Identification of QTL linked to heat tolerance in rice (Oryza sativa L.) using SSR markers through bulked segregant analysis

Identification of loci and linked markers enable the marker-assisted selection for transferring the reproductive phase heat tolerance in rice. Microsatellite marker-based bulked segregant analysis (BSA) for heat tolerance was performed in F₃ progenies of the cross between temperature sensitive high yielding variety Uma and tolerant variety N22. Hightemperature stress ranged from 23.33 to 38.99 °C at the booting-stage, and spikelet-fertility was considered as a direct measure of tolerance. N22 has exhibited a high spikelet-fertility of 90.92 per cent against 2.62 per cent, 44.78 per cent in Uma and F₃ plants, respectively. Of the 197 microsatellite markers screened, 41 were found to be polymorphic and used for BSA of tolerant and susceptible F₃ bulk along with both the parents. Marker RM5749 on chromosome 4 had co-segregated with tolerance, whereas, previously reported markers for heat tolerance in rice did not have an effect in the study population. The LOD value obtained during single marker analysis for the linkage between marker RM5749 and spikelet fertility was 6.86, indicating a strong linkage with the spikelet fertility under heat stress. The failure of the reported markers in our population suggests that the reproductive phase heat tolerance mechanisms in rice vary across the populations and the markers have to be validated for each population before being employed in MAS.