Unraveling a Genetic Roadmap for Improved Taste in the Domesticated Apple

Abstract Although taste is an important aspect of fruit quality, our understanding of its genetic control remains elusive in apple and other fruit crops. Genomic sequence analysis of 497 Malus accessions revealed an erosion of genetic diversity caused by apple breeding and possible independent domestication events of dessert and cider apples. Signatures of selection for fruit acidity and size were detected during the process of both domestication and improvement, but not for fruit sugar content. Single mutations in major genes affecting fruit taste, including Ma1, MdTDT, and MdSOT2, dramatically decrease malate, citrate and sorbitol accumulation, respectively, and correspond to important domestication events. The pleiotropic effects of Ma1 on organic acid content and sugar:acid ratio suggest its vital role in determining fruit taste. Fruit taste is unlikely to have been negatively affected by linkage drag associated with selection for larger fruit that resulted from the pyramiding of multiple genes with minor effects on fruit size. Our study provides insights into genetic basis of fruit quality and its evolutionary roadmap during apple domestication, and also points out target genes for fruit taste genetic manipulation.