Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

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Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 × raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable for breeding and for identifying agronomically important genes in rice.

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Figure 1: Population structure of Asian rice.
Figure 2: Linkage disequilibrium differences between wild and cultivated rice groups.
Figure 3: Significant outlier regions (genes) in ROD distribution.


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We thank C.-H. Shi (Zhejiang University, China) and X.-H. Wei (China National Rice Research Institute) for assistance in growing rice materials. We are grateful to the International Rice Research Institute (Los Banos, Philippines) for providing most seed samples. This work was supported by the Chinese 973 program (2007CB815700), the National Natural Science Foundation of China (30990242), the Provincial Key Grant of Yunnan Province (2008CC017; 2008GA002), the Shenzhen Municipal Government and the Yantian District local government of Shenzhen, the Ole Rømer grant from the Danish Natural Science Research Council, and a CAS-Max Planck Society Fellowship and the 100 talent program of CAS to W.W., J.W. and S.G. We also acknowledge funding support from the Chinese Ministry of Agriculture (948 program), the Shenzhen Municipal Government of China and grants from Shenzhen Bureau of Science Technology & Information, China (ZYC200903240077A; CXB200903110066A).

Author information

W.W., Jun Wang, S.G., X.X., R.N. and F.H. designed the project. X.X., X. Liu, X. Li, J.D.J., M.W., L.F., G.Z., W.H., X. Zheng., Y.L. and R.N. analyzed the data. W.W., X.X., R.N., R.N.G., X. Liu, S.M., K.K. and Jun Wang wrote the manuscript. S.G., F.H., L.H. and F.Z. prepared the samples. X. Zhang, Jian Wang, C.Y., J.L. and Y.D. conducted the experiments.

Correspondence to Rasmus Nielsen or Jun Wang or Wen Wang.

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Supplementary information

Supplementary Text and Figures

Supplementary Tables 1,2,5,6,8–16, Supplmentary Notes and Supplementary Figures 1–23 (PDF 4530 kb)

Supplementary Table 3

Annotation information of novel genes identified from unmapped contigs. (XLSM 156 kb)

Supplementary Table 4

Information of lost genes. (+ means not lost in that individual, - mean lost supported by both pairs and coverage information, P means only supported by pair-end information, C means only supported by coverage information.) (XLSM 202 kb)

Supplementary Table 7

CNV regions. (XLSM 72 kb)

Supplementary Data Set 1 (ZIP 7415 kb)

Supplementary Data Set 2 (ZIP 20621 kb)

Supplementary Data Set 3 (ZIP 17633 kb)

Supplementary Data Set 4 (ZIP 25994 kb)

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Xu, X., Liu, X., Ge, S. et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30, 105–111 (2012) doi:10.1038/nbt.2050

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