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Genome-wide association studies of 14 agronomic traits in rice landraces


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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Figure 1: Divergence and geographic origins of 517 rice landraces.
Figure 2: Population structures of Chinese landraces of both subspecies.
Figure 3: Influence of populational and experimental factors on the performance of the KNN-based imputation method.
Figure 4: Genome-wide association studies of grain width and heading date.
Figure 5: Regions of the genome showing strong association signals near previously identified genes.
Figure 6: Contributions of identified loci to phenotypic variance of each of 14 agronomic traits.

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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.

Author information

Authors and Affiliations



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.

Corresponding author

Correspondence to Bin Han.

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The authors declare no competing financial interests.

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).

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