Novel QTLs from Wild Rice Oryza longistaminata Confer Strong Tolerance to High Temperature at Seedling Stage

doi:10.1016/j.rsci.2023.07.004

Abstract

Abstract:

Global warming poses a threat to rice production. Breeding heat-tolerant rice is an effective and economical approach to address this challenge. African rice is a valuable genetic resource for developing heat-tolerant crops due to its intricate mechanism for adapting to high temperatures. Oryza longistaminata, a widely distributed wild rice species in Africa, may harbor an even richer gene pool for heat tolerance, which remains untapped. In this study, we identified three heat tolerance QTLs from O. longistaminata at the seedling stage, including novel heat tolerance loci qTT4 and qTT5. Our findings demonstrated that the O. longistaminata alleles for these two QTLs can enhance the heat tolerance of rice seedlings. Remarkably, qTT5 was mapped to a region spanning approximately 287.2 kb, which contains 46 expressing genes. Through the analysis of Gene Ontology and expression differences under heat induction, we identified four candidate genes. Our results lay the foundation for discovering heat tolerance genes underlying O. longistaminata and developing new genetic resources for heat-tolerant rice breeding.

Key words: wild rice, Oryza longistaminata, heat tolerance, QTL

Fan Fengfeng, Cai Meng, Luo Xiong, Liu Manman, Yuan Huanran, Cheng Mingxing, Ayaz Ahmad, Li Nengwu, Li Shaoqing. Novel QTLs from Wild Rice Oryza longistaminata Confer Strong Tolerance to High Temperature at Seedling Stage[J]. Rice Science, 2023, 30(6): 577-586.

Figures/Tables 7

Fig. 1. Identification of heat tolerance in backcross inbred line (BIL) population and their correlations at seedling stage. A, Phenotypes correspond to heat resistance grade after high temperature treatment. Scale bar, 10 cm. B, Phenotypes of heat tolerant and heat sensitive lines after high temperature treatment. Scale bar, 10 cm. C and D, Distributions of seedling survival rate under heat stress (C) and heat tolerance grade (D) of BIL population in two tests. Three replicates were performed for each BIL in each test. E and F, Correlation between heat tolerance grade and seedling survival rate under heat stress in two tests.

Table 1. Heat tolerance phenotypic variations in 9311 and backcross inbred lines (BILs) in two tests.

Trait	Test	9311	BILs
Trait	Test	9311	Mean ± SD	CV (%)	Range	Heritability (%)
Survival rate under heat stress (%)	Test 1	35.7 ± 7.5	41.8 ± 27.3	65.3	0.0‒100.0	73.59
Survival rate under heat stress (%)	Test 2	28.5 ± 3.3	40.3 ± 25.6	63.5	0.0‒96.3	73.59
Heat tolerance grade	Test 1	6.5 ± 1.0	5.7 ± 1.8	31.6	1.7‒9.0	69.86
Heat tolerance grade	Test 2	7.0 ± 0.0	5.9 ± 1.7	28.8	1.5‒9.0	69.86

Fig. 2. QTLs for heat tolerance at seedling stage detected in Oryza longistaminata.

Fig. 3. Validation of function of qTT4 and qTT5. A and B, Analysis of heat tolerance of qTT4 and qTT5 in backcross inbred line population. C?F, Heat tolerance phenotypes of qTT4 (C and D) and qTT5 (E and F). Scale bars, 10 cm. qTT4(qTT5)9311 represents lines containing qTT4(qTT5) from 9311, qTT4(qTT5)O. longistaminata represents lines containing qTT4(qTT5) from O. longistaminata. **** indicates significant differences at the 0.0001 level, by the Student’s t-test.

Fig. 4. qTT5 improves heat tolerance of rice at seedling stage. A, Phenotypes of heat tolerance for qTT5-carrying chromosome segment substitution line (CSSL) and its recurrent parent 9311. Scale bars, 10 cm. B, Seedling survival rate and heat tolerance grade of qTT5-carrying CSSL and 9311 under heat stress. Data are Mean ± SD (n = 3). * and ** indicate significant differences at the 0.05 and 0.01 levels, respectively, by the Student’s t-test.

Fig. 5. Analysis of qTT5 candidate genes. A, Genotype of progeny testing for qTT5 delimited the locus to a 287.2-kb stretch flanked by Bin8-130 and Bin8-131. Seedling survival rate under heat stress was shown for recombinant backcross inbred lines and parental 9311. Data are Mean ± SD (n = 3). The different lowercase letters represent significant differences (P < 0.05) as determined by the Student’s t-test. B, A total of 46 putative genes was annotated within the localization interval. C, Gene Ontology (GO) analysis of 46 candidate genes in the localization interval. D, Expression levels of 20 genes under the GO term of metabolic process and response to stimulus. The expression levels of five heat sensitive lines (white) and five heat resistant lines (black) were calibrated to rice Ubiquitin gene expression. Date are Mean ± SD (n = 5). ** and *** indicate significant differences at the 0.01 and 0.001 levels, respectively, by the Student’s t-test.

Fig. 6. Expression analysis of candidate genes in plants exposed to 45 ºC heat stress in a phytotron for different time periods. The transcript level is shown as the expression relative to the Ubiquitin gene expression. Data are Mean ± SD (n = 5). *, **, and *** indicate significant differences at the 0.05, 0.01 and 0.001 levels, respectively, by the Student’s t-test.

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