If the parents were both stable (i.e. homozygous) lines, then all seeds, from all fruits, from all F1 progeny plants will have the same genotype. In the F2 generation all plants will have a different genotype, with independent segregation for each gene that differed between the original parents. The F3 seed produced on those F2 plants will again segregate. To maximize the chance of getting the "perfect" combination of the best genes from each parent, you need to plant as many F2 progeny plants as possible. Once you harvest seed from the best F2 plants, it's about finding F3 progeny that continue to express the favorable gene combinations - and again large population size helps. If you are confident there is no cross pollination, fruit number is irrelevant, it's seed (i.e. progeny) number that counts.
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