Natural variation in GS5 plays an important role in regulating grain size and yield in rice

Journal name:
Nature Genetics
Year published:
Published online

Increasing crop yield is one of the most important goals of plant science research. Grain size is a major determinant of grain yield in cereals and is a target trait for both domestication and artificial breeding1. We showed that the quantitative trait locus (QTL) GS5 in rice controls grain size by regulating grain width, filling and weight. GS5 encodes a putative serine carboxypeptidase and functions as a positive regulator of grain size, such that higher expression of GS5 is correlated with larger grain size. Sequencing of the promoter region in 51 rice accessions from a wide geographic range identified three haplotypes that seem to be associated with grain width. The results suggest that natural variation in GS5 contributes to grain size diversity in rice and may be useful in improving yield in rice and, potentially, other crops2.

At a glance


  1. Map-based cloning of GS5.
    Figure 1: Map-based cloning of GS5.

    (a) Locations of GS5 and qSW5/GW5 in the genetic map. (b,c) Fine mapping of the GS5 region using two mapping population, with 4,374 and 5,265 plants, respectively. The thick bar represents the genomic region; numbers underneath the bars indicate the numbers of recombinants between GS5 and the molecular marker, and numbers in parentheses indicate the numbers of recombinants (for recombinants no. 30, 8936 and 57-5) whose phenotypes were affected by the qSW5/GW5 genotype and that were not used in fine mapping. (d) Genotypes of the recombinants assayed by sequencing an 8-kb region between C62 and G8, including the entire coding sequence and 2-kb promoter region (only three well-spaced SNP markers in the promoter region are placed in the map). Each recombinant was phenotyped by progeny testing to deduce the genotype of GS5 (Supplementary Table 2). Genotypes of qSW5/GW5 was determined using two functional markers N1212 and Indel2. A, homozygous for Zhenshan 97 genotype; B, homozygous for H94 genotype; H, heterozygote; No., identification number for each recombinant. (e) GS5 gene structure and natural variations between alleles from Zhenshan 97 and H94.

  2. Effects of GS5 on grain size and filling.
    Figure 2: Effects of GS5 on grain size and filling.

    (a) Grains of Zhenshan 97, H94, NIL(ZS97), NIL(H94), Zhonghua 11 and Minghui 63. (b) Grains of the transformants. OX (+) indicates grains from T1 plants expressing the coding sequence of GS5 from H94 driven by the 35S promoter; ZpHc (+) indicates grains from T1 plants expressing the coding sequence of GS5 driven by the promoter from Zhenshan 97. OX (−) and ZpHc (−) are the corresponding negative segregants. (c,d) Time-course of grain weight (n = 90 grains for each point). Blue line, NIL(ZS97); black line, NIL(H94).

  3. The effect of GS5 on cell number and size in lemma/palea.
    Figure 3: The effect of GS5 on cell number and size in lemma/palea.

    (a) Spikelets of NIL(ZS97) (left) and NIL(H94) (right) 4 d before heading. (b,c) Cross-sections of palea (b) and lemma (c) cut horizontally at the middle of the spikelets shown in a. Scale bars, 200 μm for both b and c. (d,e) Comparisons of cell number (d) and cell size (e) between NIL(ZS97) and NIL(H94) in the cross-sections of the inner parenchyma cell layer of spikelets. All P values are based on two-tailed t-tests. Black bars, NIL(ZS97); yellow bars, NIL(H94). Error bars, s.e.m.

  4. Regulation by GS5 of the expression of genes involved in the cell cycle.
    Figure 4: Regulation by GS5 of the expression of genes involved in the cell cycle.

    (a) Transcript levels of genes associated with cell cycle regulation in GS5 overexpressor OX(+) relative to negative segregants OX(−). Black bars, OX(−); light bars, OX(+). (b) Transcript levels of genes associated with cell cycle regulation in the gs5 mutant, relative to wild type. Black bars, wild type; gray bars, mutant. Expression levels were determined by qRT-PCR using 6- to 8-cm young panicles from at least five plants, in at least three biological samples and three replicates. Error bars, s.e.m. All P values are based on two-tailed t-tests.

Accession codes

Referenced accessions

NCBI Reference Sequence



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Author information


  1. National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.

    • Yibo Li,
    • Chuchuan Fan,
    • Yongzhong Xing,
    • Yunhe Jiang,
    • Lijun Luo,
    • Liang Sun,
    • Di Shao,
    • Chunjue Xu,
    • Xianghua Li,
    • Jinghua Xiao,
    • Yuqing He &
    • Qifa Zhang


Y.L. conducted most of the experiments, including fine mapping, gene cloning, genetic transformation, expression analysis, mutant analysis, histological analysis and other functional analysis; C.F., Y.X. and L.L. conducted the QTL primary mapping analysis and developed the NILs; Y.J. and L.S. carried out part of the cell division and expression analysis; D.S., C.X., X.L. and J.X. participated in the promoter sequencing; Y.H. and Q.Z. designed and supervised the study; and Y.L. and Q.Z. analyzed the data and wrote the paper. All of the authors discussed the results and commented on the manuscript.

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The authors declare no competing financial interests.

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    Supplementary Tables 1–10 and Supplementary Figures 1–5

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