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


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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Figure 1: GL7 regulates grain length and quality.
Figure 2: Elevated expression of GL7 increases grain length.
Figure 3: Correlation between genomic structure variations and grain length diversity.
Figure 4: Relationship between GL7 or Os07g0603400 and other grain size–related loci.
Figure 5: Application of GL7 in breeding.

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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

Authors and Affiliations



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.

Corresponding authors

Correspondence to Xudong Zhu, Jiayang Li or Qian Qian.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–22 and Supplementary Tables 1 and 2. (PDF 3109 kb)

Supplementary Table 3

Allelic variations of grain length–related genes and grain lengths of 96 accessions. (XLSX 21 kb)

Supplementary Table 4

Polymorphic analysis of grain length–related genes in 96 accessions. (XLSX 45 kb)

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Wang, Y., Xiong, G., Hu, J. et al. Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat Genet 47, 944–948 (2015).

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