@article{2fc3ce99a8144725baff6fd481648bae,
title = "Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes",
abstract = "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.",
author = "Xun Xu and Xin Liu and Song Ge and Jensen, {Jeffrey D.} and Fengyi Hu and Xin Li and Yang Dong and Gutenkunst, {Ryan N.} and Lin Fang and Lei Huang and Jingxiang Li and Weiming He and Guojie Zhang and Xiaoming Zheng and Fumin Zhang and Yingrui Li and Chang Yu and Karsten Kristiansen and Xiuqing Zhang and Jian Wang and Mark Wright and Susan McCouch and Rasmus Nielsen and Jun Wang and Wen Wang",
note = "Funding Information: 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 R{\o}mer 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).",
year = "2012",
month = jan,
doi = "10.1038/nbt.2050",
language = "English (US)",
volume = "30",
pages = "105--111",
journal = "Nature biotechnology",
issn = "1087-0156",
publisher = "Nature Research",
number = "1",
}