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

Xun Xu; Xin Liu; Song Ge; Jeffrey D. Jensen; Fengyi Hu; Xin Li; Yang Dong; Ryan N. Gutenkunst; Lin Fang; Lei Huang; Jingxiang Li; Weiming He; Guojie Zhang; Xiaoming Zheng; Fumin Zhang; Yingrui Li; Chang Yu; Karsten Kristiansen; Xiuqing Zhang; Jian Wang; Mark Wright; Susan McCouch; Rasmus Nielsen; Jun Wang; Wen Wang

doi:10.1038/nbt.2050

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

Xun Xu, Xin Liu, Song Ge, Jeffrey D. Jensen, Fengyi Hu, Xin Li, Yang Dong, Ryan N. Gutenkunst, Lin Fang, Lei Huang, Jingxiang Li, Weiming He, Guojie Zhang, Xiaoming Zheng, Fumin Zhang, Yingrui Li, Chang Yu, Karsten Kristiansen, Xiuqing Zhang, Jian WangMark Wright, Susan McCouch, Rasmus Nielsen, Jun Wang, Wen Wang

553 Citations (Scopus)

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.

Original language	English
Journal	Nature Biotechnology
Volume	30
Issue number	1
Pages (from-to)	105-111
Number of pages	7
ISSN	1087-0156
DOIs	https://doi.org/10.1038/nbt.2050
Publication status	Published - Jan 2012

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Xu, X., Liu, X., Ge, S., Jensen, J. D., Hu, F., Li, X., Dong, Y., Gutenkunst, R. N., Fang, L., Huang, L., Li, J., He, W., Zhang, G., Zheng, X., Zhang, F., Li, Y., Yu, C., Kristiansen, K., Zhang, X., ... Wang, W. (2012). Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology, 30(1), 105-111. https://doi.org/10.1038/nbt.2050

Xu, X, Liu, X, Ge, S, Jensen, JD, Hu, F, Li, X, Dong, Y, Gutenkunst, RN, Fang, L, Huang, L, Li, J, He, W, Zhang, G, Zheng, X, Zhang, F, Li, Y, Yu, C, Kristiansen, K, Zhang, X, Wang, J, Wright, M, McCouch, S, Nielsen, R, Wang, J & Wang, W 2012, 'Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes', Nature Biotechnology, vol. 30, no. 1, pp. 105-111. https://doi.org/10.1038/nbt.2050

@article{43e91466599f46d5a88c36dfe8bce2f1,

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",

year = "2012",

month = jan,

doi = "10.1038/nbt.2050",

language = "English",

volume = "30",

pages = "105--111",

journal = "Nature Biotechnology",

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T1 - Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

AU - Xu, Xun

AU - Liu, Xin

AU - Ge, Song

AU - Jensen, Jeffrey D.

AU - Hu, Fengyi

AU - Li, Xin

AU - Dong, Yang

AU - Gutenkunst, Ryan N.

AU - Fang, Lin

AU - Huang, Lei

AU - Li, Jingxiang

AU - He, Weiming

AU - Zhang, Guojie

AU - Zheng, Xiaoming

AU - Zhang, Fumin

AU - Li, Yingrui

AU - Yu, Chang

AU - Kristiansen, Karsten

AU - Zhang, Xiuqing

AU - Wang, Jian

AU - Wright, Mark

AU - McCouch, Susan

AU - Nielsen, Rasmus

AU - Wang, Jun

AU - Wang, Wen

PY - 2012/1

Y1 - 2012/1

N2 - 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.

AB - 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.

U2 - 10.1038/nbt.2050

DO - 10.1038/nbt.2050

M3 - Journal article

C2 - 22158310

SN - 1087-0156

VL - 30

SP - 105

EP - 111

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 1

ER -

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

Abstract

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