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Genetic engineering methods based on the use of transgenes have been successfully adopted to improve crops. A novel all-native DNA gene technology consists of the creation of intragenic constructs by isolating genetic elements from a crop, rearranging them in vitro, and inserting them back into the plant. The ever-increasing genomic information and the elucidation of the molecular mechanisms that control fruit development could be exploited to confer the desired fruit phenotypes using endogenous DNA. The spatial/temporal regulation of genes can be modified by using appropriate endogenous regulatory elements, such as fruit-specific promoters. In addition, intragenic silencing can be employed to downregulate fruit-related genes. Here, we describe the available tools for intragenic manipulation of early phases of fleshy fruit initiation.