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

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	Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
	Xu X 1,2,3; Liu X 2; Ge S 4; Jensen JD 5; Hu FY 6; Li X 1; Dong Y 1; Gutenkunst RN 7; Wang J2,9; Wang W[1; wangj@genomics.org.cn ; rasmus_nielsen@berkeley.edu ; wwang@mail.kiz.ac.cn
	2012
发表期刊	NATURE BIOTECHNOLOGY
卷号	30 期号:1 页码:105-U157
合作性质	其它
摘要	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 x 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
资助者	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). ; 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). ; 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). ; 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).
收录类别	SCI
语种	英语
资助者	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). ; 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). ; 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). ; 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).
WOS记录号	WOS:000299110600027
引用统计
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/353002/6897
专题	基因起源组遗传资源与进化国家重点实验室
通讯作者	wangj@genomics.org.cn; rasmus_nielsen@berkeley.edu; wwang@mail.kiz.ac.cn
作者单位	1.CAS-Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China 2.BGI-Shenzhen, Shenzhen, China 3.Graduate University of Chinese Academy Sciences, Beijing, China 4.State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China 5.5 School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland 6.Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China 7.Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA 8.South China University of Technology, Guangdong, China 9.Department of Biology, University of Copenhagen, Copenhagen, Denmark 10.Department of Plant Breeding & Genetics, Cornell University, Ithaca, New York, USA 11.Departments of Integrative Biology and Statistics, University of California, Berkeley, USA
推荐引用方式 GB/T 7714	Xu X,Liu X,Ge S,et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes[J]. NATURE BIOTECHNOLOGY,2012,30(1):105-U157.
APA	Xu X.,Liu X.,Ge S.,Jensen JD.,Hu FY.,...&wwang@mail.kiz.ac.cn.(2012).Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes.NATURE BIOTECHNOLOGY,30(1),105-U157.
MLA	Xu X,et al."Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes".NATURE BIOTECHNOLOGY 30.1(2012):105-U157.

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