Subsituting soy for wheat leads to deforestation in Brazil, according to story in Science just before Christmas. According to the Smithsonian Tropical Research Institute'
many American soy farmers are shifting to corn to qualify for the government subsidies. Since 2006, US corn production rose 19% while soy farming fell by 15%.
Its worth reading the short extract on the Smithsonian Tropical Research Institute's website by William Laurence