A 725-bp quadruple repeat in the promoter of SmMYB113 is associated with light-independent anthocyanin regulation in eggplant

Eggplant exhibits a diverse range of fruit colors, making it an excellent model for studying fruit pigmentation and its genetic regulation. While genes responsible for green and photosensitive purple fruit have been identified, the genetic basis of the nonphotosensitive (NPS) fruit trait in eggplant has remained elusive. In this study, we characterized a major quantitative trait locus (QTL), SmNPS10.1, on chromosome 10 using QTL-seq. By combining linkage-based gene mapping with progeny testing, we fine-mapped SmNPS10.1 to a 33.58-kb interval, within which we identified SmMYB113, an R2R3-MYB transcription factor that regulates anthocyanin biosynthesis, as the candidate gene. Sequence analysis identified a unique 725-bp tandem repeat in the SmMYB113 promoter, present in four copies in NPS eggplant variety 21E27 but only a single copy in photosensitive varieties. This suggests that increased copy number of the repeat may drive light-independent expression of SmMYB113. Transgenic complementation confirmed the additional three copies of the 725-bp repeat in the promoter of SmMYB113 contributes to light-independent anthocyanin regulation. Additionally, we validated the KASP markers 21QP381 (linked to anthocyanin-present fruit color) and 23QP715 (linked to NPS fruit color) across multiple populations, providing powerful tools for marker-assisted selection in eggplant breeding. Our findings offer new insights into the molecular mechanisms controlling fruit color in eggplant and lay the groundwork for the development of molecular markers to facilitate breeding for NPS and other fruit color variants.