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A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication

Nature Plants volume 3, Article number: 17064 (2017) Cite this article

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Abstract

Grain size is one of the most important components of grain yield and selecting large seeds has been a main target during plant domestication. Surprisingly, the grain of African cultivated rice (Oryza glaberrima Steud.) typically is smaller than that of its progenitor, Oryza barthii. Here we report the cloning and characterization of a quantitative trait locus, GL4, controlling the grain length on chromosome 4 in African rice, which regulates longitudinal cell elongation of the outer and inner glumes. Interestingly, GL4 also controls the seed shattering phenotype like its orthologue SH4 gene in Asian rice. Our data show that a single-nucleotide polymorphism (SNP) mutation in the GL4 gene resulted in a premature stop codon and led to small seeds and loss of seed shattering during African rice domestication. These results provide new insights into diverse domestication practices in African rice, and also pave the way for enhancing crop yield to meeting the challenge of cereal demand in West Africa.

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Figure 1: Characterization of the grains traits between African cultivated rice IRGC102305 and introgression line GIL25.
Figure 2: Map-based cloning of GL4.
Figure 3: Identification of the causative mutation for the GL4 gene.
Figure 4: Comparison of the effects of different GL4 alleles.
Figure 5: Evolutionary analysis of GL4/SH4.

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Acknowledgements

We thank the International Rice Research Institute and the United States Department of Agriculture Research Service for providing the wild rice and cultivated rice samples. This research was supported by the National Key R&D Program for Crop Breeding (2016YFD0100901), the Ministry of Agriculture of China (2016ZX08009-003) and the National Natural Science Foundation of China (Grant 31471457). We acknowledge the NSF Plant Genome Program for support to Meyer (1202803). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Author information

Author notes

  1. Wenguang Wu, Xiaoyun Liu & Muhua Wang

    Present address: Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, 72076, Germany

  2. Muhua Wang: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Plant Genetics and Breeding, National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, China Agricultural University, 100193, Beijing, China

    Wenguang Wu, Xiaoyun Liu, Lubin Tan, Hongwei Cai, Chuanqing Sun, Xiangkun Wang & Zuofeng Zhu

  2. Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, 85721, Arizona, USA

    Muhua Wang, Jianwei Zhang & Rod A. Wing

  3. Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, 90095, California, USA

    Rachel S. Meyer

  4. State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 200433, Shanghai, China

    Xiaojin Luo

  5. Africa Rice Centre, 2031, Cotonou, Benin

    Marie-Noelle Ndjiondjop

  6. Advanced Genomics Breeding Section, Institute of Crop Science, National Agriculture and Food Research Organization, 305-8602, Tsukuba, Japan

    Jianzhong Wu

  7. State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, 100193, Beijing, China

    Chuanqing Sun

  8. International Rice Research Institute, T.T. Chang Genetic Resources Centre, Los Baños, Laguna, Philippines

    Rod A. Wing

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  1. Wenguang Wu
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Contributions

Z.Z. and R.A.W. designed and supervised this study. W.W. conducted characterization of introgression line, map-based cloning, genetic transformation, gene expression analysis. W.W. and X. Liu constructed the introgression lines. M.W., R.S.M. and J.Z. performed evolutionary analysis of GL4. X. Luo bred the NIL-GL4Og. M.-N.N., L.T., J.W., H.C., C.S. and X.W. conducted the collection of rice germplasm and phenotypic data. Z.Z., R.S.M. and R.A.W. wrote the manuscript.

Corresponding authors

Correspondence to Rod A. Wing or Zuofeng Zhu.

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The authors declare no competing financial interests.

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Supplementary Figures 1–14, Supplementary Table 1–4. (PDF 1564 kb)

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Wu, W., Liu, X., Wang, M. et al. A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nature Plants 3, 17064 (2017). https://doi.org/10.1038/nplants.2017.64

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