Genotype and Water Regime Interaction on Morphological Traits

42 and Ciherang. Meanwhile, INPARA 3 and INPARI 29 were identified as sensitive genotypes. MRP indicates performance of average relative. Genotype with high value of MRP is identified as tolerant, and low value indicates sensitive. Based on MRP, IR 64, INPARI 30 and Ciherang were indicated as tolerant genotypes. INPARA 3 and IR 42 were identified as sensitive genotype Table 3.9. According to the six tolerance index methods, generally INPARA 3 was identified as susceptible to stagnant flooding stress. Ciherang was identified as tolerant based on 5 methods. IR 42 identified as tolerant based on 3 methods, and as susceptible based on 3 methods. Therefore, the levels of tolerance of the tested genotypes still needs to be confirmed by further experiments on several seasons. Table 3.9 Stagnant flooding response index of rice genotypes Genotype STI REI MRP SSI TOL SSSI INPARA 3 0.58 0.79 1.78 1.4 2.37 0.11 INPARA 7 0.82 1.12 2.12 0.95 1.81 -0.01 IRRI 119 0.76 1.04 2.03 0.96 1.79 -0.01 INPARA 4 0.77 1.05 2.05 0.79 1.39 -0.06 INPARA 5 0.62 0.85 1.84 0.84 1.38 -0.04 INPARI 30 0.88 1.21 2.20 0.84 1.56 -0.04 IR 64 0.95 1.3 2.28 1.02 2.08 0.01 IR 42 0.50 0.68 1.65 0.73 1.03 -0.07 Ciherang 0.90 1.24 2.22 0.71 1.37 -0.08 INPARI 29 0.60 0.82 1.82 1.49 2.64 0.13 Coefficient of correlation among tolerance parameters indicated that STI correlated with REI and MRP. SSI correlated with TOL and SSSI. The significance was also showed by the consistency of tolerant genotypes that were identified using the six methods above. The genotype which was identified as tolerant by STI was also identified as tolerant based on REI and MRP. IR 42 is consistent as susceptible genotype based on STI, REI and MRP methods. Likewise for tolerant genotypes based on SSI, it also showed similar tolerance levels based on TOL and SSSI Table 3.10. Table 3.10 Correlation coefficient among stress index of rice SSI TOL REI SSSI MRP STI -0.3347 -0.0433 0.9999 -0.3330 0.9990 SSI 0.9532 -0.3377 0.9993 -0.3170 TOL -0.0468 0.9533 -0.0251 REI -0.3360 0.9989 SSSI -0.3159 STI may be useful in identifying genotype which have high yield under normal condition and can produce well under severe stress. TOL and SSI proposed for identifying genotype that perform well under stress environment. MRP and REI are respectively the sum and product of two ration, a genotype control meanoverall control mean and b genotype stress meanoverall stress mean. The index values are increase if a or b is higher. If b high, the genotype enters the set of top performers though the performance under normal condition is not the top- most and vice versa. So, MRP and REI are not very effective in distinctively discriminating genotypes that perform well under both normal and stress condition Raman et al. 2012. Based on correlation analysis, stress tolerant index could be grouped into two groups. First is tolerance index group involving STI, REI, and MRP. The second is sensitive index group involving SSI, TOL, and SSSI. Level of tolerance based on the six indices was determined using standardizes of index. For first group, STI was selected to be standardized with three sensitive index. Standardized STI was corrected with standardized index of sensitive group so that resulting new standardized index, namely STI Table 3.11. Table 3.11 Standardized stress tolerance index of rice Genotype STIStd-ssi STIStd-tol STIStd-sssi INPARA 3 -2.61 -2.27 -2.61 INPARA 7 0.61 0.39 0.61 IRRI 119 0.19 0.05 0.19 INPARA 4 0.87 0.89 0.87 INPARA 5 -0.25 -0.03 -0.25 INPARI 30 1.42 1.27 1.42 IR 64 1.20 0.70 1.20 IR 42 -0.63 -0.12 -0.63 Ciherang 2.03 1.81 2.03 INPARI 29 -2.83 -2.69 -2.83 Abbreviation: STIStd-ssi, STIStd-tol, STIStd-sssi = standardized STI corrected by standardized SSI, TOL, dan SSSI, respectively The STI showed STIStd-ssi was no different with STIStd-sssi. This may be both of index had same derivate of formula. Three STIStd were consistent to identified tolerant and sensitive genotypes. High index values indicating tolerant genotype, vice versa lowest index value indicating sensitive genotype. Based on three index, Ciherang and INPARI 30 were tolerant genotypes, while INPARA 3 and IR 42 were sensitive genotypes. IR 64 was consistent in high value based on STIStd-ssi and STIStd-sssi, but was moderate based on STIStd-tol. IRRI 119 which identified tolerant based on previous study, however in our study it showed moderate sensitive. 3.3.4 Modelling Stress Tolerance Index Regression analysis described the effect of one or more characters designed as independent variables on a single character designed as dependent variable by expressing the latter as a function of the former. In regression, the character of major importance, for example, grain yield, usually becomes the dependent variable and the factors of character that influence grain yield become independent variables Gomez 1976. Linear regression with tolerance index as Y and grain yield as x showed that the fitted model for determining stagnant flooding stress was ̂ = -0.371 + 0.235GY Table 3.13 and 3.14. It could be showed that grain yield independently could be explain by 87.76 of the tolerance variation. It means that level of tolerance greatly affect the grain yield. To determine the level precision of STI predictive value than STI actual, it was correlated between variables which was calculated from each genotypes. Correlation analysis between STI and predictive value of STI was significant with r = 0.9567 Table 3.12. It was indicated that STI predictive is accurate to estimate actual value of STI. Table 3.12 Descriptive statistic and correlation of STI Variable Min Max Mean Stdv r coefficient p value STI actual 0.50 0.95 0.74 0.1543 0.9567 0.00000 STI predictive 0.81 1.25 1.05 0.1477 Large proportion of variance contributed by grain yield to SF stress tolerance index indicating the grain yield independently could distinguished tolerant and sensitive genotype. The implication for screening method is further experiment just need stressed condition SF without normal site to select the tolerant genotypes. It will increase the efficiency and effectiveness of screening method especially in relation to the cost of research. Table 3.13 Analysis of variance of linear regression of rice Source DF Sum of Square Mean Square F Value Pr F Adj R 2 Model 1 0.1952 0.1952 65.5 0.000 0.8776 Error 8 0.0238 0.003 Total 9 0.219 Table 3.14 Parameter estimates of linear regression of rice Variable Estimate Std. Error t value Pr|t| Intercept -0.371 0.138 -2.690 0.028 Grain yield 0.235 0.029 8.090 0.000 Linear multiple regression with tolerance index as Y and morphological traits as x showed the fitted model to explain the stagnant flooding tolerance was STI = -3.17 + 0.08W1000 – 0.14PL – 0.56SD + 0.11SPAD + 0.04 SL with R 2 adjusted 0.923 Table 3.15 and 3.16. Variance of STI could be explained by 92.3 of weight of 1000 grain W1000, panicle length PL, stem diameter SD, intensity of leaf green colour SPAD, and stem length SL. Table 3.15 Analysis of variance of multiple linear regression of rice Source DF Sum of Square Mean Square F Value Pr F Adj R 2 Model 5 0.212 0.042 22.64 0.005 0.923 Error 4 0.008 0.002 Total 9 0.219 One of five traits, weight of 1000 grain is observed at generative stage Table 3.16. For simplifying selection process, it is better to select traits which expressed at seedling or vegetative stage. Therefore, we tried to exclude weight of 1000 grain from the model. It resulted no significance of the model and R 2 became very low 0.1045, which was largely explained by stem diameter. The implication for the breeding is selection cannot only using vegetative traits, but also need to consider generative traits. Table 3.16 Parameter estimates of multiple linear regression of rice Variable Estimate Std. Error t value Pr|t| Intercept -3.17 0.791 -4.01 0.016 1000 grain weight 0.08 0.016 5.08 0.007 Panicle length -0.14 0.017 -8.06 0.001 Stem diameter -0.56 0.094 -5.94 0.004 Intensity of leaf green color 0.11 0.017 6.23 0.003 Stem length 0.04 0.008 5.10 0.007

3.3.5 Correlation among Traits

Correlation analysis was to know level of correlation between traits observed under stagnant flooding stress. Plant height was significantly correlated with morphological traits such as stem length, stem diameter, length of leaf blade, panicle length, and also weight of 1000 grain. Stress Tolerance Index STI was significantly correlated with grain yield. Grain yield only correlated with number of tillers Table 3.17. Number of productive tiller is one of yield components. The traits may be considered as one of selection criterion for stagnant flooding tolerance Ismail et al. 2012; Singh et al. 2011; Kato et al. 2014; Suwignyo 2014, although in this study showed there was no correlation between number of productive tiller and STI. Other yield components such as number of filled grain and weight of 1000 grains correlated biologically with grain yield, in this case, both of them were not correlated statistically. This may because the variance of number of filled grain and weight of 1000 grains of genotypes tested were scanty varied therefore it could not raise the correlation. . 22 Table 3.17 Correlation among traits of rice genotypes under stagnant flooding stress plot-basis Traits PT FG W1000 GY SPAD SL SD LB WB PE PL STI PH -0.347 0.023 0.356 -0.193 -0.070 0.850 0.584 0.569 0.107 0.196 0.516 -0.130 PT -0.330 -0.314 0.368 0.108 -0.469 -0.305 -0.304 -0.011 -0.262 -0.294 0.178 FG -0.014 0.077 -0.197 0.082 0.064 -0.044 0.052 0.346 -0.033 -0.032 W1000 -0.026 -0.211 0.416 0.263 0.112 0.315 0.399 0.569 0.151 GY -0.102 -0.204 -0.394 -0.326 0.035 0.225 -0.277 0.866 SPAD -0.117 -0.293 -0.243 -0.207 -0.264 0.014 -0.043 SL 0.578 0.662 0.348 0.322 0.535 -0.129 SD 0.467 0.214 -0.030 0.183 -0.332 LB 0.422 0.125 0.436 -0.250 WB 0.048 0.313 0.080 PE 0.351 0.291 PL -0.099 Abbreviation: PH, plant height; PT, number of productive tiller; FG, number of filled grain; W1000, weight of 1000 grains; GY, grain yield; SL, stem length; SD, stem diameter; LB, length of leaf blade; WB, width of leaf blade; PE, panicle exertion; PL, panicle length; STI, Stress Tolerance Index

3.3.6 Genetic Variability and Heritability

Under stagnant flooding stress, all observed traits except panicle length showed broad of phenotypic variability, and their genetic variability were varied among the traits Table 3.18. It mean that the variation greatly influenced by environment not only by genetic per se. Most of the report identified that grain yield was quantitative trait which is controlled by minor gene and had low heritability. In this study, the heritability of grain yield under stagnant flooding was high. Nugraha et al. 2013 suggested that the flooding stress was obvious discriminator between tolerance and sensitive genotypes resulting a consistent grain yield in a given environment hence the heritability also was high. Our study showed variability of grain yield was narrow although effect of genotype variance was significantly different data not shown. Narrowness of grain yield variability may be caused by the narrowness of genetic background of genotypes used. It could be explained through some varieties come from same parent. INPARA 5 IR 64 SUB1, INPARI 30 Ciherang SUB1, IR 64, Ciherang have a close genetic relationship. However, the selection based on grain yield under stagnant flooding stress could be done at early generations using bulk segregation. Plant height, intensity of leaf green color, stem length, panicle exertion and panicle length had broad genetic variability and high heritability. It mean that it would be relative easily to select the traits under flooding stress. The traits can be recommended as secondary trait for stagnant flooding tolerance. The selection can be done at early generation, using bulk segregation or pedigree method. Table 3.18 Genetic and phenotypic variability of rice traits under stagnant flooding stress in dry season of 2015 Traits Stagnant Flooding Stress � ± �� Criteri a � ± �� Criteri a H Criteri a Plant height 55.16 ± 25.43 B 59.54 ± 1.39 B 0.93 H Intensity of leaf green color 2.28 ± 0.99 B 2.32 ± 0.01 B 0.98 H Number of Productive tillers 4.99 ± 3.31 N 7.27 ± 0.80 B 0.66 H Number of filled grain 64.14 ± 69.30 N 171.60 ± 0.80 B 0.43 M Weight of 1000 grain 0.97 ± 1.36 N 3.53 ± 0.60 B 0.34 M Grain yield 0.30 ± 0.17 N 0.36 ± 0.60 B 0.77 H Stem length 33.93 ± 15.92 B 32.08 ± 1.05 B 0.91 H Stem diameter 0.09 ± 0.06 N 0.12 ± 1.05 B 0.68 H Length of leaf blade 7.26 ± 6.05 N 14.14 ± 1.95 B 0.54 M Width of leaf blade 0.00 ± 0.00 N 0.01 ± 1.95 B - 0.86 N Panicle exertion 7.31 ± 3.28 B 6.59 ± 0.12 B 0.95 H Panicle length 2.27 ± 1.05 B 2.46 ± 0.06 B 0.93 H Abbreviation: � ± �� is genotypic variance and its standard deviation; � ± �� is phenotypic variance and its standard deviation; h 2 is heritability; B = broad; N = narrow; H = high; M = medium; L=low

3.4 Conclusion and Suggestion

A linear model involving weight of 1000 grain, panicle length, stem diameter, intensity of leaf green color, and stem length could explain 92.30 of the variance of stress tolerance index. Intensity of leaf green color, panicle length and stem length had relatively broad genetic variability and high heritability under flooding stress, and therefore may be used for selection. Number of productive tillers was correlated with grain yield under SF and highly heritable, hence it may also suggest as one of determining characters for stagnant flooding tolerance. Based on STIStd, Ciherang, and INPARI 30 had good performance under 50 – 60 cm of water depth while IR 42 did not. The tolerance levels of the genotypes need to be confirmed by further experiments across several seasons. 4 INHERITANCE STUDY OF AGRONOMICAL TRAITS OF RICE UNDER STAGNANT FLOODING AND NORMAL CONDITION Abstract Information of genetic model related to stagnant flooding tolerance is essential in the utilization of rice germplasm for improving the effectiveness of breeding program. This study aimed to elucidate genetic control and heritability of agronomic traits under stagnant flooding stress and normal conditions. The rice genotype IRRI 119 was used as a tolerant parent and IR 42 as a sensitive parent. The materials used were six population which were obtained from crossing of the genotypes. The materials were grown at the stagnant flooding stress and normal spot. The experiment was conducted at the Experimental Station of Indonesian Center for Rice Research in the wet season of December 2015 to April 2016. The grain yield and yield components did not fit to additive-dominant model, which indicating the presence of non-allelic interaction. Joint scaling test with six parameter revealed duplicate and complementary epistasis fitted to explain gene action model. The heritability estimates under stress condition were lower compared to the ones in the controlled condition. The strategy for breeding program to improving grain yield under stagnant flooding stress is delaying the selection after several generations until high level of gene fixation was attained. Additionally, it could be useful to conduct shuttle breeding between stress and controlled environment. Key words: generation mean analysis, joint scaling test, stagnant flooding, rice

4.1 Introduction

Rice is often the only cereal that can be grown in flood-prone ecosystem. Rice fields in these flood-prone areas are subject to either transient flash floods leading to total submergence or to long-term partial floods stagnant flooding, SF, and both often occur in the same field within one cropping season Mackill et al. 1996. Stagnant flooding prolonged partial flooding; medium deep occurs in areas when floodwater of 25 –50 cm stagnates in the field from a few weeks to several months. Rice varieties respond to the slowly rising water of stagnant flooding by elongating their stems or leaves escape. Internode elongation keeps the top leaves above the water surface, thereby facilitating respiration. Moderate shoot elongation rate strongly and positively correlated with grain yield under stagnant flooding. However, elongation at rates of 2.0 cm day -1 was associated with reduced harvest index due to a smaller panicle size and the increased lodging. Tolerant varieties should be inherently tall or elongate moderately along with the rising of the water. Improvement of stagnant flooding tolerant should involve combination of both of these traits to develop an appropriate phenotype Kato et al. 2014. The improvement of tolerance to abiotic stress has been a major goal in many breeding projects; however, there is no unanimous opinion regarding the best strategy to deploy and which traits to target Blum 1988. The slow progress