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Reference genome sequences and population-scale resequencing of vegetable crops enabled the reconstruction of the evolutionary history of their domestication and breeding.We collaborated with an international team to develop a multi-disciplinary tool that combines population genomics,molecular biology,and biochemistry.The successful application of the tool is examplified by the identification of genetic variants that rendered the loss of bitterness in cucumber and the increase of fruit size in tomato.Cucurbitacins confer a bitter taste in cucurbits that were domesticated from their ancestors carrying extremely bitter fruits.In cucumber,cucurbitacin C is mainly attributed to a bitter taste,and the gene Bi confers bitterness to the entire plant.We firstly uncovered the genetic variants associated with Bi using a genome-wide association strategy based on the variation map of 115 diverse cucumber lines.Together with genetic analysis and yeast expression system,we demonstrated that Bi encodes a cucurbitadienol synthase.Then we showed that Bi is activated by Bl in leaves and by Bt in fruits.We further found out that nine genes are coexpressed with Bi and they are activated by Bl and Bt.In summary we discovered that two transcription factors Bl and Bt regulate nine genes in the Cucurbitacin C biosynthetic pathway.In tomato,we reported a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions.Modern tomato fruit is around 100 times larger than its ancestor,and this huge transition is mainly resulting from two independent sets of quantitative trait loci(QTLs).The first set QTLs are loaced within the domestication sweeps and likely contribute to the shift from small-sized fruit to middle-sized fruit.The second set QTLs are located within improvement sweeps and likely contribute to the shift from middlesized fruit to big-sized fruit.