The R2R3-type MYB transcription factor MdMYB90-like is responsible for the enhanced skin color of an apple bud sport mutant

The anthocyanin content in apple skin determines its red coloration,as seen in a Fuji apple mutant.Comparative RNA-seq analysis was performed to determine differentially expressed genes at different fruit development stages between the wild-type and the skin color mutant.A novel R2R3-MYB transcription factor,MdMYB90-like,was uncovered as the key regulatory gene for enhanced coloration in the mutant.The expression of MdMYB90-like was 21.3 times higher in the mutant.MdMYB90-like regulates anthocyanin biosynthesis directly through the activation of anthocyanin biosynthesis genes and indirectly through the activation of other transcription factors that activate anthocyanin biosynthesis.MdMYB90-like bound to the promoters of both structural genes(MdCHS and MdUFGT)and other transcription factor genes(MdMYB1 and MdbHLH3)in the yeast one-hybrid system,electrophoretic mobility shift assay,and dual-luciferase assay.Transgenic analysis showed that MdMYB90-like was localized in the nucleus,and its overexpression induced the expression of other anthocyanin-related genes,including MdCHS,MdCHI,MdANS,MdUFGT,MdbHLH3,and MdMYB1.The mutant had reduced levels of DNA methylation in two regions(−1183 to−988 and−2018 to−1778)of the MdMYB90-like gene promoter,which might explain the enhanced expression of the gene and the increased anthocyanin content in the mutant apple skin.