Abstract
Submergence is a widespread problem of rice production, especially in low-lying areas in South and Southeast Asia. Despite the success of Sub1 mega varieties, repeated instances of prolonged and severe flooding in stress-prone areas suggests that the SUB1 gene is no longer sufficient in those regions and requires improved varieties with increased tolerance. A study was conducted to identify quantitative trait loci (QTLs) associated with submergence tolerance using 115 F7 recombinant inbred lines (RILs) derived from the cross of Ciherang-Sub1, a popular Indonesian cultivar carrying the SUB1 gene that has relatively higher tolerance to submergence compared to the performance of most other Sub1 lines and the submergence and stagnant flooding tolerant IR10F365. As the tolerant allele at SUB1A on chromosome 9 was fixed in this mapping population, additional QTLs responsible for submergence tolerance were expected to be revealed. Genotyping with an Infinium 6K SNP chip resulted in 469 polymorphic markers that were then used for QTL mapping. Phenotyping was performed under complete submergence with two replicates. A major QTL for submergence derived from Ciherang-Sub1, named qSUB8.1, was detected on chromosome 8 with a LOD score of 10.3 and phenotypic variance of 27.5%. Additionally, a smaller QTL, also derived from Ciherang-Sub1, was detected on chromosome 2 with a LOD score of 3.5 and phenotypic variance of 12.7%. There was no digenic interaction detected between these QTLs suggesting their independent action. The QTLs detected in this study can be used in marker-assisted selection to further improve the tolerance of other Sub1 varieties.
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Acknowledgements
We thank R. Garcia, E. Suiton, J. Mendoza, G. Perez, J. Borgonia, R. Formaran, V. Bartolome and the IRRI GSL team for technical assistance. The work reported here was supported in part by a grant from the Bill and Melinda Gates Foundation (BMGF) through the project on “Stress-tolerant rice for Africa and South Asia (STRASA)”, Global Rice Science Partnership (GRiSP), and the National Institute of Food and Agriculture, U.S. Department of Agriculture, Hatch project 1009300.
Authors’ contributions
E.M.S. designed the experiments. B.C.Y.C developed the RIL population using rapid generation advance (RGA). J.C. performed the seed multiplication of the mapping population. Z.J.C.G and A.S. performed the DNA extraction, and J.C. and Z.J.C.G performed the phenotyping under the supervision of E.M.S. M.J.T. supervised the SNP genotyping in the Genotyping Service Lab (GSL). Z.J.C.G., A.S., and E.M.S. analyzed the data. Z.J.C.G. and E.M.S. wrote the manuscript. B.C.Y.C. and M.J.T. edited the manuscript. All authors read and approved the manuscript.
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Supplementary Table 1
Recombinant Inbred Lines (RILs) with average survival rates above the tolerant check FR13A containing combinations of the identified QTLs (90–100% survival rates). (DOCX 13 kb)
Supplementary Figure 1
A representative figure showing the QTLs for submergence tolerance from Ciherang-sub1/IR10F365 population identified by QTLNetwork. The red balls indicate the QTLs with additive effects. (DOCX 49 kb)
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Gonzaga, Z.J.C., Carandang, J., Singh, A. et al. Mapping QTLs for submergence tolerance in rice using a population fixed for SUB1A tolerant allele. Mol Breeding 37, 47 (2017). https://doi.org/10.1007/s11032-017-0637-5
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DOI: https://doi.org/10.1007/s11032-017-0637-5