Just like the arguments about evolution in general, you have to ask, why couldn't it have been done the usual way? Just selecting and propagating good food plants. If someone in the distant past were really able to alter individual genes, you'd think they would have removed undesirable characteristics like the binding of niacin in maize that requires soaking in lime-water to release the vitamin. Large European populations suffered pellagra when maize was first introduced into Europe and people started relying on it as a staple food. Rice has a similar problem with an enzyme that blocks iron absorption. This is one of the reasons that Asians of many ethnicities, from Chinese and Japanese to Filipinos and Indians have tended to be smaller than Westerners. Iron deficiency is a serous problem in Asia down to the present, largely because of the dominance of rice in the Asian diet.
The convenient mechanical crop characteristics of these plants such as larger seeds were developed, the inconvenient nutritional problems were not eliminated. Just what you would expect from crops developed by selection and re-propagation instead of direct genetic manipulation.
Like ancient Rome, we today are once more importing every form of exotic superstition in the hope of finding the right remedy for our sickness.
-- C. G. Jung
Richard Wilhelm: In Memoriam (1930), CW 15: pg. 60