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Bayesian Network Development Based on Genomic and Phenomic Characterization of Multi-Parent Advanced Generation Intercrosses (MAGIC)-Derived Population in Rice (Oryza sativa L.)
Dissertation Abstract:
Tolerance to salinity, cold, anaerobic germination, zinc deficiency at seedling stages, grain yield, and related traits were investigated using 444 MAGIC Indica lines through GBS, involving 27041 SNPs to investigate the potential putative SNPs for the detection of a specific trait and establish the marker and trait network (Bayesian Networks, BNs) in International Rice Research Institute (IRRI) and Myanmar. The significant SNPs—namely, Sl_5656605, Sl_6593442, and Sl_6640911 for salinity tolerance; S6_6686862, S6_6698403, S6_6701738, S6_6701762, and S6_6703357 for cold tolerance; S5_102763 for AG; and S4_31666827, S4_31992079, and S4_320007019 for zinc deficiency tolerance were detected. Only one strong SNP (S6_3077965) for days to 50 percent flowering (DTF); nine novel SNPs (S1_33996022, Sl_33996762, Sl_34010713, Sl_34010721, S1_37535892, S1_37543937, S1_38620942, S1_38636497, and S1_38949958) for plant height (HT); S6_18859143 for the number of tillers; and three robust SNPs (S6_2962502, S6_3077965, and S6_2939487) for grain yield (GY) were also identified. Thus, these markers could be used in marker-assisted rice breeding. According to BNs, DTF and HT affect GY. Therefore, DTF and correspondingly HT should be considered to obtain the desired GY. Furthermore, salinity tolerant lines (MIB-4608, MIB-4361, MIB-3604, MIB-4198, and MIB-4546); cold tolerant lines (MIB-4524, MIB-4389, MIB-4425, MIB-4445, MIB-4289, MIB-3814, and MIB-4620); three lines (MIB-3930 and MIB-4707) with high AG; and zinc-deficiency tolerant lines (MIB-4050, MIB-3442, and MIB-4198) were identified for their probable utilization in designing rice breeding strategies.