An LTR retrotransposon in the promoter of a gene associated with the regulation of fruit flesh color in Japanese plum.

Japanese plums exhibit wide diversity of fruit coloration. The red to black hues are caused by the accumulation of anthocyanins, while their absence results in yellow, orange or green fruits. In , genes are determinants for anthocyanin accumulation. In peach, QTLs for red plant organ traits map in an LG3 region with three copies (, and ). In Japanese plum the gene copy number in this region differs with respect to peach: there are at least three copies of , with the expression of one of them ( correlating with fruit skin color. The objective of this study was to determine a possible role of LG3-PsMYB10 genes in the natural variability of the flesh color trait and to develop a molecular marker for marker-assisted selection (MAS). We explored the variability within the LG3-PsMYB10 region using long-range sequences obtained in previous studies through CRISPR-Cas9 enrichment sequencing. We found that the gene was only expressed in red flesh fruits. Its role in promoting anthocyanin biosynthesis was validated by transient overexpression in Japanese plum fruits. The analysis of long-range sequences identified an LTR retrotransposon in the promoter of the expressed gene that explained the trait in 93.1% of the 145 individuals analyzed. We hypothesize that the LTR retrotransposon may promote the expression and activate the anthocyanin biosynthesis pathway. We propose for the first time the gene as candidate for the flesh color natural variation in Japanese plum and provide a molecular marker for MAS.