Mapping QTL for heat tolerance at flowering stage in rice using SNP markers

Abstract

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.

Genome-Wide Association Mapping of Fertility Reduction upon Heat Stress Reveals Developmental Stage-Specific QTLs in Arabidopsis thaliana

“…Such a common response mechanism is promising for the translation of findings from model species to crops. Unfortunately, comparison of the QTLs observed in this study with earlier identified QTLs in other mapping studies in crops aiming to identify heat tolerance genes during flowering is difficult because most QTLs have not been cloned yet (Grilli et al, 2007;Ye et al, 2012;Lucas et al, 2013). All earlier studies were done in low-resolution biparental mapping populations; therefore, the associated regions still contain many genes.…”

“…Moreover, such studies reveal the actual genetic regulators driving a specific response, in contrast to identifying transcriptional differences upon heat stress in gene expression studies, which identifies many downstream effects of the response. Biparental mapping populations have been developed and used for quantitative trait locus (QTL) mapping of heat tolerance in various crops, such as rice (Ye et al, 2012), cowpea (Vigna unguiculata) (Lucas et al, 2013), and tomato (Grilli et al, 2007). These studies identified multiple QTLs (from 2 to 18) with an explained variance between 2 and 20%.…”

Field level evaluation of rice introgression lines for heat tolerance and validation of markers linked to spikelet fertility

“…Several QTLs have been mapped for heat tolerance at flowering stage (Ye et al 2011;Jagadish et al 2010a;Zhang et al 2008;Xiao et al 2011). In our study, RM250 and RM88 were associated with days to flowering in normal and poly cover house methods respectively but same type of alleles were observed in both susceptible and tolerant checks indicating they are not specific to a haplotype.…”

“…Exploring the thermo tolerance diversity in rice plants will provide useful information for the improvement of traits to cope with the projected climate warming scenarios in the future (IPCC: Intergovernmental panel on climate change 2007). The impact of heat stress on rice yield depends on the genotype, the growth stage at which heat stress is received and the period of the stress (Liao et al 2014;Poli et al 2013;Zhou et al 2012;Ye et al 2011;Jagadish et al 2010a;Prasad et al 2006;Morita et al 2005). In general, when rice plants are exposed to temperature greater than 35°C for more than one hour at anthesis, it results in increased sterility (Jagadish et al 2007).…”

“…Genetic variation in the ability of rice to maintain spikelet fertility and seed set under heat stress allows selection of genotypes with increased tolerance to heat stress. QTL mapping and gene expression studies for heat tolerance have been carried out in rice at different stages such as booting, flowering and grain filling stage (Bui et al 2014;Wei et al 2013;Liao et al 2014;Poli et al 2013;Xue et al 2012;Xiao et al 2011;Ye et al 2011;Jagadish et al 2010a;Zhang et al 2008;Chen et al 2008;Zhao et al 2006). QTLs for heat tolerance were mapped on all chromosomes except chromosome 7 but fine mapping of these QTLs has not been reported.…”