability is an important attribute of stagnant flooding tolerance so that rice plants can
grow ahead of rising water. However, if elongation is too much, plants will be lodge after the water recedes, therefore this trait needs to be combined with lodging
resistance.
IRRI119 was considered to be stagnant flooding tolerant in rice breeding program at IRRI Collard et al. 2013, Kato et al. 2014, and Vergara et al. 2014.
The plant height under stagnant flooding stress is 135-140 cm and with days to flowering is ± 94 days. IRRI119 is semidwarf types under well-drained conditions
Collard et al. 2013.
IRRI119 was developed using conventional breeding and was not specifically bred for stagnant flooding trait. Elucidating the genetic basis, that are
heritability, genetic control, mapping QTL of stagnant flooding tolerance is major objective of the IRRI breeding and research programs. Classical QTL mapping
efforts are currently underway Collard et al. 2013.
A bulk-pedigree method was used to develop IRRI119. Submergence screening is done at F2 and F3 generations using bulk selection at F2 generation.
At F3 generation, screening of submergence is repeated to ensure there are few escapes. At F4 to F6 generations, selection are done based on plant type, yield, grain
quality, and insect and disease resistance. Screening of stagnant flooding stress was done at F7-F8 generations. IRRI119 was considered to be stagnant flooding tolerant
in the rice breeding program at IRRI Collard et al. 2013.
IR 42 is IRRI line which is derived from crossing of IR1561-228-1- 2IR1737CR94-13. IR42 is susceptible for submergence stress Das et al. 2009;
Serres et al. 2010; Sarkar et al. 2011. IR42 is determined as stagnant flooding susceptible by Vergara et al. 2014 and Yullianida et al. 2015. Under stagnant
flooding stress, the yield reduction of IR42 is 57 , stem elongation is 36.7 cm, stem elongation rate is 1 cm day
-1
and the number of tillering are 3 Yullianida et al. 2015. Meanwhile the yield reduction higher 85 based on Vergara et al.
2014.
2.5 Selection Criterion
Under stagnant flooding stress, yield is primary selection criterion based on visual selection. There are sufficient genetic variation for yield in IRRI material,
although heritability of the trait is low to medium. For improving of phenotyping method, that is easy to measure physiological traits, it is need to look for traits which
are highly correlated with yield or relatively yield under stagnant flooding stress. The traits are preferably non-destructive and pre-flowering phase. Collard et al.
2013 suggest that number of tillers, elongation ability at vegetative stage, leaf area development, and lodging resistance can be used to estimate tolerance. All traits,
except lodging resistance can be measured at one month after transplanting.
Singh et al. 2011 and Kato et al. 2014 also recommended that reduction in tiller number directly affected rice yield under stagnant flooding. Therefore,
anatomical, biochemical and molecular studies on this temporal tiller suppression
