Abstract
Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified ∼3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS explained ∼36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.
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Acknowledgements
We thank the China National Rice Research Institute for providing the landrace samples, R.A. Wing for critical reading of the manuscript, P. Hu for helping assay rice grain quality and Z. Ning for assistance with sequence alignment. This work was supported by the Chinese Academy of Sciences (KSCX2-YW-N-024), China's Ministry of Science and Technology (2006AA10A102) and Ministry of Agriculture (2008ZX08009-002) and the National Natural Science Foundation of China (30821004) to B.H.
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B.H. conceived the project and its components. J.L., Q.-F.Z., T.S. and B.H. contributed to the original concept of the project. Q.F., D.F., Y.G., L.D., Wenjun Li, Y.L. and Q.W. performed the genome sequencing. X.H., Q.Z., Y.Z., C.Z., T.L., K.L. and T.H. performed GWAS and data analysis. Y.Z., Q.Z., C.Z. and X.H. developed the imputation program for data analyses. X.H., Y.Z. and T.S. performed statistical simulations. Z.Z., M.L., Y.Z. and E.S.B. performed GWAS using the compressed mixed linear model. X.W., C.L., A.W., L.W., T.Z., Y.J., Wei Li, Z.L. and Q.Q. collected samples and performed the phenotyping. Q.Z., T.L., Y.Z. and X.H. prepared figures and tables. X.H., T.S. and B.H. analyzed all the data and wrote the paper.
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Supplementary information
Supplementary Text and Figures
Supplementary Note; Supplementary Tables 2–4, 7 and 8; Supplementary Figs. 1–25 (PDF 6688 kb)
Supplementary Table 1
The list of 517 landrace accessions sampled in this study. (XLS 71 kb)
Supplementary Table 5
The list of genes over-represented for large-effect changes. (XLS 31 kb)
Supplementary Table 6
The list of genes that contained large-effect complete-differentiation SNPs. (XLS 31 kb)
Supplementary Table 9
The genotype dataset of indica landraces on the causal polymorphic sites of three known genes. (XLS 79 kb)
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Huang, X., Wei, X., Sang, T. et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42, 961–967 (2010). https://doi.org/10.1038/ng.695
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DOI: https://doi.org/10.1038/ng.695