A minimal two-amino-acid deletion converts SmMYB1 from a transcriptional activator into a dominant repressor that causes anthocyaninless eggplant fruit during domestication.

Eggplant fruits exhibit remarkable natural variation in both the intensity and spatial distribution of anthocyanin pigmentation, but the genetic bases of 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 in 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. Although SmMYB1alf-D has lost its ability to bind the promoters of its target genes, it retains the complete protein-interaction network of wild-type SmMYB1, thereby sequestering essential partners and suppressing the expression of anthocyanin biosynthetic genes. The strong suppression of anthocyanin structural genes by SmMYB1alf-D enables reliable prediction of fruit color and provides a breeding strategy for precise manipulation of anthocyanin metabolism. Unlike previously reported dominant-negative mutants, which often arise from large protein truncations, SmMYB1alf-D represents a rare case in which the 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 in 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 worldwide. Collectively, our findings reveal how a single, minimally altered natural allele originated, spread, and reshaped the pigmentation of eggplant fruit, offering a potential tool for precise trait engineering during molecular breeding.