The nutrient content, or chemical profile, of the food we eat is very important to maintaining our health and well-being. Your question does a good job recognizing that the way our food is grown can impact its nutrient content, but to understand how this happens we need to look in more detail than conventional vs. GM vs. organic. Let me explain what years of research shows.
Many studies conclude that factors such as farming practices (row spacing, seeding rate, fertilization, irrigation) or location (country, state, county, field, or even location in a field!) can have an impact on the vitamins, minerals, and other nutritional components in a crop. One good example in conventional (or as you refer to it, standard) crops includes a study by Seguin et al. (2010) showing how row spacing, fertilization, and date of planting can affect the amount of vitamin E in soybean. There are also many studies available that show how crops grown in different locations can have large differences in nutrient levels, including one by Shewry et al. (2010) as part of the EU HEALTHGRAIN initiative, which showed how fibers and other nutrients in wheat and other cereals can be affected by environment.
Even different varieties of the same crop naturally have different levels of nutrients. For example, consider tomatoes, which come in many different sizes, shapes, and colors. On a recent visit to the grocery store,I had my choice of yellow, orange, red, and purple tomatoes. These differences in colors are a result of differences in the types and levels of nutrients called carotenoids. Regardless of the farming practice, the varieties were developed for these different colors, and thus, for different nutrient content. So every day, we’re choosing to eat a variety of different nutrient profiles, even in consuming the same types of foods! Another example is multi-colored corn (traditionally called “Indian corn”) where even on a single cob there are kernels with different nutrient content! I’m sure you’re anxious to know, I chose the purple tomatoes – I had never seen them before so was very eager to try something new. My daughter seemed a little perplexed, which is not surprising since we all get used to certain types of foods, even if they are vastly different than what was available to our ancestors.
There are many examples of the wide variability in crop nutrient content (or composition) due to variety and environment. The International Life Sciences Institute maintains an online Crop Composition Database (https://www.cropcomposition.org/query/index.html) that contains nutrient content information for conventional corn, cotton, and soybeans; the data contained within exemplifies this wide variability. As an example of effects of environment and genetics, if you look at only protein in non-GM corn grown in the US during 2005, the average value was 9.02%. But, protein ranged between 5.87% and 13.50%. That’s almost a 3-fold difference from low to high!
There are also numerous comparisons of the composition of GM crops to non-GM counterparts in the published literature; one example is a study in Nature Biotech by Harrigan et al. (2010) on corn and soybean, and another example is a study by Venneria et al. (2008) on wheat, corn, and tomatoes . There are no instances where a harmful compound has appeared in one but not the other, or has been elevated in one and not the other to an extent that would affect human or animal health. There are many of these types of studies because before a GM crop is commercialized, extensive scientific analyses are conducted, including a compositional analysis, that contribute to the overall safety assessment of these crops. These are very comprehensive studies that include multiple geographies that span up to 1000 miles to get a variety of environmental and soil conditions, with multiple plots within a location and analysis of up to 80 analytes. The overwhelming conclusion of these studies is that the composition of the GM crops is nutritionally equivalent to the non-modified variant, and that factors such as environment have a much bigger effect on composition.
The exception to this is when the composition of a crop is intentionally altered, either to increase levels of beneficial nutrients (biofortification), or decrease levels of naturally-occurring compounds in the crop that are not beneficial and in some cases may be harmful. This alteration can be achieved by conventional breeding methods or through GM technology. Examples of conventional breeding for biofortification include a recent example from Blair (2013) where common bean, the most important directly consumed legume in underdeveloped African countries, has been bred for increased amounts of iron and zinc to promote healthy metabolism and fight childhood infections. GM examples include golden rice (http://irri.org/index.php?option=com_k2&view=item&id=10202) which has been developed to contain beta-carotene (pro-vitamin A) to help prevent 670,000 deaths a year that are a result of Vitamin A deficiency, and SDA omega-3 soybean, which contains stearidonic acid that is readily converted in the body to EPA (eicosapentaenoic acid) omega-3 – one of two main omega-3s that has been clinically shown to promote heart health.1
There has been a lot of debate around whether organic produce has “more-nutrition” than conventionally-raised crops. Studies comparing input systems (conventional vs. organic farming) on the nutrient content of crop have shown little difference. One example is corn (Rohlig and Engel, 2010) where input system had little effect, but as expected, there was a large influence of environment and variety on the nutrient content. Thus, there is no credible evidence that suggests organic crops have more/better nutrients than conventional crops.
To sum this up, food that we purchase at the grocery store or farmer’s market are all different crop varieties, and have been grown using different farming practices, in different locations. All of these differences contribute to differences in the nutrient content, regardless of whether they are GM, non-GM, or grown using traditional or organic methods. In regards to achieving a healthy diet, quantity and variety of fruits and vegetables appears to be a simple and achievable approach.
Blair (2013): http://pubs.acs.org/doi/pdf/10.1021/jf400774y
Seguin et al. (2010): http://pubs.acs.org/doi/pdf/10.1021/jf100455f
Shewry et al. (2010): http://pubs.acs.org/doi/pdf/10.1021/jf100039b
Röhlig, R.M. and Engel, K.-H. Influence of the Input System (Conventional versus Organic Farming) on Metabolite Profiles of Maize (Zea mays) Kernels J. Ag. Food Chem. 2010, 58 (5), 3022–30: http://pubs.acs.org/doi/full/10.1021/jf904101g
Harrigan et al., 2010: http://www.nature.com/nbt/journal/v28/n5/full/nbt0510-402.html
1 FDA, in considering the relationship between EPA and the risk of cardiovascular disease, has issued qualified health claim that “supportive but not conclusive” research shows that consumption of EPA “may reduce the risk” of CVD.