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In the evolution of wheat, there are two instances of chromosomal doubling, when Emmer wheat Triticum turgidum was formed from Einkorn wheat, and when Triticum aestivum was formed from Emmer wheat.

When allopolyploids are artificially made, chromosome doubling is done by chemicals. Here, it occurred by natural endoreplication. But for the entire plant to turn out with allotetraploidy and allohexaploidy respectively, wouldn't it be necessary for endoreplication to occur just after zygote formed--quickly, so all, or most, cells of the plant would have this genotype?

Isn't the probability of that happening twice in the process of evolution, both times in those incidences when the wheat crossed with the goatgrass species, very low? Is it just coincidence that it happened this way, at the right time, to allow for the allohexaploid species to develop naturally?

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But for the entire plant to turn out with allotetraploidy and allohexaploidy respectively, wouldn't it be necessary for endoreplication to occur just after zygote formed--quickly, so all, or most, cells of the plant would have this genotype?

Yes, it should have happened right after the embryo was formed in nature. But in artificial settings, this can be done after growing the seed to a small seedling then dipping its roots in colchicine for 12-24 hours.

Isn't the probability of that happening twice in the process of evolution, both times in those incidences when the wheat crossed with the goatgrass species, very low?

Yes, it is very low, but consider the fact that nature never sleeps. Einkorn existed for millions of years before the Emmer wheat came into existence. And hexaploid wheat only came line 8000-10000 year ago (about half a million years later). You don't see these events in nature that frequently. So it is slow.

Is it just coincidence that it happened this way, at the right time, to allow for the allohexaploid species to develop naturally?

Yes, it was part coincidence that it occurred naturally. Right conditions at the right time. But really important was the role of early hunter gatherers turned farmers who identified the potential of the new allohexaploid and selected it to grow grains.

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