Abstract
Seed vigor is an important seed quality trait in rice (Oryza sativa L.) that profoundly affects seedling morphogenesis in different environments. Generally, highly vigorous seeds have many advantages in agricultural production, such as resistance to adverse stresses, rapid emergence, and yield improvement. In the present study, one germplasm collection and one recombinant inbred line (RIL) population were used to identify quantitative trait loci (QTLs) for seed vigor. A total of 19 single nucleotide polymorphisms (SNPs) were found to be significantly associated with seed vigor (−log10(P) > 6) in the germplasm collection, which consisted of 200 rice cultivars. Nine loci responsible for seed vigor were identified via QTL mapping by using a high-density bin map. To screen the candidate genes more efficiently, we selected six loci that were co-localized in GWAS and QTL mapping, overlapped previous reports, repeat detected across two seasons, or high contribution rate as reliable loci. A total of 44 differentially expressed genes were obtained from the reliable loci via gene expression profile analysis. Among these 44 genes, Os06g0108600, Os06g0110200, Os06g0253100, Os06g0282000, Os07g0583600, Os07g0592600, and Os09g0432300 were the most promising candidates associated with seed vigor.
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Abbreviations
- GR:
-
germination rate
- GP:
-
germination potential
- GI:
-
germination index
- VI:
-
vigor index
- QTL:
-
quantitative trait loci
- GWAS:
-
genome-wide association study
- DSR:
-
direct-seeded rice
- WS:
-
wet season
- DS:
-
dry season
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Acknowledgments
We thank Novogene Co., Ltd., for assisting in sequencing and bioinformatics analyses. We thank the assistant scientist Berlaine Quime from International Rice Research Institute for the critical reading and modification of the manuscript. We also thank Ling Su and Meng Yang for their suggestions and help for experiments and data analyses.
Funding
Financial support for this research was provided in part by a grant from the Breeding New Varieties of Rice Suitable for Light and Simple Cultivation and Mechanized Production (no. 2017YFD0100104), the National Key Technology Research and Development Program of China (no. 2016YFD0102102), the Science and Technology Project of Guangdong Province (no. 2015B020231011), and the earmarked fund for Modern Agro-Industry Technology Research System (no. CARS-01-12).
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Z.C. and H.W. designed the project and J.Y. performed all the experiments and T.G. wrote the manuscript. D.L., K.S., L.L., W.X., J.W., Y.L., and S.W. assisted in conducting experiments and data analysis. H.W. and Z.C. provided the direction for the study and the correction of the manuscript. All authors read and approved the final manuscript.
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National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
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Fig. S1
Differentially expressed genes between parents at different periods. (PNG 84 kb)
Table S1
Primers used for qRT-PCR. (XLSX 9 kb)
Table S2
Phenotypic data of all germplasms. (XLSX 49 kb)
Table S3
Annotated function of 44 differentially expressed genes identified from the six reliable loci. (XLSX 15 kb)
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Guo, T., Yang, J., Li, D. et al. Integrating GWAS, QTL, mapping and RNA-seq to identify candidate genes for seed vigor in rice (Oryza sativa L.). Mol Breeding 39, 87 (2019). https://doi.org/10.1007/s11032-019-0993-4
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DOI: https://doi.org/10.1007/s11032-019-0993-4