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OsSPL13 controls grain size in cultivated rice

Nature Genetics volume 48, pages 447–456 (2016)Cite this article

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Abstract

Although genetic diversity has a cardinal role in domestication, abundant natural allelic variations across the rice genome that cause agronomically important differences between diverse varieties have not been fully explored. Here we implement an approach integrating genome-wide association testing with functional analysis on grain size in a diverse rice population. We report that a major quantitative trait locus, GLW7, encoding the plant-specific transcription factor OsSPL13, positively regulates cell size in the grain hull, resulting in enhanced rice grain length and yield. We determine that a tandem-repeat sequence in the 5′ UTR of OsSPL13 alters its expression by affecting transcription and translation and that high expression of OsSPL13 is associated with large grains in tropical japonica rice. Further analysis indicates that the large-grain allele of GLW7 in tropical japonica rice was introgressed from indica varieties under artificial selection. Our study demonstrates that new genes can be effectively identified on the basis of genome-wide association data.

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Figure 1: GWAS analysis and molecular characterization of the large-grain trait.
Figure 2: Comparative analyses of the OsSPL13 locus between the small-grain and large-grain haplotypes.
Figure 3: Analyses of grain shape for wild-type Dongjing, transgenic plants and a T-DNA mutant.
Figure 4: Analyses of yield traits for Dongjing and transgenic plants.
Figure 5: Associations of transcript and protein levels of OsSPL13 with changes in cell size in the hull.
Figure 6: In situ hybridization of OsSPL13 in hulls during floret development and identification of the SRS5 gene as a direct target of OsSPL13.
Figure 7: The level of genetic differentiation (FST) across chromosome 7 between different subspecies.

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Acknowledgements

We thank J. Wang and W. Cai for help in the construction of the MIM156 vector, K. Chong (Institute of Botany, Chinese Academy of Sciences) for providing the pTCK303 vector, P. Hu and G. Jiao for the measurements of grain quality, and J. Li, Xiaoyan Gao and Xiaoshu Gao for microscopy experiments. This work was supported by the Chinese Academy of Sciences (XDA08020101), the National Natural Science Foundation of China (91535202 and 31421093) and the Ministry of Science and Technology of China (2013CBA01404).

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Authors and Affiliations

  1. National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

    Lizhen Si, Jiaying Chen, Xuehui Huang, Hao Gong, Jianghong Luo, Qingqing Hou, Taoying Zhou, Tingting Lu, Jingjie Zhu, Yingying Shangguan, Erwang Chen, Chengxiang Gong, Qiang Zhao, Yufeng Jing, Yan Zhao, Yan Li, Lingling Cui, Danlin Fan, Yiqi Lu, Qijun Weng, Yongchun Wang, Qilin Zhan, Kunyan Liu & Bin Han

  2. State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China

    Xinghua Wei

  3. Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea

    Kyungsook An & Gynheung An

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  1. Lizhen Si
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Contributions

B.H. and L.S. designed and conducted the research. L.S., J.C., J.L., Q.H., T.Z., J.Z., Y.S., E.C., C.G., Y.J., Y.W., D.F., Y. Lu, Q.W., Q. Zhan, L.C. and Y.W. performed research. L.S., X.H., H.G., T.L., Y.Z., Y. Li, K.L. and Q. Zhao analyzed data. X.W. collected rice cultivars. K.A. and G.A. performed the generation of mutant rice. L.S. and B.H. wrote the manuscript.

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Correspondence to Bin Han.

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Supplementary information

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Supplementary Figures 1–24 and Supplementary Tables 1–5, 7 and 8. (PDF 11352 kb)

Supplementary Table 6

RNA-seq results with wild-type Dongjing and glw7 plants in panicles. (XLSX 292 kb)

Supplementary Data Set

Supporting data for the supplementary figures. (XLS 111 kb)

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Si, L., Chen, J., Huang, X. et al. OsSPL13 controls grain size in cultivated rice. Nat Genet 48, 447–456 (2016). https://doi.org/10.1038/ng.3518

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