A minimal two-amino-acid deletion in SmMYB1 converts an activator into a dominant repressor, reshaping global eggplant anthocyanin pigmentation during domestication.

Abstract

Eggplant fruits exhibit remarkable natural variation in both the intensity and spatial distribution of anthocyanin pigmentation, yet the genetic bases underlying the dominant anthocyaninless fruit (ALF) phenotype in many white- and green-fruited accessions remain unclear. Using bulked segregant analysis, we identified a 6-bp deletion within the coding sequence of SmMYB1 as the causal mutation underlying the ALF trait. Functional characterization revealed that this deletion converts the core fruit coloration regulator SmMYB1 from a transcriptional activator into a dominant-negative repressor, designated SmMYB1alf-D. While SmMYB1alf-D loses its ability to bind target gene promoters, it retains the complete protein-interaction network of the wild-type SmMYB1, thereby sequestering essential partners and effectively suppressing the expression of anthocyanin biosynthetic genes. This strong suppression of anthocyanin structural genes by SmMYB1alf-D enables reliable prediction of fruit color and provides a breeding strategy to precisely manipulate anthocyanin metabolism. Notably, unlike previously reported dominant-negative mutants that often involve large protein truncations, this study uncovers a rare case in which a deletion of just two amino acids is sufficient to generate a potent dominant-negative regulator. Phylogenetic, geographic, haplotypic and historical evidence strongly suggests that alf-D originated as a spontaneous mutation from a purple eggplant cultivar in North China approximately 1200 years ago. Moreover, its emergence and subsequent introgression represent a major mechanism underlying the origin of green/white-fruited eggplant varieties globally. Collectively, these findings highlight how a single, minimally altered natural allele originated, spread, and reshaped eggplant fruit pigmentation and offer a potential tool for precise phenotype engineering in molecular breeding.