Highlight qEMF3, a novel QTL for the early-morning flowering trait to mitigate heat-induced spikelet sterility at flowering in rice, was identified using a wild rice, Oryza officinalis, as a genetic resource.

No abstract

Wild relatives of rice in the genus Oryza (composed of 24 species with 11 different genome types) have been significantly contributing to the varietal improvement of rice (Oryza sativa). More than 4000 accessions of wild rice species are available and they are regarded as a “genetic reservoir” for further rice improvement. DNA markers are essential tools in genetic analysis and breeding. To date, genome-wide marker sets for wild rice species have not been well established and this is one of the major difficulties for the efficient use of wild germplasm. Here, we developed 541 genome-wide InDel markers for the discrimination of alleles between the cultivated species O. sativa and the other seven AA-genome species by positional multiple sequence alignments among five AA-genome species with four rice varieties. The newly developed markers were tested by PCR-agarose gel analysis of 24 accessions from eight AA genome species (three accessions per species) along with two representative cultivars (O. sativa subsp. indica cv. IR24 and subsp. japonica cv. Nipponbare). Marker polymorphism was validated for 475 markers. The number of polymorphic markers between IR24 and each species (three accessions) ranged from 338 (versus O. rufipogon) to 416 (versus O. longistaminata) and the values in comparison with Nipponbare ranged from 179 (versus O. glaberrima) to 323 (versus O. glumaepatula). These marker sets will be useful for genetic studies and use of the AA-genome wild rice species.

The enhancement of heat stress tolerance at anthesis is an important strategy to achieve sustainable rice production in the context of predicted global warming. In this study, we genetically analysed spikelet fertility under high temperature treatment (38°C) at anthesis using the three rice varieties, namely, Koshihikari and Takanari, which were developed in Japan, and IR64, which was developed in the Philippines. Genetic analysis of the F 2 population between Takanari and IR64 revealed a quantitative trait locus (QTL) on chromosome 4 that increased spikelet fertility with the Takanari allele and that was likely qHTSF4.1, a previously fine-mapped major QTL. Genetic analysis using chromosome segment substitution lines (CSSLs) carrying Koshihikari chromosome segments in the IR64 genetic background did not show any QTLs. In contrast, genetic analysis using CSSLs carrying Koshihikari chromosome segments in the Takanari genetic background revealed some QTLs, including chromosomes 4 and 9. These results suggest that the expression of QTLs may depend on genetic background. The two CSSLs, SL1313 and SL1330, which carried the QTLs on chromosomes 4 and 9, respectively, exhibited a spikelet fertility of over 80% and relatively large anther dehiscence compared with Takanari. These results suggest that the Koshihikari allele of QTLs may be related to improved anther dehiscence, which may lead to successful pollination and ultimately increased spikelet fertility under heat stress conditions. The findings in the present study should be useful to enhance heat stress tolerance at anthesis in rice in future breeding programs.