Repairing a deleterious mutation acquired during tomato domestication accelerates yield

During the domestication of crops, humans selectively breed plants for desirable traits. This process often involves selecting a small number of plants with specific traits from a larger, genetically diverse population. This strong selection pressure and the narrowing of genetic diversity is referred to as a "genetic bottleneck", and can result in the accumulation of deleterious mutations that negatively impact the plant's function or fitness. These mutations are difficult to remove by natural selection because the bottleneck reduces the population size and diversity, limiting the ability of the population to "weed out" harmful genetic changes. New technologies such as genome editing have been proposed to eliminate such harmful mutations, although they have never been tested for this purpose.

In this article we identified a deleterious mutation in the tomato transcription factor SUPPRESSOR OF SP2 (SSP2), involved in the control of flowering time and inflorescence architecture. This mutation became prevalent during tomato domestication. 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 may allow predictable crop improvement.