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Duplication of an upstream silencer of FZP increases grain yield in rice


Transcriptional silencer and copy number variants (CNVs) are associated with gene expression. However, their roles in generating phenotypes have not been well studied. Here we identified a rice quantitative trait locus, SGDP7 (Small Grain and Dense Panicle 7). SGDP7 is identical to FZP (FRIZZY PANICLE), which represses the formation of axillary meristems. The causal mutation of SGDP7 is an 18-bp fragment, named CNV-18bp, which was inserted ~5.3 kb upstream of FZP and resulted in a tandem duplication in the cultivar Chuan 7. The CNV-18bp duplication repressed FZP expression, prolonged the panicle branching period and increased grain yield by more than 15% through substantially increasing the number of spikelets per panicle (SPP) and slightly decreasing the 1,000-grain weight (TGW). The transcription repressor OsBZR1 binds the CGTG motifs in CNV-18bp and thereby represses FZP expression, indicating that CNV-18bp is the upstream silencer of FZP. These findings showed that the silencer CNVs coordinate a trade-off between SPP and TGW by fine-tuning FZP expression, and balancing the trade-off could enhance yield potential.

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We thank K. Kaufmann at Potsdam University for providing the pSPUTK expression vector. We thank D. Zhang at Shanghai Jiao Tong University for kindly providing the antiserum for OsBZR1, and S. Sun at Huazhong Agricultural University for kindly providing the OsBZR1-activation plants. This work was financially supported through grants from the National Natural Science Foundation of China (91535301), the National Key Research and Development Program of China (2016YFD0100403), the National Special Program for Research of Transgenic Plants of China (2014ZX0800944B) and Hubei Collaborative Innovation Center for Grain Industry (2015ZD003).

Author information

X.B. performed fine mapping of the quantitative trait locus, in situ hybridization, qRT–PCR, RNA-seq analysis, ChIP analysis, phenotypic observation and data analysis. Y.Hua. conducted genetic transformation and SEM. Y.Hu performed yeast one-hybrid assays and transcriptional activity assays. H.L. performed electrophoretic mobility shift assays. B.Z. collected some phenotype data. C.S. constructed the vectors for expression of the OsBZR1 protein. G.H. and Z.H. performed the nucleotide diversity analysis. Y.X. designed the experiments and wrote the paper together with X.B.

Competing interests

The authors declare no competing financial interests.

Correspondence to Yongzhong Xing.

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Fig. 1: Mapping and cloning of SGDP7.
Fig. 2: Performance of FZP RNAi plants in the genetic background of NIL-NN.
Fig. 3: The effect of FZP on cell number contributes to grain length.
Fig. 4: OsBZR1 repressed gene expression by binding to CNV-18bp.
Fig. 5: Comparison analysis and nucleotide diversity analysis of FZP.