Marker development for the identification of rice seed color

Pigmented traits in rice seeds are regarded as important breeding goals for crop improvement. Marker-assisted 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 programs.