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Plant Cell Advance Online Publication
Published on November 25, 2008; 10.1105/tpc.108.060426

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Received April 30, 2008
Returned for revision October 9, 2008
Accepted November 7, 2008

Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication

Yanchun Yu 1, Tian Tang 2, Qian Qian 3, Yonghong Wang 1, Meixian Yan 3, Dali Zeng 3, Bin Han 4, Chung-I Wu 5*, Suhua Shi 2, and Jiayang Li 1

1 State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
2 State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China
3 State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
4 National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
5 State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China; Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

* To whom correspondence should be addressed. E-mail: ciwu{at}uchicago.edu.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reflect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1; here, we report the cloning of Phr1, which encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar. Phr1 is defective in all japonica lines but functional in nearly all indica and wild strains. Phylogenetic analysis showed that the defects in Phr1 arose independently three times. The multiple recent origins and rapid spread of phr1 in japonica suggest the action of positive selection, which is further supported by several population genetic tests. This case may hence represent an example of artificial selection driving the differentiation among domesticated varieties.






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