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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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, **aoyan Gao and **aoshu 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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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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Supplementary Text and Figures
Supplementary Figures 1–24 and Supplementary Tables 1–5, 7 and 8. (PDF 11352 kb)
Supplementary Table 6
RNA-seq results with wild-type Dong**g 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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DOI: https://doi.org/10.1038/ng.3518
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