The genetic constitutions of complementary genes Pp and Pb determine the purple color variation in pericarps with cyanidin-3-O-glucoside depositions in black rice

The purple pericarp color in rice was controlled by two dominant complementary genes, Pb and Pp. Crossing black rice ‘Heugnambyeo’ variants with three varieties of white pericarp rice gave a segregation ratio of 9 purple: 3 brown: 4 white. The Pp genes were segregated by homozygous PpPp alleles for the dark purple pericarps, heterozygous Pppp alleles for the medium and mixed purple pericarps, and homozygous pppp alleles for either brown or white pericarps with a 1 PpPp: 2 Pppp: 1 pppp segregation ratio, indicating that the Pp allele in rice is incompletely dominant to the recessive pp allele. Among the purple seeds, the amount of cyanidin-3-O-glucoside was higher in the dark purple seeds (Pb_PpPp) than in the medium purple seeds (Pb_Pppp). Moreover, no cyanidin-3-glucoside was detected in brown (Pb_pppp) or white pericarp seeds (pbpbpppp). These findings indicated that the level of cyanidin-3-glucoside was determined by the copy number of the Pp allele. Further genotype investigation of the F₃ progeny demonstrated that the dominant Pb allele was present in either purple or brown pericarp. A 2-bp (GT) deletion from the DNA sequences of the dominant and functional Pb was found in the same DNA sequences of the recessive and non-functional pb allele. These findings suggested that the presence of at least a dominant Pb allele was an essential factor for color development in rice pericarps. In conclusion, the Pp allele in rice is incompletely dominant to the recessive pp allele; thus, the number of dominant Pp alleles determines the concentration of cyanidin-3-O-glucoside in black rice.