Black rice has high accumulation of anthocyanins on pericarp tissues. OsB1 and OsC1
genes are important for the controls of anthocyanin biosynthesis in rice. OsDFR gene is structural
gene that encodes the vital enzyme in anthocyanin biosynthesis pathway. In this study, DNA
makers specific to OsB1, OsC1 and OsDFR were investigated to select rice with black pericarp and
identify F1 hybrid of the cross between white pericarp rice as a receptor and black pericarp rice as a
donor. Sequence analysis of OsB1 gene at exon 7 showed 2-bp insertion in white rice. CAPS
(Cleaved amplified polymorphic sequences) maker of OsB1 was tested. The results showed that
CAPS marker could be used to distinguish between white and black rice and to detect F1 hybrid.
Analysis of nucleotide sequences of OsDFR at -450 promoter region revealed 11-bp insertion in
white rice. Indel marker was developed and the results showed that the Indel marker could select
black rice from white rice and identify F1 hybrid. In addition, sequence analysis of OsC1 showed
that white rice had 10-bp deletion in exon 3. Indel marker of OsC1 was studied. It was found that
the Indel marker could discriminate black rice form red and white rice and also select F1 hybrid.
Analysis of anthocyanin contents and antioxidant activity of rice seeds revealed that black rice had
higher anthocyanins than white and red rice. However, red rice had the highest antioxidant activity,
followed by black rice and white rice, respectively. Therefore, gene-specific markers in this study
will be beneficial for selection of black rice in the early stage of development which will facilitate
selection and shorten the time in breeding Thai rice for high anthocyanins and antioxidant activity.