A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica)

Journal name:
Nature Genetics
Year published:
Published online

Foxtail millet (Setaria italica) is an important grain crop that is grown in arid regions. Here we sequenced 916 diverse foxtail millet varieties, identified 2.58 million SNPs and used 0.8 million common SNPs to construct a haplotype map of the foxtail millet genome. We classified the foxtail millet varieties into two divergent groups that are strongly correlated with early and late flowering times. We phenotyped the 916 varieties under five different environments and identified 512 loci associated with 47 agronomic traits by genome-wide association studies. We performed a de novo assembly of deeply sequenced genomes of a Setaria viridis accession (the wild progenitor of S. italica) and an S. italica variety and identified complex interspecies and intraspecies variants. We also identified 36 selective sweeps that seem to have occurred during modern breeding. This study provides fundamental resources for genetics research and genetic improvement in foxtail millet.

At a glance


  1. Geographic distribution and genetic structures of 916 foxtail millet varieties.
    Figure 1: Geographic distribution and genetic structures of 916 foxtail millet varieties.

    (a) The geographic distribution of the varieties, each of which is represented by a red dot on the world map. (b) Neighbor-joining tree of all varieties calculated from whole-genome SNPs. The two divergent groups, type 1 and type 2, are shown in yellow and dark brown, respectively. The scale bar indicates the simple matching distance. (c) Comparisons of the average heading dates of the two divergent groups (color as in b) in five environments. Error bars, s.d. Statistical significance for each environment was determined by t test, and the differences were all significant (P = 7 × 10−65 in Sanya, P = 7 × 10−39 in Anyang, P = 2 × 10−59 in Changzhi, P = 3 × 10−7 in Beijing and P = 3 × 10−19 in Chaoyang). Alti., altitude.

  2. Regions of the genome showing association signals underlying multiple agronomic traits.
    Figure 2: Regions of the genome showing association signals underlying multiple agronomic traits.

    (a) Local Manhattan plots for grain weight in Beijing. −log10 P values calculated with EMMAX are plotted against position on the foxtail millet genome. The horizontal dashed lines indicate the genome-wide significance threshold (10−7). (b) Local Manhattan plots for grain weight in Anyang. (c) Local Manhattan plots for branch number per main stem in Sanya. (d) Local Manhattan plots for branch number per main stem in Changzhi. (e) Local Manhattan plots for heading date in Beijing. (f) Local Manhattan plots for heading date in Anyang. (g) Local Manhattan plots for panicle length in Anyang. (h) Local Manhattan plots for bristle length in Sanya. (i,j) Local Manhattan plots for hull color in Chaoyang. (k,l) Local Manhattan plots for pericarp color in Changzhi. The horizontal lines indicate the genome-wide significance threshold of the GWAS (10−7).

  3. Whole-genome screening and functional annotations of selective sweeps during modern breeding.
    Figure 3: Whole-genome screening and functional annotations of selective sweeps during modern breeding.

    (a) Whole-genome screening of selective sweeps in foxtail millet. The πl/πm values are plotted against position on each of the nine chromosomes. The blue horizontal line indicates the genome-wide threshold of selection signals (πl/πm > 3). The selective sweeps that overlapped with characterized GWAS loci are shown in dark red. (be) Four strong selective sweeps that were found to be associated with tiller number (b), panicle number (c), hull color (d) and leaf architecture (e). In be, the GWAS −log10 P values for the corresponding traits are plotted against position on the chromosomes. The blue horizontal dashed lines indicate the genome-wide significance threshold of the GWAS (10−7).

Accession codes

Primary accessions

European Nucleotide Archive


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Author information

  1. These authors contributed equally to this work.

    • Guanqing Jia,
    • Xuehui Huang,
    • Hui Zhi &
    • Yan Zhao


  1. Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China.

    • Guanqing Jia,
    • Hui Zhi,
    • Yang Chai,
    • Lifang Yang,
    • Hangfei Hao,
    • Hongkuan Liu,
    • Ping Lu &
    • Xianmin Diao
  2. National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

    • Xuehui Huang,
    • Yan Zhao,
    • Qiang Zhao,
    • Wenjun Li,
    • Kunyan Liu,
    • Hengyun Lu,
    • Chuanrang Zhu,
    • Yiqi Lu,
    • Congcong Zhou,
    • Danlin Fan,
    • Qijun Weng,
    • Yunli Guo,
    • Tao Huang,
    • Lei Zhang,
    • Tingting Lu,
    • Qi Feng &
    • Bin Han
  3. State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.

    • Ning Zhang &
    • Jiayang Li
  4. Institute of Millet Crops, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China.

    • Yuhui Li &
    • Erhu Guo
  5. Institute of Millet Crops, Anyang Academy of Agricultural Sciences, Anyang, Henan, China.

    • Shujun Wang,
    • Suying Wang &
    • Jinrong Liu
  6. Institute of Soil and Water Conservation, Liaoning Academy of Agricultural Sciences, Chaoyang, Liaoning, China.

    • Wenfei Zhang,
    • Guoqiu Chen &
    • Baojin Zhang
  7. Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China.

    • Wei Li,
    • Yongfang Wang,
    • Haiquan Li &
    • Xianmin Diao
  8. College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China.

    • Baohua Zhao &
    • Xianmin Diao


B.H., X.D. and J. Li conceived the project and its components. H.Z., P.L., B. Zhao and X.D. collected samples. H.Z., G.J., H. Liu, Y.C., Y. Li, E.G., Shujun Wang, J.L., Suying Wang, W.Z., G.C., B. Zhang, L.Y., H.H., Y.W., Wei Li, N.Z. and H. Li performed the phenotyping. L.Z. contributed to evolutionary and functional analyses. G.J., Wenjun Li, Y.G., Y. Lu, C. Zhou, D.F., Q.W. and Q.F. performed the genome sequencing. X.H. and Y.Z. performed GWAS and population genetics analysis. Q.Z., K.L., H. Lu, C. Zhu, T.H., L.Z. and T.L. performed genome data analysis. Y.Z. and X.H. prepared figures and tables. X.H., X.D. and B.H. analyzed the total data and wrote the paper.

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The authors declare no competing financial interests.

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Supplementary information

PDF files

  1. Supplementary Text and Figures (16.1 MB)

    Supplementary Figures 1–54, Supplementary Tables 2–15

Excel files

  1. Supplementary Table 1 (168 KB)

    The list of 916 foxtail millet accessions (Setaria italica) sampled in the collection.

Additional data