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

Abstract

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.

Acknowledgements

We thank Ying Zhang for providing the eggplant variety 24AE005. This study was funded by the Yuelushan Laboratory Breeding Program (YLS-2025-ZY02013), the Natural Science Foundation of Guangdong Province (2023A1515030070), Science and Technology Special Commissioner Research Project of Jiangmen City (2024760000490010406), and the Key-Area Research and Development Program of Guangdong Province (2022B020208003).

Author contributions

Z.Q. and B.C. conceived and designed the experiments. Z.X. conducted the experiment and wrote the paper. M.Y., B.Y., T.W., D.W., Q.L., and M.S. offered professional assistance in conduction experimentation and analyzing data, and revising the manuscript. Z.Q., B.C., and S.Y. designed aspects of the study and revised the manuscript. All authors read and approved the final manuscript.

Data availability

The data that support the findings of this study are available in the Supporting Information.

Conflicts of interest statement

All authors declare no conflicts of interest.

Supplementary material

Supplementary material is available at Horticulture Research online.

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