6 GENERAL DISCUSSION
6.1 Agro-morphological Traits Associated with Stagnant Flooding Tolerance in Rice
The experiment was less favourable because of leaking ponds and technical obstacles on irrigation. When the water reached 40 cm of depth, the water receded
to 20 cm for 2-3 days at the end of the vegetative stage. This condition caused the plant recovered so that it carried out metabolic activity and saving assimilates. Thus,
when the stressed water was occurred, the plant used the reserve of assimilate to survive. This may explain the why the decreasing of grain yield were not extreme.
Plants were also attacked by stem borer at the low to moderate intensity.
Water regime based on Vergara et al. 2014, which was gradual flooding with maximum of the depth of 50-60 cm. This condition was less effective because
it is difficult to distinguish between tolerant and susceptible genotypes. As shown by grain yield of IRRI 119 tolerant check was not significantly different with IR
42 check-sensitive. The effectiveness of screening methods depends on water level and light intensity. The flood stress level besides depends on water level, also
depends on light intensity, temperature, turbidity of water, soil fertility, and age of crops Setter et al. 1997; Das et al. 2009. For artificial selection, the water level
should be increased because the floods could reach at 100 cm of depth in swampy area. A flooded environment can also suffer from low light- thus reducing
photosynthesis, and from high concentration of toxic soil compound Bailey-Serres and Voesenek 2008. Artificial screening should be conducted in wet season to get
similar condition in swampy area, where rice is only grown in wet season.
Genotypes tested have narrow genetic diversity, as shown by several genotypes which having the closer genetic background. IR64, Ciherang, INPARA
4 IR 64 SUB1, and INPARI 30 Ciherang SUB1 had the same parent Source: Official documents of released plant varieties. The closer relationship caused
similar response of stress on grain yield, as shown by genotype x water regimes interaction were not significantly different on traits number of productive tiller,
number of filled grain, 100-grain weight, grain yield, stem length, stem diameter, and length of leaf blade. This means that the tolerant genotypes based STI classified
as intermediate tolerant.
Previous study reported that the performance of Swarna SUB1 INPARA 5 under stagnant flooding was uncertain, as the first generation of variety introgressed
with SUB1 were relatively short, and if water depth remains at above the canopy level for longer than two weeks, the plants may not elongate sufficiency. The SUB1
mediated suppression of elongation could limit the growth of the variety and render it more sensitive to stagnant floods, particularly if the floods persist after a period
of complete submergence Vergara et al. 2006; Kotera et al. 2007; Septiningsih et al. 2009; Barley-Serres et al. 2010. However, in our study performed that
percentage of grain yield decreasing of varieties with SUB1 gene INPARA 4, INPARA 5, INPARI 29, INPARI 30 were relatively low. It may because screening
method in our study was different. In our study, the complete submergence was never occur so that the SUB1 varieties were still could elongated their stem.
Therefore they still could produce grain yield relatively higher.
The genotypes with good performance based on the STI were irrigation varieties, namely IR 64, Ciherang, and INPARI 30. The genotypes have high yield
potential. Ciherang and INPARI 30 never have been tested in stagnant flooding stress. IR 64 identified as sensitive in previous studies Sigh et al. 2011. However,
Yullianida et al. 2015 reported that IR64 was still able to grow well and had 9.68 of decreasing grain yield from normal to stagnant flooding condition. Good
response of the three genotypes was new information and still need to be confirmed especially regarding the tolerance level both in the field and molecular basis.
The traits which determined stress tolerance index were weight of 1000 grain, panicle length, stem diameter, intensity of leaf green colour, and stem length.
These traits could be explained by the model STI = -3.17 + 0.08W1000 – 0.14PL –
0.56SD + 0.11SPAD + 0.04 SL with R
2
adjusted 0.923. Based on the regression coefficients, stem diameter has a negative value and the greatest influence than the
others. Stem diameter correlated with the mechanism of plant resistance to water lodging. In this case, stem diameter of tolerant genotype was not too large, although
all genotypes increased diameter at stress condition. This condition may be explained through compensation mechanism of assimilate distribution among stem
diameter and yield components. Plants with higher grain yield translocated more reserve of assimilate for yield components than stem. However, the genetic
diversity of traits is small so it would not be effective if used as trait selection.
The regression coefficient of leaf green color intensity was positive and quite large. Measurement of leaf green color using SPAD was correlated with
chlorophyll content Ruttanaprasert et al. 2012. SPAD reading at all stages also was positively correlated with rice yield Tari et al. 2013. It is come to attention
that SPAD readings can be affected by factors such as leaf anatomy that may be influenced by factors such as drought, salinity or light level. The color leaves of
tolerant plants were greener and more chlorophyll content so photosynthesis process were better.
Traits selected based on multiple linear regression and genetic variability analysis were stem length, intensity of leaf green color, and panicle length. The
traits were easy and non-destructive in measurement. The traits would be candidate as secondary trait for stagnant flooding selection. These traits may be relevant when
studying intermediate genotypes with tolerance. However, reviews their relevance as selectable traits still needs to be assessed.
6.2 Inheritance Study of Agronomical Traits of Rice under Stagnant Flooding and Normal Condition
The possibility of epistasis estimation for a significant proportion of genetic variance has been investigated. The result showed that beside additive and
dominant effects, epistatic components have also contributed to genetic variation of most traits studied under stagnant flooding condition. However, the relative
magnitude varied across different traits.
The result showed that gene action estimated in stress and normal condition provided similar information on plant height and weight of 100 grain with different
rate. The traits were controlled by epistatic gene action. However, number of productive tiller and length of panicle were controlled by additive-dominant gene
action under normal condition, and epistatic gene action under stress condition. Epistatic effects interaction more strongly with the environment than additive and
dominance gene effect has been reported in maize Azizi et al. 2006; Adetirimin et al. 2001; Eta-Ndu et al. 1999; Moreno-Gonzalez et al. 1981.
Non-consistency in estimation was more obvious for epistasis effects for most traits at different environment, as reported by Nugraha 2016, and Azizi et
al. 2006. Martine and Hallauer 1976 reported that interaction between epistatic effect and environment in maize is important. Interaction between environment and
genetic parameters depends on the number of genes involved and, as the number increases the influence, of the environment becomes greater Upadhyaya et al.
1998. Therefore, widespread and unpredictable epistasis caused by environmental interaction emphasizes the need for wide and repeated testing.
Confounding epistasis effect in the model suggested that inheritance of the traits is complex and polygenic. Because one or more type of epistatic effects were
detected for all traits under stress condition, estimations of the additive and dominant components for these traits would have been biased because of non-
orthogonality if they had been estimated using procedures that assume no epistasis Upadhyaya et al. 1998. For this reason, the estimate of epistasis attained is likely
to be minimum value. The assumption of no epistasis is one of the most common made in quantitative genetic models. The amount of epistasis present in crop species
may have major consequences on both the reliability of prediction and the design of breeding programs.
The signs associated with estimates of [i], [j], and [l] types of epistasis indicate the direction in which gene effect influence the mean of the population.
For [i] and [j], the sign also provides information on the association or dispersal of genes in the parents Mather and Jinks 1982. With two exceptions, all the other
signs of [i] and [j] type of detected epistasis were negative. Also, a negative sign for any of the two parameters suggests an interaction between increasing and
decreasing alleles, thus providing evidence for some level of dispersal in the inbred parents. A negative sign for each of these two parameters suggests that it should be
possible to improve further the level of the traits.
Mather and Jinks 1982 reported that presence of epistasis interaction caused estimation of additive variance D was greater than the actual value. The
kind of epistasis generally hinders the improvement through selection and, hence, a higher magnitude of dominant and its interaction [l] effects would not be expected.
The presence of interaction effect on inheritance of trait caused genetic gain estimation based on genetic parameters should be done carefully. Selection should
be delayed after several generations until high level of gene fixation was gained. Subsequent inter-mating between promising lines may be important in
accumulating favourable genes.
6.3 Implication of Genetic Study of Stagnant Flooding Tolerance in Rice for Breeding Program
Study of morphological and agronomical traits associated stagnant flooding tolerance aimed to evaluate traits associated with grain yield decreasing at stress
environment. The selected traits can be candidate for selection criteria in developing new varieties. Based on study in Chapter 3, it was obtained three traits
selected by linear regression model using stepwise method, viz. stem length, intensity of leaf green color, and panicle length. These traits have a broad genetic
variability and high heritability so that it can be used as selection criteria. Stem length and intensity of the green color of leaves can be observed in the vegetative
stage, while panicle length can be observed in the reproductive stage.
Weight of 1000 grain and stem diameter has a narrow geneticvariability so that it is difficult for breeder to use these characters as selection criteria. However,
if 1000 grain weight were excluded from the model, the linear model was non significant. It is indicating that the breeder should be still consider character of 1000
grain weight in the selection process.
Coefficient of regression of stem diameter in this study is negative. The implication is selection should be done for plants with medium thickness of stem.
Stem diameter associated with susceptibility of lodging. In addition to the narrow genetic diversity, it is relatively difficult to observe stem diamater in stress
environment. Selection can be done in reproductive stage by choosing plants that still stand after the water receded.
Grain yield in stagnant flooding environment could explain 87.76 of stress tolerance variation. This indicates that stress environment can distinguish tolerant
and susceptible genotype so that selection can be done only in stress environment. It can improve the effectiveness and efficiency of selection.
The genetic study in stagnant flooding and normal condition in Chapter 4 revealed a complex inheritance involving epistasis, and low heritability. Therefore
selection should be delayed in later generation when favorable gene are fixed Fehr, 1987; Kersey and Ponni 1996. Alternative approach can be proposed is shuttle
breeding selection which has been reported success in drought tolerance in wheat Reynold et al. 2001, drought tolerance in Maize Said, 2014. The favorable
environments are most suitable for fixing some favor gene of good agronomy performance, yield components and grain yield under normal condition while under
stagnant flooding or stressed environment can be done for selection of tolerant- stress progenies Nugraha 2016.
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