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, Xun; Liu, Xin; Ge, Song; Jensen, Jeffrey D.; Hu, Fengyi; Li, Xin; Dong, Yang; Gutenkunst, Ryan N.; Fang, Lin; Huang, Lei; Li, Jingxiang; He, Weiming; Zhang, Guojie; Zheng, Xiaoming; Zhang, Fumin; Li, Yingrui; Yu, Chang; Kristiansen, Karsten; Zhang, Xiuqing; Wang, Jian; Wright, Mark; McCouch, Susan; Nielsen, Rasmus; Wang, Jun; Wang, Wen.
In: Nature Biotechnology, Vol. 30, No. 1, 2012, p. 105-111.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
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
Y1 - 2012
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 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.
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 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.
U2 - 10.1038/nbt.2050
DO - 10.1038/nbt.2050
M3 - Journal article
C2 - 22158310
VL - 30
SP - 105
EP - 111
JO - Nature Biotechnology
JF - Nature Biotechnology
SN - 1087-0156
IS - 1
ER -
ID: 40903649