The New York Times starkly covers the farmer v. farmer issues in GMO, or “traited,” crops.  In this case, corn in the Midwest.  Roundup (glyphosate)-resistant seeds, bioengineered by Monsanto, may also affect the soil, according to the article:

http://www.nytimes.com/2013/09/20/business/misgivings-about-how-a-weed-killer-affects-the-soil.html