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Genetic control of rice plant architecture under domestication

Nature Genetics volume 40, pages 1365–1369 (2008)Cite this article

Abstract

The closely related wild rice species Oryza rufipogon is considered the progenitor of cultivated rice (Oryza sativa)1,2,3,4,5. The transition from the characteristic plant architecture of wild rice to that of cultivated rice was one of the most important events in rice domestication; however, the molecular basis of this key domestication transition has not been elucidated. Here we show that the PROG1 gene controls aspects of wild-rice plant architecture, including tiller angle and number of tillers. The gene encodes a newly identified zinc-finger nuclear transcription factor with transcriptional activity and is mapped on chromosome 7. PROG1 is predominantly expressed in the axillary meristems, the site of tiller bud formation. Rice transformation experiments demonstrate that artificial selection of an amino acid substitution in the PROG1 protein during domestication led to the transition from the plant architecture of wild rice to that of domesticated rice.

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Figure 1: Plant architecture phenotypic characterization in Teqing and NIL(PROG1).
Figure 2: Map-based cloning of PROG1 and genetic complementation test.
Figure 3: PROG1 structure and mutation analysis.
Figure 4: Subcellular localization, transcription activity assay and expression pattern analysis of PROG1.

References

  1. Oka, H.I. Origin of Cultivated Rice (Japan Scientific Society Press, Tokyo, 1988).

    Google Scholar 

  2. Chang, T.T. in Evolution of Crop Plants 2nd edn. (eds. Smartt, J. & Simmonds, N.W.) Rice: Oryza sativa and Oryza glaberrima (Gramineae-Orzeae) 147–155 (Longman Scientific and Technical, Essex, UK, 1995).

    Google Scholar 

  3. Khush, G.S. Origin, dispersal, cultivation and variation of rice. Plant Mol. Biol. 35, 25–34 (1997).

    Article  CAS  Google Scholar 

  4. Sharma, S.D., Tripathy, S. & Biswal, J. in Rice Breeding and Genetics: Research Priorities and Challenges (ed. Nanda, J.S.) 349–369 (Science Publications, Enfield, New Hampshire, 2000).

    Google Scholar 

  5. Kovach, M.J., Sweeney, M.T. & McCouch, S.R. New insights into the history of rice domestication. Trends Genet. 23, 578–587 (2007).

    Article  CAS  Google Scholar 

  6. Vaughan, D.A., Morishima, H. & Kadowaki, K. Diversity in the Oryza genus. Curr. Opin. Plant Biol. 6, 139–146 (2003).

    Article  CAS  Google Scholar 

  7. Cheng, C. et al. Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Mol. Biol. Evol. 20, 67–75 (2003).

    Article  CAS  Google Scholar 

  8. Vitte, C., Ishii, T., Lamy, F., Brar, D. & Panaud, O. Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol. Genet. Genomics 272, 504–511 (2004).

    Article  CAS  Google Scholar 

  9. Li, C., Zhou, A. & Sang, T. Rice domestication by reducing shattering. Science 311, 1936–1939 (2006).

    Article  CAS  Google Scholar 

  10. Konishi, S. et al. An SNP caused loss of seed shattering during rice domestication. Science 312, 1392–1396 (2006).

    Article  CAS  Google Scholar 

  11. Sweeney, M.T., Thomson, M.J., Pfeil, B.E. & McCouch, S. Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell 18, 283–294 (2006).

    Article  CAS  Google Scholar 

  12. Hao, W., Jin, J., Sun, S.Y., Zhu, M.Z. & Lin, H.X. Construction of chromosome segment substitution lines carrying overlapping chromosome segments of the whole wild rice genome and identification of quantitative trait loci for rice quality. J. Plant Physiol. Mol. Biol. 32, 354–362 (2006).

    CAS  Google Scholar 

  13. Ren, Z.H. et al. A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat. Genet. 37, 1141–1146 (2005).

    Article  CAS  Google Scholar 

  14. Li, P.J. et al. LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res. 17, 402–410 (2007).

    Article  CAS  Google Scholar 

  15. Yu, B. et al. TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J. 52, 891–898 (2007).

    Article  CAS  Google Scholar 

  16. Miller, J., McLachlan, A.D. & Klug, A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 4, 1609–1614 (1985).

    Article  CAS  Google Scholar 

  17. Wolfe, S.A., Nekludova, L. & Pabo, C.O. DNA recognition by Cys2His2 Zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct. 29, 183–212 (2000).

    Article  CAS  Google Scholar 

  18. Sakamoto, H. et al. Arabidopsis Cys2/His2-type zinc-finger proteins function as transcription repressors under drought, cold, and high-salinity stress conditions. Plant Physiol. 136, 2734–2746 (2004).

    Article  CAS  Google Scholar 

  19. Lin, R. et al. Transposase-derived transcription factors regulate light signaling in Arabidopsis. Science 318, 1302–1305 (2007).

    Article  CAS  Google Scholar 

  20. Doebley, J., Stec, A. & Hubbard, L. The evolution of apical dominance in maize. Nature 386, 485–488 (1997).

    Article  CAS  Google Scholar 

  21. Wang, R.L., Stec, A., Hey, J., Lukens, L. & Doebley, J. The limits of selection during maize domestication. Nature 398, 236–239 (1999).

    Article  CAS  Google Scholar 

  22. Frary, A. et al. fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289, 85–88 (2000).

    Article  CAS  Google Scholar 

  23. Liu, J., Van Eck, J., Cong, B. & Tanksley, S.D. A new class of regulatory genes underlying the cause of pear-shaped tomato fruit. Proc. Natl. Acad. Sci. USA 99, 13302–13306 (2002).

    Article  CAS  Google Scholar 

  24. Wang, H. et al. The origin of the naked grains of maize. Nature 436, 714–719 (2005).

    Article  CAS  Google Scholar 

  25. Doebley, J.F., Gaut, B.S. & Smith, B.D. The molecular genetics of crop domestication. Cell 127, 1309–1321 (2006).

    Article  CAS  Google Scholar 

  26. Cong, B., Barrero, L.S. & Tanksley, S.D. Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nat. Genet. 40, 800–804 (2008).

    Article  CAS  Google Scholar 

  27. Hiei, Y., Ohta, S., Komari, T. & Kumashiro, T. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium tumeficience and sequence analysis of the boundaries of the T-DNA. Plant J. 6, 271–282 (1994).

    Article  CAS  Google Scholar 

  28. Pfaffl, M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29, e45 (2001).

    Article  CAS  Google Scholar 

  29. Coen, E. et al. Floricaula: a homeotic gene required for flower development in Antirrhinum majus. Cell 63, 1311–1322 (1990).

    Article  CAS  Google Scholar 

  30. Li, X. et al. Control of tillering in rice. Nature 422, 618–621 (2003).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank Z.-Z. Piao and X.-M. Li for technical assistance. We thank S. Luan for critically reading the manuscript. This work was supported by grants from the Ministry of Science and Technology of China, the National Natural Science Foundation of China, the Chinese Academy of Sciences and the Shanghai Science and Technology Development Fund to H.-X.L.

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Authors and Affiliations

  1. National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China

    Jian Jin, Wei Huang, Ji-Ping Gao, Jun Yang, Min Shi, Mei-Zhen Zhu, Da Luo & Hong-Xuan Lin

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  1. Jian Jin
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  2. Wei Huang
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  3. Ji-Ping Gao
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  4. Jun Yang
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  6. Mei-Zhen Zhu
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  7. Da Luo
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  8. Hong-Xuan Lin
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Contributions

H.-X.L. designed the experiments. J.J. performed most of the experiments. W.H., J.-P.G., J.Y., M.S., M.-Z.Z., D.L. and H.-X.L. performed some of the experiments. H.-X.L. wrote the manuscript.

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Correspondence to Hong-Xuan Lin.

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Supplementary Figures 1–3, Supplementary Tables 1 and 2 (PDF 149 kb)

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Jin, J., Huang, W., Gao, JP. et al. Genetic control of rice plant architecture under domestication. Nat Genet 40, 1365–1369 (2008). https://doi.org/10.1038/ng.247

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