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We established an orange (L) and a tangerine (D) colored callus line by repeatedly subculturing rice callus line (N). The L line accumulated lycopene, β-carotene, and two lycopene isomers, while the D line accumulated much higher concentration of lycopene as well as a lycopene isomer than the L line. Genomic sequencing revealed the presence of SNP that results in the incomplete lycopene β-cyclase (β LCY) enzyme in the D line. We analyzed expression levels of carotenoid biosynthetic genes by qRT-PCR. Regarding the 2-C-methyl-D-erythritol-4-phosphate pathway genes, expression of the gene encoding geranylgeranyl diphosphate synthase 1 (GGPS1) was enhanced in both L and D lines as compared to the N line. Regarding the carotenoid pathway genes, the transcript amounts of the genes encoding phytoene synthase 2, phytoene desaturase, and ζ-carotene desaturase, were larger in the L line than in the N line; however, this pattern was not found in the D line. The expression levels of β LCY and lycopene ε-cyclase (ε LCY) gene in the D line and ε LCY in the L line were lower than in the N line. The transcript amounts of two carotenoid oxygenase genes were decreased both in L and D lines. We concluded that increased expression of GGPS1 and reduced expression of ε LCY, β LCY, and carotenoids oxygenase genes might allow an excess accumulation of carotenoids in L and D lines, and that the mutation in β LCY is responsible for the conspicuous phenotype in the D line as compared to the L line.

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