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Copy number variation at the GL7 locus contributes to grain size diversity in rice

Nature Genetics volume 47, pages 944948 (2015) | Download Citation


Copy number variants (CNVs) are associated with changes in gene expression levels and contribute to various adaptive traits1,2. Here we show that a CNV at the Grain Length on Chromosome 7 (GL7) locus contributes to grain size diversity in rice (Oryza sativa L.). GL7 encodes a protein homologous to Arabidopsis thaliana LONGIFOLIA proteins, which regulate longitudinal cell elongation. Tandem duplication of a 17.1-kb segment at the GL7 locus leads to upregulation of GL7 and downregulation of its nearby negative regulator, resulting in an increase in grain length and improvement of grain appearance quality. Sequence analysis indicates that allelic variants of GL7 and its negative regulator are associated with grain size diversity and that the CNV at the GL7 locus was selected for and used in breeding. Our work suggests that pyramiding beneficial alleles of GL7 and other yield- and quality-related genes may improve the breeding of elite rice varieties.

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We thank the National Medium Rice Genebank at the China National Rice Research Institute for providing rice accessions. This work was supported by grants from the Ministry of Science and Technology of China (2013CBA01400) and the National Natural Science Foundation of China (31221004, 31201004 and 31201194).

Author information

Author notes

    • Yuexing Wang
    • , Guosheng Xiong
    •  & Jiang Hu

    These authors contributed equally to this work.


  1. State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.

    • Yuexing Wang
    • , Jiang Hu
    • , Jie Xu
    • , Yunxia Fang
    • , Erbo Xu
    • , Jing Xu
    • , Weijun Ye
    • , Ruifang Liu
    • , Hongqi Chen
    • , Xudong Zhu
    •  & Qian Qian
  2. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.

    • Yuexing Wang
    • , Guosheng Xiong
    • , Liang Jiang
    • , Hong Yu
    • , Xiangbing Meng
    • , Yanhui Jing
    • , Yonghong Wang
    •  & Jiayang Li
  3. National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.

    • Yuexing Wang
    • , Guosheng Xiong
    • , Liang Jiang
    • , Hong Yu
    • , Xiangbing Meng
    • , Yanhui Jing
    • , Yonghong Wang
    •  & Jiayang Li
  4. Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.

    • Guosheng Xiong
    • , Longjun Zeng
    • , Ruifang Liu
    •  & Qian Qian


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Yuexing Wang, G.X. and J.H. designed research, performed experiments, analyzed data and wrote the manuscript. L.J., Jie Xu, Y.F., L.Z., E.X., Jing Xu, W.Y., X.M., H.C. and Y.J. performed the experiments. H.Y., R.L. and Yonghong Wang designed research and analyzed data. J.L., Q.Q. and X.Z. conceived the project and designed research. J.L. and Q.Q. supervised the project, analyzed data and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Xudong Zhu or Jiayang Li or Qian Qian.

Supplementary information

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  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–22 and Supplementary Tables 1 and 2.

Excel files

  1. 1.

    Supplementary Table 3

    Allelic variations of grain length–related genes and grain lengths of 96 accessions.

  2. 2.

    Supplementary Table 4

    Polymorphic analysis of grain length–related genes in 96 accessions.

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