Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice

• Published in: The Plant cell 2006-02, Vol.18 (2), p.283-294
• Main Authors: Sweeney, Megan T, Thomson, Michael J, Pfeil, Bernard E, McCouch, Susan
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Basic Helix-Loop-Helix Transcription Factors; Chromosomes, Plant - genetics; Corn; Crop production; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Domestication; Exons - genetics; Gene Expression Profiling; Gene Expression Regulation, Plant - genetics; Genes, Plant - genetics; Molecular Sequence Data; Mutation - genetics; Oryza - metabolism; Oryza rufipogon; Oryza sativa; Phenotype; Phylogeny; Physical Chromosome Mapping; Plant Proteins - chemistry; Plant Proteins - genetics; Plant Proteins - metabolism; Polymorphism, Genetic; Quantitative Trait Loci - genetics; RNA, Messenger - genetics; RNA, Messenger - metabolism; Sequence Analysis, DNA; Transcription Factors - genetics; Transcription Factors - metabolism; Zea mays
• ISSN: 1040-4651; 1532-298X; 1532-298X
• DOI: 10.1105/tpc.105.038430

Rc is a domestication-related gene required for red pericarp in rice (Oryza sativa). The red grain color is ubiquitous among the wild ancestors of O. sativa, in which it is closely associated with seed shattering and dormancy. Rc encodes a basic helix-loop-helix (bHLH) protein that was fine-mapped to an 18.5-kb region on rice chromosome 7 using a cross between Oryza rufipogon (red pericarp) and O. sativa cv Jefferson (white pericarp). Sequencing of the alleles from both mapping parents as well as from two independent genetic stocks of Rc revealed that the dominant red allele differed from the recessive white allele by a 14-bp deletion within exon 6 that knocked out the bHLH domain of the protein. A premature stop codon was identified in the second mutant stock that had a light red pericarp. RT-PCR experiments confirmed that the Rc gene was expressed in both red- and white-grained rice but that a shortened transcript was present in white varieties. Phylogenetic analysis, supported by comparative mapping in rice and maize (Zea mays), showed that Rc, a positive regulator of proanthocyanidin, is orthologous with INTENSIFIER1, a negative regulator of anthocyanin production in maize, and is not in the same clade as rice bHLH anthocyanin regulators.