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Is it possible to identify the gender of Papaya seeds without using DNA analysis?

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You can't, as a seed - and not only that, papaya are variable, some years producing all male flowers, in some seasons producing male and female (perfect) flowers, and sometimes just female flowers. The link below explains a bit more

https://www.crfg.org/pubs/ff/papaya.html

There is information that male seedlings produce a single straight root, whereas female seedlings produce two or more branched rootlets, (https://arlene1027.wordpress.com/2009/05/11/how-to-recognize-a-female-and-male-plant-seed/) but the trouble with that is, they hate root disturbance, so in order to distinguish which is which, you'd inevitably have to disturb them. Probably the simplest thing is to germinate and wait for them to get two true leaves, then, when you prick them out, check out the root system at that point, preferably without causing too much disturbance to the rootlets.

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