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- Genetic Study of Stagnant Flooding Tolerance in Rice
Genetic Study of Stagnant Flooding Tolerance in Rice
Thesis Abstract:
The major constraint in cultivating rice in flood-prone ecosystem is the lack of appropriate varieties. In the flood-prone ecosystem, common modern rice varieties are unlikely to grow normally due to water depth. To contribute to the rice breeding program, this is a study on the genetic basis of stagnant flooding tolerance in rice.
The first objective in this study aimed to identify major morphological and agronomical traits associated with stagnant flooding tolerance. The water regime was in normal condition (shallow flooding of 5 cm) and gradual flooding, which started at 30 days after transplanting (DAT) with 20 cm water depth, then gradually increased weekly by 5 cm up to 50–60 cm. When 50–60 cm had been reached, it was maintained until the maturity. A linear model involving weight of 1,000 grains, panicle length, stem diameter, intensity of leaf green color, and stem length could explain 92.30 percent of the variance of stress tolerance index (STI). Stem length, intensity of leaf green color, and panicle length had broad genetic variability and high heritability, therefore it would be relatively easy to select the characters under flooding stress. Number of productive tillers was correlated with grain yield under stagnant flooding stress and highly heritable. The characters were easy to observe and non-destructive in measurement. The characters would be candidate for secondary character for stagnant flooding selection. These characters may be relevant when studying intermediate genotypes with tolerance. However, their relevance as selectable traits still needs to be assessed. It was identified that IR 64, Ciherang, and INPARI 30 had good performance, while IR 42 under 50–60 cm of water depth, did not. However, the levels of tolerance of the genotypes still needs to be confirmed by further experiments across several seasons.
The second objective aimed to identify the inheritance of stagnant flooding tolerance. The population of crossing IR 42 x IRRI 119 was evaluated using six generation mean analysis under stress and normal condition. In the stagnant flooding site, the plants were situated at 2–3 cm of water depth from zero to seven days after transplanting (DAT). Then the water was increased twice a week at a rate of 1.43 cm day-1 during early vegetative stage (from seven to 21 DAT); and three times a week at a rate of 2.14 cm day-1 during the late vegetative stage (from 21 to 35 DAT). Then, a water depth of 50–80 cm was maintained from 35 DAT until maturity. The grain yield and yield components did not fit to additive-dominant model, which indicated 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 estimated under stress condition were lower compared to the ones in the controlled condition. To improve grain yield under stagnant flooding stress, the strategy for breeding program was delaying the selection after several generations until high level of gene fixation was attained. Also, it is important to combine the shuttle breeding between stress and controlled environment.
The third objective was to identify SNP markers linked with agronomical traits related to stagnant flooding tolerance in rice. The characters selected were plant height and number of productive tillers. The phenotypical data were collected from bi-parental population of IR 42 and IRRI 119. IR 42 was sensitive parent and IRRI 119 was tolerant. The genotyping was carried out using 384 SNPs Golden Gate Illumina assay. Association analysis between SNP markers and phenotypical data were performed using general linear model in Tassel version 5.0 software program. Based on GLM association analysis, the significant marker for plant height with p value < .05 were TBGI275345, TBGI275367, and TBGI424383. The significant marker for number of tiller were TBGI000722, TBGI258600, TBGI270843, TBGI271066, TBGI271076, TBGI272122, TBGI272241, and TBGI327790. Two of them, TBGI424383 and TBGI271066, were expected to be associated with family of protein kinase, which play a role in plant stress signaling.