Abstract
Large-scale genomic variations are fundamental resources for crop genetics and breeding. Here we sequenced 1,904 genomes of broomcorn millet to an average of 40× sequencing depth and constructed a comprehensive variation map of weedy and cultivated accessions. Being one of the oldest cultivated crops, broomcorn millet has extremely low nucleotide diversity and remarkably rapid decay of linkage disequilibrium. Genome-wide association studies identified 186 loci for 12 agronomic traits. Many causative candidate genes, such as PmGW8 for grain size and PmLG1 for panicle shape, showed strong selection signatures during domestication. Weedy accessions contained many beneficial variations for the grain traits that are largely lost in cultivated accessions. Weedy and cultivated broomcorn millet have adopted different loci controlling flowering time for regional adaptation in parallel. Our study uncovers the unique population genomic features of broomcorn millet and provides an agronomically important resource for cereal crops.
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Data availability
The raw sequencing data of 1,904 diversity accessions was deposited with the NCBI genome database under project no. PRJNA917713 (SRR23330656–SRR23330837, SRR23330861–SRR23331110, SRR23331663–SRR23332055, SRR23332224–SRR23332338, SRR23332341–SRR23332395, SRR23338406–SRR23338647, SRR23344772–SRR23345046, SRR23366736–SRR23366900, SRR23378377–SRR23378603). The Longmi4 reference genome sequences were obtained from the NCBI GenBank assembly (www.ncbi.nlm.nih.gov/datasets/genome; GCA_002895445.2). The SNPs, indels and SVs, and the details of each phenotypic information, are available at Zenodo88 (https://doi.org/10.5281/zenodo.10783997). Data availability has no restrictions. Source data are provided with this paper.
Code availability
The custom code used in this study is available at Zenodo88 (https://doi.org/10.5281/zenodo.10783997). The code can be freely used and redistributed without any restrictions.
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Acknowledgements
We thank C. J. Yang (Scotland’s Rural College) and W. Xue (Agronomy College of Shenyang Agricultural University) for their valuable suggestions and comments. We thank the Tongzhou Yujiawu International Seed Industry Park and the Yujiawu Professor Workstation for providing the space that facilitated collaboration. We thank the High-performance Computing (HPC) Platform of China Agricultural University for its support of large-scale computation. We thank Beijing PARATERA Tech (https://paratera.com/) for providing the HPC resources that have contributed to the research results reported in this study. This work was supported by the National Key R&D Program of China (no. 2021YFD1200700 to W.S.), the National Natural Science Foundation of China (no. 32271541 to W.S., no. 32272143 to H.M.Z. and no. 62031003 to B.X.), the Science and Technology Innovation (STI) 2030 (no. 2022ZD04020 to H.M.Z.), a key project of maize germplasm improvement (no. 2022010202 to W. S. and no. B21HJ0509 to J.L.), the Chinese Universities Scientific Fund (no. 2023TC019 to H.N.Z.) and the STI 2030-Major Projects (no. 2023ZD04074 to H.N.Z.).
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W.S. and J.L. conceived the research. Q.L., Y.Z., H.G., X.D., L.C., Y.H.B., B.L. and X.H. conducted the experiments. Q.L. and T.L. extracted the DNA. Q.L., H.N.Z. and Z.Z. performed the data analyses. G.L., H.Q.L., P.L., M.L., F.W., L.W., Z.L. and H.L. provided the cultivated broomcorn millet accessions. W.S. and H.Y.Z. collected the weedy broomcorn millet. L.Z., W.M., C.L., Y.B., B.X., J.C., H.M.Z. and L.E. contributed to the discussion. H.N.Z., Q.L., Z.Z., H.M.Z. and W.S. wrote the paper. B.X. and J.C. revised the paper.
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Lu, Q., Zhao, H., Zhang, Z. et al. Genomic variation in weedy and cultivated broomcorn millet accessions uncovers the genetic architecture of agronomic traits. Nat Genet 56, 1006–1017 (2024). https://doi.org/10.1038/s41588-024-01718-6
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DOI: https://doi.org/10.1038/s41588-024-01718-6
