Plants do sexual reproduction through pollination. This induces the production of fruit, and, because it is sexual reproduction, the child plant acquires traits of both parent plants. That is useful for hybridization.
When did civilization discover all this? It's far from obvious: pollen is microscopic. Was it reasoned from analogy? Maybe humans familiar with human sexual reproduction reasoned that plants must be doing something similar, so looked for an analogous mechanism, despite plants being sessile organisms. But it's quite a leap to assume human and plant reproduction are similar.
Our modern agriculture is a product of a lot -- millennia? -- of old school genetic engineering, including intentional hybridization, done by people who must have understood that aspect of plant biology.
Inspired by the huge amount of crosses that make up modern citrus varieties.
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