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.

Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication

“…Previous studies reported that Phr1 participates in the formation of black hull (Kuriyama and Kudo, 1967) and that Phr1 in japonica is a nonfunctional allele (Yu et al, 2008). We transferred the Bh4 gene into the two subspecies of cultivated rice, indica (Guangluai 4, Kasalath) and japonica (Nipponbare).…”

“…These results are consistent with previous genetic analyses. As multiple mutations occurred in Rc (Sweeney et al, 2006) and Phr1 (Yu et al, 2008) genes, Bh4 also had multiple mutations. All three of these genes are related to color changes in grains and seeds.…”

“…Phr1 localizes on the long arm of chromosome 4 and encodes a polyphenol oxidase. The frequency of Ph is high in the indica type and low in the japonica type (Yu et al, 2008). In another study, using an F2 population developed from the cross between the weedy strain SS18-2 and the breeding line EM93-1, the two loci qHC4 and qHC7 that explained a major and a minor proportion of the phenotypic variation in black pigmentations on the hull were identified (Gu et al, 2005).…”

“…Over the long time of domestication, large arrays of morphological traits have changed as a result of artificial selection, including the loss of seed shattering, changing of grain coloration, enlarging of the seed size, and changing from prostrate to erect growth habit. There are a number of genes known to control seed-shattering habit (Konishi et al, 2006;Li et al, 2006), red grain pericarp (Sweeney et al, 2006), grain discoloration (Yu et al, 2008), grain size (Shomura et al, 2008), shoot gravitropism (Li et al, 2007), and prostrate growth (Jin et al, 2008;Tan et al, 2008). Examination of these genes will help us understand the forces driving the evolution of phenotypes during domestication.…”

Complementary Genes That Cause Black Ripening Hulls in F1Plants of Crosses betweenIndicaandJaponicaRice Cultivars

“…Maekawa (1984) reported that three complementary genes, termed Bh-a, Bh-b and Bh-c, controlled the black hull phenotype. Among them, Bh-c was suggested to correspond to Phr1, which encodes polyphenol oxidase (Kuriyama and Kudo, 1967;Maekawa, 1984;Yu et al, 2008). Phr1 causes the phenol reaction-positive phenotype of seeds, in which the hull color turns black after being soaked in a phenol solution (Yu et al, 2008).…”