Repairing a deleterious domestication variant in a floral regulator of tomato by base editing

Abstract

ABSTRACTCrop genomes accumulated deleterious mutations, a symptom known as the cost of domestication. Precision genome editing has been proposed to eliminate such potentially harmful mutations, however, experimental demonstration is lacking. Here, we identified a deleterious mutation in the tomato transcription factorSUPPRESSOR OF SP2(SSP2), which became prevalent in the domesticated germplasm and diminished DNA-binding to genome-wide targets. We found thatSSP2acts partially redundant with its paralogSSPto regulate shoot and inflorescence architecture. However, redundancy was compromised during tomato domestication and completely lost in the closely-related speciesPhysalis grisea, in which a single ortholog regulates shoot branching. We applied base editing to directly repair the deleterious mutation in cultivated tomato and obtained plants with compact growth that provide an early fruit yield. Our work shows how deleterious variants sensitized modern genotypes for phenotypic tuning and illustrates how repairing deleterious mutations with genome editing allows for predictable crop improvement.