NOTE: Research by Dr Don Huber and others has found a strong association between glyphosate applications and crop infection with a mould called fusarium, which produces a toxin called fumonisin (see GMO Myths and Truths at www.earthopensource.org). 

As most GM crops are engineered to tolerate being sprayed with large amounts of glyphosate, fusarium is a concern with these crops. As a result, GM companies are strongly focused on developing fusarium-resistant GM crops.

That hasn't stopped pro-GM/anti-organic pundits like Henry Miller scaremongering about how organic corn is more likely than GM corn to contain fusarium and concluding that GM corn is the healthier choice:
 http://cei.org/op-eds-and-articles/kernals-truth-henry-miller

Miller's evidence seems partial at best. For example, it ignores a Spanish study that compared fusarium infection and fumonisin production in corn from conventional farms against corn from organic farms. The study found that "The organic farming system, with well-balanced crop rotation, tillage, and compost fertilization, produced corn that was less likely to be contaminated with Fusarium species, although no significant difference in fumonisin concentrations was found between the two types of contaminated corn."
 http://www.ncbi.nlm.nih.gov/pubmed/17265874

An important factor that's often ignored in the fusarium discussion, as in similar scaremongering stories about E. coli and organic food, is the type of fusarium mould that is found and whether it's disease-causing or not.

Just as most strains of E. coli are not pathogenic (disease-causing) and can be beneficial, so not all strains of fusarium are pathogenic.

A study published in 2011 (abstract below) found that fusarium in organic systems tended to be dominated by non-disease causing species, whereas pathogenic fusarium were more abundant in high-input chemical systems.
 https://www.agronomy.org/publications/aj/abstracts/103/3/756?access=0&view=article

It seems that the Western Producer inaccurately reported this study in an otherwise excellent article that we circulated in December 2012, titled "Scientist raises concerns about GM crops and glyphosate". The article says:

"Myriam Fernandez, a plant disease specialist with Agriculture Canada, found that fusarium in organic systems tended to be dominated by saprophytic species (not disease causing) whereas pathogenic fusarium (causing disease) were more abundant in other systems where GM crops and glyphosate were commonly used."
 http://www.gmwatch.org/latest-listing/51-2012/14542

In fact Dr Fernandez pointed out that there were no GM crops in her research project. The comparator with the organic system was a high-input chemical + tillage + fertilizer system.

So if you're concerned about pathogenic strains of fusarium, the message from this and other studies is: avoid GM herbicide-tolerant crops, avoid chemically grown food, and eat organic.
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Fernandez, M. R., et al. (2011). Crop management effects on root and crown rot of wheat in West-Central Saskatchewan, Canada

 Agronomy Journal 103(3): 756–765.
 https://www.agronomy.org/publications/aj/abstracts/103/3/756?access=0&view=article

ABSTRACT 

The impact of cropping system management on root and crown rot of spring wheat (Triticum aestivum L.) was examined on a Dark Brown Chernozem (Typic Boroll) soil in the Canadian Prairies. This systems approach tried to reflect the most common practices of organic and conventional producers in this region. The study consisted of a factorial combination of three input levels (high, with tillage, fertilizer and pesticides; reduced [RED], with conservation tillage, targeted fertilizer and weed control; and organic [ORG] with tillage and N-fixing legumes); and three levels of cropping diversity (low diversity with wheat and sum- merfallow or legume green manure fallow; diversified using annual grain crops; and diversified using annual grain crops and perennial forages). All rotations were 6 yrs long. Subcrown internodes and crowns/lower culms of wheat plants were scored for discoloration, and fungi in discolored tissue were identified and quantified. Overall, input level had a greater impact on disease levels and fungal frequency than cropping diversity. Discoloration severity was lowest in the RED systems, which was attributed to lower percentage isolation of Cochliobolus sativus, the most common pathogen. Fusarium species varied with input level. The pathogens F. avenaceum and F. culmorum were most associated with RED and/or least associated with ORG systems, whereas the weak pathogen/saprophyte F. equiseti was most associated with ORG systems. Thus, ORG management helped to reduce populations of F. avenaceum and F. culmorum, two of the most important Fusarium pathogens in the Canadian Prairies.