title: The Birth of a Black Rice Gene and Its Local Spread by Introgression.
abstract: The origin and spread of novel agronomic traits during crop domestication are complex events in plant evolution. Wild rice (Oryza rufipogon) has red grains due to the accumulation of proanthocyanidins, whereas most cultivated rice (Oryza sativa) varieties have white grains induced by a defective allele in the Rc basic helix-loop-helix (bHLH) gene. Although the events surrounding the origin and spread of black rice traits remain unknown, varieties with black grains due to anthocyanin accumulation are distributed in various locations throughout Asia. Here, we show that the black grain trait originated from ectopic expression of the Kala4 bHLH gene due to rearrangement in the promoter region. Both the Rc and Kala4 genes activate upstream flavonol biosynthesis genes, such as chalcone synthase and dihydroflavonol-4-reductase, and downstream genes, such as leucoanthocyanidin reductase and leucoanthocyanidin dioxygenase, to produce the respective specific pigments. Genome analysis of 21 black rice varieties as well as red- and white-grained landraces demonstrated that black rice arose in tropical japonica and its subsequent spread to the indica subspecies can be attributed to the causal alleles of Kala4. The relatively small size of genomic fragments of tropical japonica origin in some indica varieties indicates that refined introgression must have occurred by natural crossbreeding in the course of evolution of the black trait in rice.
authors.affiliation: Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Oikawa
authors.affiliation: Toyama Prefectural Agricultural, Forestry and Fisheries Research Center, Toyama, Toyama 939-8153, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Maeda
authors.affiliation: Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Taichi
authors.initials: T
authors.lastname: Oguchi
authors.affiliation: Toyama Prefectural Agricultural, Forestry and Fisheries Research Center, Toyama, Toyama 939-8153, Japan.
authors.forename: Takuya
authors.initials: T
authors.lastname: Yamaguchi
authors.affiliation: Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Noriko
authors.initials: N
authors.lastname: Tanabe
authors.affiliation: Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Kaworu
authors.initials: K
authors.lastname: Ebana
authors.affiliation: Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Yano
authors.affiliation: Toyama Prefectural Agricultural, Forestry and Fisheries Research Center, Toyama, Toyama 939-8153, Japan.
authors.forename: Takeshi
authors.identifier: http://orcid.org/0000-0002-5726-1610
authors.initials: T
authors.lastname: Ebitani
authors.affiliation: Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan tizawa@affrc.go.jp.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Izawa
mesh_terms: D000217:Acyltransferases / Q000235:genetics / Q000378:metabolism; D000429:Alcohol Oxidoreductases / Q000235:genetics / Q000378:metabolism; D000483:Alleles; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics; D005075:Biological Evolution; D018556:Crops, Agricultural / Q000235:genetics; D019175:DNA Methylation; D018506:Gene Expression Regulation, Plant; D012275:Oryza / Q000235:genetics* / Q000502:physiology; D010105:Oxygenases / Q000235:genetics / Q000378:metabolism; D010858:Pigmentation; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D030821:Plants, Genetically Modified; D011401:Promoter Regions, Genetic
chemical_list: D000217:Acyltransferases; D000429:Alcohol Oxidoreductases; D051792:Basic Helix-Loop-Helix Proteins; D010105:Oxygenases; D010940:Plant Proteins; C056570:dihydroflavanol 4-reductase; C105763:leucoanthocyanidin dioxygenase; C020141:flavanone synthetase