The Rc locus was positionally cloned from rice. A mapping population between a cultivar (Jefferson) with the recessive, null allele, rc was crossed with a dominant allele ( Rc) Oryza sativa with red pericarp. By recombination analysis, a small stretch of genomic sequence was delimited within which an open reading frame annotated as a bHLH containing protein was identified. The null allele in Jefferson was found to be identical to that of Nipponbare, and has a 14bp indel that introduces a frameshift resulting in a premature stop codon. This frameshift,resulting in a white pericarp, occurs upstream of the basic helix-loop-helix motif responsible for the regulation of proanthocyanidin production. A second functional allele, Rc-s was cloned from an indica cultivar and confirmed that the Rc locus was the source of the red pericarp phenotype.