Abstract
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.
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Acknowledgements
We thank J. Chen from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, for discussion about the manuscript. We thank Z. Ning for assistance with sequence alignment. This work was supported by the China Agricultural Research System (CARS07-12.5-A02), the National Natural Science Foundation of China (31171560, 30630045 and 31121063), the National High Technology Research and Development Program of China (863 Program) (2013AA102603), the National Fund for Genetically Modified Organisms of China (2009ZX08009-093B), the Ministry of Agriculture of China (2011ZX08009-002) and the Chinese Academy of Sciences.
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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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Supplementary Text and Figures
Supplementary Figures 1–54, Supplementary Tables 2–15 (PDF 15733 kb)
Supplementary Table 1
The list of 916 foxtail millet accessions (Setaria italica) sampled in the collection. (XLS 163 kb)
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Jia, G., Huang, X., Zhi, H. et al. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet 45, 957–961 (2013). https://doi.org/10.1038/ng.2673
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DOI: https://doi.org/10.1038/ng.2673
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