To identify quantitative trait loci (QTL) controlling heat tolerance in rice, the progeny of BC 1 F 1 and F 2 populations derived from an IR64 · N22 cross were exposed to 38/24°C for 14 days at the flowering stage, and spikelet fertility was assessed. A custom 384-plex Illumina GoldenGate genotyping assay was used to genotype the F 2 and selected BC 1 F 1 plants. Four single nucleotide polymorphisms were associated with heat tolerance in the BC 1 F 1 population using selective genotyping and single marker analysis, and four putative QTL were found to be associated with heat tolerance in the F 2 population. Two major QTL were located on chromosome 1 (qHTSF1.1) and chromosome 4 (qHTSF4.1). These two major QTL could explain 12.6% (qHTSF1.1) and 17.6% (qHTSF4.1) of the variation in spikelet fertility under high temperature. Tolerant allele of qHTSF1.1 was from the susceptible parent IR64, and that of qHTSF4.1 was from tolerant parent N22. The effect of qHTSF4.1 on chromosome 4 was confirmed in selected BC 2 F 2 progeny from the same IR64 · N22 cross, and the plants with qHTSF4.1 showed significantly higher spikelet fertility than other genotypes.

BackgroundClimate change is affecting rice production in many countries. Developing new rice varieties with heat tolerance is an essential way to sustain rice production in future global warming. We have previously reported four quantitative trait loci (QTLs) responsible for rice spikelet fertility under high temperature at flowering stage from an IR64/N22 population. To further explore additional QTL from other varieties, two bi-parental F2 populations and one three-way F2 population derived from heat tolerant variety Giza178 were used for indentifying and confirming QTLs for heat tolerance at flowering stage.ResultsFour QTLs (qHTSF1.2, qHTSF2.1, qHTSF3.1 and qHTSF4.1) were identified in the IR64/Giza178 population, and two other QTLs (qHTSF6.1 and qHTSF11.2) were identified in the Milyang23/Giza178 population. To confirm the identified QTLs, another three-way-cross population derived from IR64//Milyang23/Giza178 was genotyped using 6K SNP chips. Five QTLs were identified in the three-way-cross population, and three of those QTLs (qHTSF1.2, qHTSF4.1 and qHTSF6.1) were overlapped with the QTLs identified in the bi-parental populations. The tolerance alleles of these QTLs were from the tolerant parent Giza178 except for qHTSF3.1. The QTL on chromosome 4 (qHTSF4.1) is the same QTL previously identified in the IR64/N22 population.ConclusionThe results from different populations suggest that heat tolerance in rice at flowering stage is controlled by several QTLs with small effects and stronger heat tolerance could be attained through pyramiding validated heat tolerance QTLs. QTL qHTSF4.1 was consistently detected across different genetic backgrounds and could be an important source for enhancing heat tolerance in rice at flowering stage. Polymorphic SNP markers in these QTL regions can be used for future fine mapping and developing SNP chips for marker-assisted breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0199-7) contains supplementary material, which is available to authorized users.