gmo – Texas A&M AgriLife Organic

Residue Testing for a Global Supply Chain

The article below appears in the Fall 2025, “OMRI Materials Review” newsletter sent out by OMRI to subscribers. I thought this article was interesting since it concerns pesticide residues – a hot topic in Texas Organic Agriculture! It is reprinted with permission by OMRI.

By Doug Currier

The work to modernize residue testing in USDA organic production could impact input material review.

Residue Testing for a Global Supply Chain (RTGSC) is an ongoing discussion being led by National Organic Standards Board (NOSB) with input from public stakeholders and the National Organic Program (NOP). It is well established that organic production is based on organic system plans that, if followed, ensure adherence to the organic standards. Testing to detect residues of both prohibited substances and excluded methods is seen as an important measure of the success of those system plans, or whether those plans were followed at all. This type of testing is required within the USDA organic standard¹, but for the testing to remain “relevant” and “impactful,” changes to the USDA standard and guidance documents are being considered. This is the aim of RTGSC.

Before we consider some of these changes, it is helpful to become clear on the sources of these residues and the possible reasons they may appear in organic systems. The 2013 “Pesticide Rule”² ³ established the current residue testing requirements to ensure that organic system plans prevent commingling and contamination with prohibited substances. Testing has long focused on detecting genetically modified crops to address the commingling issue.

Because of how the “Pesticide Rule” is written, there is a focus on detecting prohibited pesticides as a way to address the contamination issue. Both GMO and pesticide residues can come from neighboring non‑organic farms through “drift” or can occur when cleanout procedures used between processing non‑organic and organic commodities are ineffective. These two examples can be referred to as “organic control points” in a production system where the risk of contamination is high. There are many facets to the strategies used to detect contamination in organic production systems—far too many to examine in this article.

The NOSB Spring 2025 meeting materials call for an in-depth description of these issues. Before we move on to the changes being discussed to modernize the current approach to testing and detection, it can be helpful to acknowledge that the “Pesticide Rule” was not necessarily written with fraud detection in mind. Also, input materials themselves can be a source of contaminant residue that are actionable from the perspective of accredited certification bodies (“certifiers”).

Positive results from residue testing impact organic growers in several ways, with perhaps the most significant being the inability to sell produce as organic. In our work, we have seen growers lose their ability to sell produce as organic because of positive test results that were traced back not to their farm, but to the input materials, just like with other sources of residues—whether due to unintentional contamination or intentional adulteration. It is therefore promising to see that within the RTGSC conversation is a proposal to redefine the definition of Unavoidable Residual Environmental Contamination (UREC) to one that acknowledges that sometimes no matter how strong the system plan, contamination can occur. This is not to say that the contamination can go unaddressed. But relieving the grower of some responsibility seems to be a step in the right direction. How that contamination is ultimately addressed, and how often, is a separate matter.

A significant focus of RTGSC is to modernize the strategies for testing for contamination in a way that more meaningfully centers on pesticides and GMOs. A “Target List” or consumer‑focused list does good work to identify materials and input materials where extraordinary high levels of heavy metals and harmful organic contaminants may exist.

With that said, the advancements in test methodologies, test sensitivities, and the realization that detection strategies—especially those used to detect fraud—are more sensitive now than ever, suggest that the RTGSC ideas coming from the NOSB for the NOP to consider could change the nature of input material review work: (1) development and adoption of accredited methods for Organic Authenticity Testing as it relates to detecting whether inorganic nitrogen is manufactured from allowed or prohibited sources, and (2) broadening the list of substances for which there is regular testing.

Regarding the former, we are supportive of this long‑needed move towards methods and accreditation. As for the latter, we are mindful that widening the net, through expansion of the substances list and more sensitive testing, could mean for us and the manufacturers with which we work.

There is still much to consider and absorb before changes that move our industry beyond the 2013 “Pesticide Rule.” Achieving RTGSC’s goal of keeping testing relevant and impactful will affect nearly everyone. OMRI will continue to monitor these developments closely and share updates as the RTGSC process moves forward.

GMO Testing in Organic Cotton: What Farmers Need to Know

Organic cotton farmers work hard to maintain their certification, ensuring that their crops are grown without synthetic chemicals, genetically modified organisms (GMOs), or prohibited inputs. Even when farmers follow organic practices to the letter, GMO contamination can still occur!

Let’s take a closer look at how GMO testing works, what the results mean, and why the final decision on certification can sometimes feel arbitrary.

How is GMO Contamination Measured?

GMO testing in Seed Cotton (raw cotton including fibers and seeds) is performed using real-time PCR analysis, a widely used method to detect genetic modification markers in cotton DNA. The gin will take samples of your seed cotton and submit those samples to their Global Organic Textile Standard (GOTS) Certifier. The GOTS Certifier will submit those samples to a lab, usually OMIC which will then run them for GMO presence. The results are then submitted back to the GOTS Certifier. Here are some things that are being investigated.

Standard Limit of Quantification (LOQ): 0.1% GMO content – This is the most commonly used threshold for accurately measuring contamination.
More Sensitive Tests: Some advanced labs claim they can detect levels as low as 0.01%, but I have not seen this as an industry-standard threshold for Seed Cotton testing. But you could see this from European labs!
Anything above a 0.1% is detectable and reported as such as you can tell from this test sheet with all the names removed!

Here is another test with some different results.

What the Test Results Mean

This sample contains GMO markers including Bt toxin (Cry1Ab/Ac) and herbicide resistance (otp/mepsps).
p35S, pFMV, and tNOS confirm genetic modification.
Organic certifiers would likely reject this cotton since GMO elements were clearly detected.
If contamination was unintentional, an investigation might be needed to determine if the cotton can still qualify for certain supply chains.

Marker	Detected?	GMO Trait Significance
SAH7 (Cotton Gene)	✔ Yes	Confirms valid cotton DNA
Cry1Ab/Ac (Bt Toxin)	✔ 1.44%	Indicates Bt Cotton (Insect Resistance)
otp/mepsps (Glyphosate Resistance)	✔ 0.47%	Possible Roundup Ready Cotton (Herbicide Resistance)
p35S (CaMV Promoter)	✔ 1.93%	Common GMO activation switch
PAT (Glufosinate Resistance)	❌ Not Detected	No Liberty Link herbicide resistance
pFMV (FMV Promoter)	✔ 1.91%	Used for GMO gene activation
tNOS (Terminator)	✔ 3.27%	Common GMO terminator sequence
GM Elements (General GMO Presence)	✔ Yes	Confirms GMO modification detected

Now What Happens?

What happens when an organic cotton sample tests positive for GMOs? That really depends on a lot of different things, and this is where farmers can get frustrated. I have provided you with some sample test results but usually you won’t even see these results. At this point the GOTS Certifier for the Gin has your test results. This is a small list of what they do:

The Global Organic Textile Standard (GOTS) Says:

No intentional use of GMOs is allowed.
If contamination is detected, the GOTS certifier launches an investigation instead of outright rejection.
If the farmer can prove they used verified non-GMO seed and followed organic practices, then there is a strong possibility that they may still be approved.

GOTS Certifier Reaches Out

The next step is for the GOTS Certifier to reach out to your Organic Certifier at the farm level. Because a “red flag” is now waving, your certifier is going to be looking at your Organic System Plan (OSP) with a fine-toothed comb! They will be looking at your cottonseed information, at your field and field locations, at every record you submitted to determine if there is anything that might have caused a “voluntary” versus “involuntary” contamination. You will probably know that something is up either by just a notice of an investigation or possibly a full-blown visit. Either way, they (your certifier) are trying to find out why the raw seed cotton is showing up with detectable levels of GMO.

Most of the time there is absolutely nothing you did to cause a detectable limit of GMO in your seed cotton. We might call this an “Act of God” because no one knows why it happens. The planting seed tested good, the field was good and there is no drift. No one knows what happened or why and so you get a clean bill of health. The system is designed with some flexibility because there can be an “Act of God” and to be honest I am glad to recognize that God is Sovereign even over cotton fields and cotton farmers!

On the other hand, it can sometimes be identified as a wrong bag of planting seed picked up, a wrong module or bale marking, or some other contamination issue along the way. Elevated levels of GMO in your raw seed cotton will throw up all kinds of red flags and could lead to a non-compliance, rejected organic cotton and a microscopic look at all other aspects of your organic operation! Let’s hope we don’t go there……

What Can Farmers Do?

Test early and often. If you suspect contamination, conduct your own tests before sending cotton to market. Newsletter Article Page 2
Maintain strong records. Prove that you sourced verified non-GMO seed and followed organic protocols.
Work with a certifier who understands the realities of farming. Some certifiers are more flexible in their investigations than others or ask the right questions instead of just assuming you are wrong.
Improve segregation. Make sure that cotton stays separate at every stage, from harvesting to ginning.

Final Thoughts

Organic farmers face an uphill battle when it comes to avoiding GMO contamination. Even with perfect compliance, your cotton test results can find GMOs, and certification decisions often depend on factors beyond the farmer’s control. Don’t panic and be willing to go the extra mile to find out why. Your organic certifier has their neck on the line too as does your ginner and we all want you to succeed. As we are at the very start of a new crop year do all you can now to stay out of this “mess” later!

Addressing the Challenges of Organic Cotton Seed

As the Extension Organic Specialist with Texas A&M AgriLife Extension Service, I work closely with organic cotton farmers to navigate the complexities of maintaining organic certification. Recently, issues surrounding the sourcing and certification of organic cotton seed have come to the forefront, particularly with the influx of imported planting seed from other countries. This situation is compounded by the stringent requirements of the Global Organic Textile Standard (GOTS) and potential conflicts in international trade.

Key Issues with GOTS and Organic Cotton Seed

Contamination Risks

GOTS certifies cotton fiber from the gin facility to the mill but does not extend this certification back to planting cotton seed. This poses a significant risk for farmers, as even with rigorous adherence to organic practices, their crops can become contaminated through cross-pollination, especially in regions like the cotton belt where GMO crops are prevalent. Contamination, detected in seed cotton samples at the gin before ginning (raw cotton from the farm), can lead to farmers being excluded from organic certification for up to five years, creating severe economic and operational challenges.

Lack of Standardized GMO Thresholds

Currently, GOTS does not establish a GMO contamination threshold for cotton seed, which complicates the situation for organic cotton farmers. While many USA cotton seed companies work to maintain low levels of GMO contamination (usually below 5%), GOTS demands strict purity in the final product. This standard requires seed cotton (seed, leaves, stems) testing because it is the only part of the cotton plant containing DNA, where contamination can be detected. However, this rigid approach does not fully account for the post-planting natural cross-pollination risks that farmers face, such as GMO pollen carried by insects into organic fields. This discrepancy between the ideal purity GOTS seeks and the realities of farming highlights the need for a practical and fair standard that supports organic farmers without penalizing them for uncontrollable factors.

To address these challenges, a multi-faceted approach involving key industry stakeholders is essential. Here’s how we can move forward:

1. Establishing a Fair GMO Contamination Standard:

Implementing a reasonable GMO contamination threshold for planting cotton seed would significantly alleviate the testing burden on farmers and prevent unjust penalties. This standard should be recognized and enforced by all organic certification bodies, including GOTS. If the plants grown from this approved cotton seed are tested and not the seed cotton at the gin the farmer would be protected from the natural potential of seed contamination.

2. Enhanced Collaboration Among Industry Stakeholders:

Seek advice and input from the industry, including farmers, Extension specialists, researchers, ginners, and manufacturers, to determine acceptable thresholds and protocols based on constraints faced by each group. This collaborative approach ensures that the standards are practical and attainable. We, here in Texas, represent the largest cotton production area in the world and want to be involved in this process.

3. Advocating for Policy Changes:

Engaging with policymakers and certifiers to establish upfront certification for cotton seed would ensure farmers have a clear understanding of the seed quality they are purchasing. Specific policies might include establishing minimum GMO thresholds and clear guidelines for contamination levels, mitigating risks, and supporting farmers in maintaining their organic certification. With upfront testing by seed companies and certifications from USDA, gins could operate more confidently, alleviating the burden not only on farmers but also on the ginning facilities themselves.

Addressing Import Issues

The reliance on non-GMO cottonseed imported from other countries, while possibly beneficial in the short run, introduces additional complications. Political and economic instability can disrupt supply chains, and without stringent testing, the risk of unintended contamination remains. Developing robust testing protocols, such as frequent sampling and standardized testing methods, for all imported seed is crucial to ensure they meet the same standards required domestically. It will also create a more transparent, open and balanced business environment for all.

Conclusion

The path to resolving these issues is through collaboration, standardization, and proactive policymaking. By working together, we can create a fair and sustainable environment for organic cotton farmers, ensuring their efforts are recognized and supported throughout the supply chain.