Genetic response to strong directional selection was studied by simulation and selection experiment of rice tolerance to critical stress. In the simulation, a balanced BC_2F_2 population with 200 individuals was constructed for randomly sampling with5,10, 20, and 30 individuals that covered all cases in the selection experiment. Two elite indica varieties of rice, IR64 from IRRI and Teqing from China, were crossed with seven donors from different countries, and backcrossed two times with IR64 and Teqing as recurrent parents. Three selection experiments with 200 individuals in the original BC_2F_2 were conducted for evaluating on genetic response: experiment I, selection on non fitness-related trait, kernel elongation (non fitness-related trait forcomparison); experiment II, selection on submergence tolerance (fitness-related trait); and experiment III, selection on drought tolerance (fitness-related trait). The selected plants at both directions in experiment I, the survived plants in experimentII and III, were used to analyze the variation of haplotype and diplotype frequencies and linkage disequilibrium with 140 anchor SSR markers representing 79 well-distributed bins.
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