A trait specific QTL survey identifies NL44, a NERICA cultivar as a novel source for reproductive stage heat stress tolerance in rice

Rice is sensitive to heat stress at gametogenesis and anthesis stages. For sustaining rice yields under the predicted threat of reproductive stage heat stress (RSHS), identification of tolerant donors as well as mapping of genes governing tolerance is crucial. Recently a NERICA (NEwRIce for AfriCA) rice genotype, NL44 has been reported tolerant to RSHS. The present study aims to survey a recombinant inbred line (RIL) population developed from the cross, Pusa Basmati 1 (PB1)/NL44 using markers linked to 54 RSHS quantitative trait loci (QTLs) through phenotypic and genotypic characterization. When exposed to RSHS, the susceptible parent PB1 and several RILs showed significant reduction for spikelet fertility and grain yield plant −1 relative to NL44. Both these traits and the estimated stress tolerance index (STI) showed a quantitative pattern of inheritance. Out of the 116 SSR markers surveyed, 31 markers were polymorphic between PB1 and NL44. No discernible associations could be found through a preliminary bulked segregant analysis with these markers. A subsequent single marker analysis revealed five minor QTLs, four for spikelet fertility under heat stress and two for STI-spikelet fertility, of which one QTL was mapped for both the traits. These QTLs, however, could explain a very low level of total phenotypic variation. Additionally, the cumulative additive effect of these QTLs could account only for a possible 30% of the contrast between PB1 and NL44. Thus, the study clearly establishes that NL44 has novel genomic regions for RSHS tolerance.