Allelic Variation of Is the Major Force Controlling Natural Variation in Skin and Flesh Color in Strawberry ( spp.) Fruit.

The fruits of diploid and octoploid strawberry ( spp) show substantial natural variation in color due to distinct anthocyanin accumulation and distribution patterns. Anthocyanin biosynthesis is controlled by a clade of R2R3 MYB transcription factors, among which MYB10 is the main activator in strawberry fruit. Here, we show that mutations in cause most of the variation in anthocyanin accumulation and distribution observed in diploid woodland strawberry () and octoploid cultivated strawberry ( ×). Using a mapping-by-sequencing approach, we identified a -transposon in that truncates the protein and knocks out anthocyanin biosynthesis in a white-fruited ecotype. Two additional loss-of-function mutations in were identified among geographically diverse white-fruited ecotypes. Genetic and transcriptomic analyses of octoploid spp revealed that , one of three homoeologs identified, regulates anthocyanin biosynthesis in developing fruit. Furthermore, independent mutations in are the underlying cause of natural variation in fruit skin and flesh color in octoploid strawberry. We identified a CACTA-like transposon () insertion in the promoter of red-fleshed accessions that was associated with enhanced expression. Our findings suggest that cis-regulatory elements in are responsible for enhanced expression and anthocyanin biosynthesis in strawberry fruit flesh.