Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Control of a key transition from prostrate to erect growth in rice domestication

Nature Genetics volume 40, pages 1360–1364 (2008)Cite this article

Abstract

The transition from the prostrate growth of ancestral wild rice (O. rufipogon Griff.) to the erect growth of Oryza sativa cultivars was one of the most critical events in rice domestication. This evolutionary step importantly improved plant architecture and increased grain yield. Here we find that prostrate growth of wild rice from Yuanjiang County in China is controlled by a semi-dominant gene, PROG1 (PROSTRATE GROWTH 1), on chromosome 7 that encodes a single Cys2-His2 zinc-finger protein. prog1 variants identified in O. sativa disrupt the prog1 function and inactivate prog1 expression, leading to erect growth, greater grain number and higher grain yield in cultivated rice. Sequence comparison shows that 182 varieties of cultivated rice, including 87 indica and 95 japonica cultivars from 17 countries, carry identical mutations in the prog1 coding region that may have become fixed during rice domestication.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

Buy

All prices are NET prices.

Figure 1: The transition from prostrate growth to erect growth.
Figure 2: Phenotype of YIL18 and Teqing.
Figure 3: Molecular identification of PROG1.
Figure 4: Expression of PROG1 and prog1.

Accession codes

Accessions

NCBI Reference Sequence

References

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  5. Lin, Z. et al. Origin of seed shattering in rice (O. sativa L.). Planta 226, 11–20 (2007).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  7. Sweeney, M. et al. 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 

  8. Tan, L. et al. Development of Oryza rufipogon and Oryza sativa introgression lines and assessment for yield-related quantitative trait loci. J. Integr. Plant Biol. 49, 871–884 (2007).

    Article  CAS  Google Scholar 

  9. Yuan, Q. et al. The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res. 31, 229–233 (2003).

    Article  CAS  Google Scholar 

  10. Takatsuji, H. Zinc-finger proteins: the classical zinc finger emerges in contemporary plant science. Plant Mol. Biol. 39, 1073–1078 (1999).

    Article  CAS  Google Scholar 

  11. Hiratsu, K., Ohta, M., Matsui, K. & Ohme-Takagi, M. The SUPPERMAN protein is an active repressor whose carboxy-terminal repression domain is required for the development of normal flowers. FEBS Lett. 514, 351–354 (2002).

    Article  CAS  Google Scholar 

  12. Yoshihara, T. & Iino, M. Identification of the gravitropism-related rice gene LAZY1 and elucidation of LAZY1-dependent and –independent gravity signaling pathways. Plant Cell Physiol. 48, 678–688 (2007).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  14. 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 

  15. Waisel, Y. Evolution of erect growth forms in domesticated wheats: possible effects of grazing. Oecologia 73, 630–632 (1987).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  17. Clark, R., Wagler, T., Quijada, P. & Doebley, J. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat. Genet. 38, 594–597 (2006).

    Article  CAS  Google Scholar 

  18. Li, X. et al. Construction of a bacterial artificial chromosome (BAC) library of common wild rice (Oryza rufipogon Griff.) for map-based cloning of genes selected during the domestication of rice. Biotechnol. Lett. 30, 555–561 (2008).

    Article  CAS  Google Scholar 

  19. Scarpella, E., Rueb, S. & Meijer, A.H. The RADICLELESS1 gene is a required for vascular pattern formation in rice. Development 130, 645–658 (2003).

    Article  CAS  Google Scholar 

  20. Thompson, J., Gibson, T., Plewniak, F., Jeanmougin, F. & Higgins, D. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876–4882 (1997).

    Article  CAS  Google Scholar 

  21. Crooks, G., Hon, G., Chandonia, J. & Brenner, S. WebLogo: a sequence logo generator. Genome Res. 14, 1188–1190 (2004).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank N. Harberd for comments on the manuscript, Y. Wang for assisting in cross sections, and the International Rice Research Institute, Chinese Rice Research Institute, Institute of Crop Sciences of Chinese Academy of Agricultural Sciences, Guangxi Academy of Agricultural Sciences and Guangdong Academy of Agricultural Sciences for providing the wild rice and cultivated rice samples. This research was supported by the National Natural Science Foundation, the Ministry of Agriculture and the Ministry of Science and Technology of China.

Author information

Authors and Affiliations

  1. Department of Plant Genetics and Breeding, State Key Laboratory of Plant Physiology and Biochemistry, National Center for Evaluation of Agricultural Wild Plants (Rice), China Agricultural University, Beijing, 100094, China

    Lubin Tan, Xianran Li, Fengxia Liu, Xianyou Sun, Chenggang Li, Zuofeng Zhu, Yongcai Fu, Hongwei Cai, Xiangkun Wang & Chuanqing Sun

  2. Department of Biological Sciences and Biotechnology, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China

    Daoxin Xie

Authors
  1. Lubin Tan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xianran Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Fengxia Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xianyou Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chenggang Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Zuofeng Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yongcai Fu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hongwei Cai
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Xiangkun Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Daoxin Xie
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Chuanqing Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

L.T. conducted characterization of introgression line, genetic mapping, gene cloning and gene expression analysis; X.L. constructed the genomic BAC library of YJCWR and screened the positive clone; F.L. helped L.T. with genetic mapping and gene expression analysis; X.S. maintained plant materials and performed the field management; C.L. performed the genetic transformation; Z.Z., Y.F., H.C. and X.W. conducted the collection of rice garmplasm and phenotypic data; C.S and D.X. designed and supervised this study; C.S., D.X. and L.T. analyzed the data and wrote the paper.

Corresponding authors

Correspondence to Daoxin Xie or Chuanqing Sun.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–4, Supplementary Figures 1–4 (PDF 551 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Tan, L., Li, X., Liu, F. et al. Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet 40, 1360–1364 (2008). https://doi.org/10.1038/ng.197

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.197

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing