Tolerance to salinity, cold, anaerobic germination, zinc deficiency at seedling stages,
grain yield, and related traits were investigated using 444 MAGIC lndica 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 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% flowering (DTF),
nine novel SNPs (SI_33996022, Sl_33996762, Sl_34010713, Sl_34010721, SI_37535892,
SI_37543937, SI_38620942, SI_38636497, and SI_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, 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.
