Abstract Pigmented traits in rice seeds are regarded as
important breeding goals for crop improvement. Markerassisted
selection is very helpful when screening for target
seed color traits in the early stages of plant development.
Among the genes involved in the biosynthesis of anthocyanins
and proanthocyanins (PAs) that are candidates for
marker development, we examined the expression of five
genes encoding CHS, CHI, F3H, DFR, and ANS in the
seeds of non-pigmented white and pigmented black and red
rice cultivars. The transcript levels of all these genes except
for CHI are higher in pigmented rice than in non-pigmented
rice. Sequence variations in these biosynthetic
genes revealed that the DFR gene harbors a single nucleotide
substitution that generates a premature stop codon in
white rice. Additional sequence variations in two regulatory
genes, OSB1 and Rc, were also compared among the
same cultivars. The sequence of the OSB1 gene in black
rice was found to differ from that in red and white rice. The
sequence of the Rc gene in red rice also differed from that
in white and black rice. Based on these variations, we
developed two CAPS markers for DFR and OSB1 genes
and an Indel marker for the Rc gene. The combined use of
these three markers could discriminate rice seeds harboring
white, black and red color. We validated the usefulness of
these markers in 34 rice cultivars. Hence, the combined
application of our three new markers may have utility to
screen the seed color prior to seed setting in rice breeding