Identifying and confirming quantitative trait loci associated with heat tolerance at flowering stage in different rice populations

Abstract

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.

Breeding efforts to mitigate damage by heat stress to spikelet sterility and grain quality

“…The heat tolerance of the nIL carrying qHTSF4.1 was increased consistently in all of the backcross populations. In BC 3 F 3 , spikelet fertility of plants with qHTSF4.1 (34.7 ± 14.2%) was significantly higher than in those without the QTL (22.5 ± 7.9%) and recurrent parent IR64 Ye et al (2015a) identified and used in our breeding programs. A thermotolerance gene (TT1) in African rice (O. glaberrima) variety CG14 was cloned .…”

“…Some of the QTLs identified in different populations are overlapped or closely linked (Table 1). Among the identified QTLs, a QTL for spikelet fertility under high temperature, qHTSF4.1 from n22, was identified in different genetic backgrounds in different studies (Jagadish et al, 2010;Xiao et al, 2011;Ye et al, 2012Ye et al, , 2015a. To fine map and validate the effect of heat tolerance QTL qHTSF4.1, PCR-based SnP markers were developed and used to genotype BC 2 F 2 , BC 3 F 2 , BC 3 F 3 , and BC 5 F 2 populations from the cross combination of IR64/n22.…”

“…n22 has many undesirable agronomic characteristics (Manigbas et al, 2014), but the results imply the importance of making best use of the landrace as a genetic resource for future breeding challenges. In the genetic analyses using Giza178 as a donor parent, some other QTLs for heat tolerance at flowering were detected (Ye et al, 2015a), and further efforts are being made to develop the series of nILs carrying the QTLs at different loci for heat tolerance at flowering. Recent studies showed that heat tolerance at flowering stage in rice is controlled by recessive genes (Fu et al, 2015;Ye et al, 2012Ye et al, , 2015b.…”

<strong>When water runs dry and temperature heats up: </strong><strong>Understanding the mechanisms in rice tolerance to drought and </strong><strong>high temperature stress conditions</strong>

“…The second QTL qSTIY5.1/qSSIY5.1, which has been previously reported was established in chromosome 5 at a narrower 331 kbp region compared to 23Mb in the original study. Although several QTLs control heat tolerance at flowering stage, QTL qHTSF4.1 can be an importance source for HTS tolerance since it was found consistently across genetic backgrounds of RILs involving crosses of IR64, N22, Giza178 and Milyang23 (Ye et al, 2015). Figure 6A shows the various published QTLs associated with heat tolerance at flowering stage in different rice genotypes including Azucena, Bala, Toyonishiki, T226, T219 and IR64 (Ye et al, 2012).…”

Molecular Mapping and Breeding of Physiological Traits

“…The identified QTLs can be used for marker assisted breeding program in wheat for improved heat tolerance. In rice, QTL qHTSF4.1 showing consistent performance across different genetic backgrounds has been identified which could be used as an important source for enhancing heat tolerance in rice at flowering stage [130].…”