title: Independent losses of function in a polyphenol oxidase in rice: differentiation in grain discoloration between subspecies and the role of positive selection under domestication.
abstract: 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.
authors.affiliation: 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.
authors.forename: Yanchun
authors.initials: Y
authors.lastname: Yu
authors.forename: Tian
authors.initials: T
authors.lastname: Tang
authors.forename: Qian
authors.initials: Q
authors.lastname: Qian
authors.forename: Yonghong
authors.initials: Y
authors.lastname: Wang
authors.forename: Meixian
authors.initials: M
authors.lastname: Yan
authors.forename: Dali
authors.initials: D
authors.lastname: Zeng
authors.forename: Bin
authors.initials: B
authors.lastname: Han
authors.forename: Chung-I
authors.initials: CI
authors.lastname: Wu
authors.forename: Suhua
authors.initials: S
authors.lastname: Shi
authors.forename: Jiayang
authors.initials: J
authors.lastname: Li
mesh_terms: D000595:Amino Acid Sequence; D004156:Catechol Oxidase / Q000235:genetics*; D003001:Cloning, Molecular; D018556:Crops, Agricultural / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant; D005816:Genetic Complementation Test; D005828:Genetics, Population; D008969:Molecular Sequence Data; D009154:Mutation; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D018514:Plant Structures / Q000235:genetics*; D030821:Plants, Genetically Modified / Q000235:genetics; D011110:Polymorphism, Genetic; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins; D004156:Catechol Oxidase