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Control of grain size and rice yield by GL2-mediated brassinosteroid responses

An Erratum to this article was published on 13 January 2016


Given the continuously growing population and decreasing arable land, food shortage is becoming one of the most serious global problems in this century1. Grain size is one of the determining factors for grain yield and thus is a prime target for genetic breeding2,3. Although a number of quantitative trait loci (QTLs) associated with rice grain size have been identified in the past decade, mechanisms underlying their functions remain largely unknown4,5. Here we show that a grain-length-associated QTL, GL2, has the potential to improve grain weight and grain yield up to 27.1% and 16.6%, respectively. We also show that GL2 is allelic to OsGRF4 and that it contains mutations in the miR396 targeting sequence. Because of the mutation, GL2 has a moderately increased expression level, which consequently activates brassinosteroid responses by upregulating a large number of brassinosteroid-induced genes to promote grain development. Furthermore, we found that GSK2, the central negative regulator of rice brassinosteroid signalling, directly interacts with OsGRF4 and inhibits its transcription activation activity to mediate the specific regulation of grain length by the hormone. Thus, this work demonstrates the feasibility of modulating specific brassinosteroid responses to improve plant productivity.

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Figure 1: Cloning and verification of GL2.
Figure 2: GL2 escapes from miR396 suppression to regulate cell volume.
Figure 3: GL2-activated brassinosteroid responses.
Figure 4: GSK2 interacts with GRF4 and inhibits its activity.


  1. 1

    Rosegrant, M. W. & Cline, S. A. Global food security: challenges and policies. Science 302, 1917–1919 (2003).

    CAS  Article  Google Scholar 

  2. 2

    Xing, Y. Z. & Zhang, Q. F. Genetic and molecular bases of rice yield. Annu. Rev. Plant Biol. 61, 421–442 (2010).

    CAS  Article  Google Scholar 

  3. 3

    Ikeda, M., Miura, K., Aya, K., Kitano, H. & Matsuoka, M. Genes offering the potential for designing yield-related traits in rice. Curr. Opin. Plant Biol. 16, 213–220 (2013).

    CAS  Article  Google Scholar 

  4. 4

    Zuo, J. & Li, J. Molecular genetic dissection of quantitative trait loci regulating rice grain size. Annu. Rev. Genet. 48, 99–118 (2014).

    CAS  Article  Google Scholar 

  5. 5

    Miura, K., Ashikari, M. & Matsuoka, M. The role of QTLs in the breeding of high-yielding rice. Trends Plant Sci. 16, 319–326 (2011).

    CAS  Article  Google Scholar 

  6. 6

    Horiguchi, G., Kim, G. T. & Tsukaya, H. The transcription factor AtGRF5 and the transcription coactivator AN3 regulate cell proliferation in leaf primordia of Arabidopsis thaliana. Plant J. 43, 68–78 (2005).

    CAS  Article  Google Scholar 

  7. 7

    Wang, L. et al. miR396-targeted AtGRF transcription factors are required for coordination of cell division and differentiation during leaf development in Arabidopsis. J. Exp. Bot. 62, 761–773 (2011).

    CAS  Article  Google Scholar 

  8. 8

    Liu, D. M., Song, Y., Chen, Z. X. & Yu, D. Q. Ectopic expression of miR396 suppresses GRF target gene expression and alters leaf growth in Arabidopsis. Physiol. Plant 136, 223–236 (2009).

    CAS  Article  Google Scholar 

  9. 9

    van der Knaap, E., Kim, J. H. & Kende, H. A novel gibberellin-induced gene from rice and its potential regulatory role in stem growth. Plant Physiol. 122, 695–704 (2000).

    CAS  Article  Google Scholar 

  10. 10

    Kim, J. H., Choi, D. S. & Kende, H. The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis. Plant J. 36, 94–104 (2003).

    CAS  Article  Google Scholar 

  11. 11

    Tong, H. N. et al. Brassinosteroid regulates cell elongation by modulating gibberellin metabolism in rice. Plant Cell 26, 4376–4393 (2014).

    CAS  Article  Google Scholar 

  12. 12

    Zhu, X. L. et al. Brassinosteroids promote development of rice pollen grains and seeds by triggering expression of Carbon Starved Anther, a MYB domain protein. Plant J. 82, 570–581 (2015).

    CAS  Article  Google Scholar 

  13. 13

    Tong, H. et al. DWARF AND LOW-TILLERING acts as a direct downstream target of a GSK3/SHAGGY-like kinase to mediate brassinosteroid responses in rice. Plant Cell 24, 2562–2577 (2012).

    CAS  Article  Google Scholar 

  14. 14

    Wang, X. L. et al. Arabidopsis MICROTUBULE DESTABILIZING PROTEIN40 is involved in brassinosteroid regulation of hypocotyl elongation. Plant Cell 24, 5193–5193 (2012).

    CAS  Article  Google Scholar 

  15. 15

    Yamamuro, C. et al. Loss of function of a rice brassinosteroid insensitive1 homolog prevents internode elongation and bending of the lamina joint. Plant Cell 12, 1591–1606 (2000).

    CAS  Article  Google Scholar 

  16. 16

    Li, J. A. et al. Mutation of rice BC12/GDD1, which encodes a kinesin-like protein that binds to a GA biosynthesis gene promoter, leads to dwarfism with impaired cell elongation. Plant Cell 23, 628–640 (2011).

    CAS  Article  Google Scholar 

  17. 17

    Kitagawa, K. et al. A novel Kinesin 13 protein regulating rice seed length. Plant Cell Physiol. 51, 1315–1329 (2010).

    CAS  Article  Google Scholar 

  18. 18

    Fujikura, U. et al. Atkinesin-13A modulates cell-wall synthesis and cell expansion in Arabidopsis thaliana via the THESEUS1 pathway. PLoS Genet. 10, e1004627 (2014).

    Article  Google Scholar 

  19. 19

    Kim, J. H. & Kende, H. A transcriptional coactivator, AtGIF1, is involved in regulating leaf growth and morphology in Arabidopsis. Proc. Natl Acad. Sci. USA 101, 13374–13379 (2004).

    CAS  Article  Google Scholar 

  20. 20

    Tong, H. & Chu, C. Brassinosteroid signaling and application in rice. J. Genet. Genomics 39, 3–9 (2012).

    CAS  Article  Google Scholar 

  21. 21

    Nelissen, H. et al. Dynamic changes in ANGUSTIFOLIA3 complex composition reveal a growth regulatory mechanism in the maize leaf. Plant Cell 27, 1605–1619 (2015).

    CAS  Article  Google Scholar 

  22. 22

    Kim, J. H. & Tsukaya, H. Regulation of plant growth and development by the GROWTH-REGULATING FACTOR and GRF-INTERACTING FACTOR duo. J. Exp. Bot. 66, 6093–6107 (2015).

    CAS  Article  Google Scholar 

  23. 23

    Omidbakhshfard, M. A., Proost, S., Fujikura, U. & Mueller-Roeber, B. Growth-regulating factors (GRFs): a small transcription factor family with important functions in plant biology. Mol. Plant 8, 998–1010 (2015).

    CAS  Article  Google Scholar 

  24. 24

    Fan, C. H. et al. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor. Appl. Genet. 112, 1164–1171 (2006).

    CAS  Article  Google Scholar 

  25. 25

    Hu, J. et al. A rare allele of GS2 enhances grain size and grain yield in rice. Mol. Plant 8, 1455–1465 (2015).

    CAS  Article  Google Scholar 

  26. 26

    Huang, X. H. et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genet. 42, 961–967 (2010).

    CAS  Article  Google Scholar 

  27. 27

    Jin, Y. et al. An AT-hook gene is required for palea formation and floral organ number control in rice. Dev. Biol. 359, 277–288 (2011).

    CAS  Article  Google Scholar 

  28. 28

    Waadt, R. et al. Multicolor bimolecular fluorescence complementation reveals simultaneous formation of alternative CBL/CIPK complexes in planta. Plant J. 56, 505–516 (2008).

    CAS  Article  Google Scholar 

  29. 29

    Sparkes, I. A., Runions, J., Kearns, A. & Hawes, C. Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants. Nature Protocols 1, 2019–2025 (2006).

    CAS  Article  Google Scholar 

  30. 30

    Guo, X. et al. The rice GERMINATION DEFECTIVE 1, encoding a B3 domain transcriptional repressor, regulates seed germination and seedling development by integrating GA and carbohydrate metabolism. Plant J. 75, 403–416 (2013).

    CAS  Article  Google Scholar 

  31. 31

    Fiil, B. K., Qiu, J. L., Petersen, K., Petersen, M. & Mundy, J. Coimmunoprecipitation (co-IP) of nuclear proteins and chromatin immunoprecipitation (ChIP) from Arabidopsis. Cold Spring Harb. Protoc. 2008, pdb.prot5049 (2008).

  32. 32

    Chen, M. L. et al. Highly sensitive and quantitative profiling of acidic phytohormones using derivatization approach coupled with nano-LC-ESI-Q-TOF-MS analysis. J. Chromatogr. B 905, 67–74 (2012).

    CAS  Article  Google Scholar 

  33. 33

    Ding, J., Mao, L. J., Wang, S. T., Yuan, B. F. & Feng, Y. Q. Determination of endogenous brassinosteroids in plant tissues using solid-phase extraction with double layered cartridge followed by high-performance liquid chromatography-tandem mass spectrometry. Phytochem. Anal. 24, 386–394 (2013).

    CAS  Article  Google Scholar 

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This work was supported by grants from National Natural Science Foundation of China (91435106, 91335203, 31170715), Ministry of Agriculture of China (2014ZX08009), Natural Science Foundation of Fujian Province (B0420002) and Youth Innovation Promotion Association CAS (2015076).

Author information




R.C. and H.T. designed the research, performed the experiments, analysed the data and wrote the paper. B.S, Y.L., S.F., Y.X., D.L., B.H., L.L. and H.W. performed the experiments. C.C. and M.Z. supervised the project, designed the research and analysed the data.

Corresponding authors

Correspondence to Mingfu Zhao or Chengcai Chu.

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The authors declare no competing financial interests.

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Che, R., Tong, H., Shi, B. et al. Control of grain size and rice yield by GL2-mediated brassinosteroid responses. Nature Plants 2, 15195 (2016).

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