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

GMO detection in organic cotton does not automatically mean a farmer intentionally used genetically modified seed. This article explains how cotton is tested, what laboratory results mean, how GOTS and organic certifiers investigate positive findings, and what farmers can do to document compliance and reduce contamination risk.

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!

A young man in overalls holds a cotton flower and a test tube in a cotton field, with an older man in a lab coat observing samples at a table labeled 'Organic Cotton' in the background.

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.

Table of Contents (just click a title)

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.¹ 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!
GMO laboratories may report analytical limits of detection (LOD) or quantification (LOQ), and some test reports provide estimated percentages for individual genetic markers. These laboratory reporting limits should not be confused with a USDA organic tolerance or allowable GMO percentage. USDA organic regulations do not establish a numerical GMO tolerance for organic crops.

The material being tested matters. Seed and seed cotton contain abundant biological material suitable for DNA analysis, while mature lint presents greater analytical limitations; consequently, a positive screening result must be interpreted in light of both the sample material and the testing method.

Report of Analysis from OMIC USA Inc., detailing the results of a real-time TaqMan PCR test for various genetic markers, including detected and not detected GM-elements.

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Here is another test with some different results.

Supplementary report of analysis from OMIC USA Inc., detailing results of a real-time TaqMan PCR test for various genetic elements in a cotton sample, including detection levels and quantification limits.

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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.
Detection of these GMO markers would likely trigger additional investigation and could affect acceptance of the cotton into a GOTS or other private textile supply chain. The result alone, however, does not establish that the producer violated USDA organic requirements.
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

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A Positive GMO Test Does Not Automatically Mean an Organic Violation

USDA organic certification is a process-based standard, not a zero-tolerance GMO standard. Genetic engineering is an excluded method and cannot be intentionally used in organic production. However, USDA National Organic Program Policy Memo 11-13 makes an important distinction between the intentional use of genetically engineered material and its inadvertent presence.² When an organic producer has used appropriate non-GMO planting seed, followed the approved Organic System Plan, and implemented reasonable measures to prevent contact with GMOs, the detection of GMO material does not by itself establish a violation of USDA organic requirements.

This distinction is especially important with cotton. A qualitative GMO screening test can establish that GM-associated DNA was detected in the sample, but that result alone does not establish how the material got there. Potential sources can include the planting seed, pollen-mediated gene flow, post-harvest mixing, transportation or storage, and commingling during ginning. The appropriate response to a positive result is therefore trace-back and investigation—not an automatic assumption that the farmer planted GMO cotton.

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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 circumstances and possible source should be investigated, including seed documentation, production practices, segregation and potential commingling.
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.

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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……

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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!

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References

Organic Cotton Accelerator. 2024. Standard Operating Procedure for GMO Sampling and Testing. Organic Cotton Accelerator. ↩︎
USDA National Organic Program. 2011. “Policy Memo 11-13: Genetically Modified Organisms.” Agricultural Marketing Service, U.S. Department of Agriculture. ↩︎

Addressing the Challenges of Organic Cotton Seed

Organic cotton growers face unique risks when planting seed contains unintended GMO material or when contamination is detected later in the supply chain. This article examines seed quality, testing, GOTS requirements, imported seed and the need for clearer, fairer protocols for organic cotton producers.

Updated October 2026: This article has been revised to clarify that GMO detection in cotton does not by itself establish the source, cause, intent, or percentage of GMO cotton present. Organic and textile certification decisions depend on investigation, documentation, traceability, sampling protocols, and compliance with applicable standards.

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 complicated by Global Organic Textile Standard (GOTS) requirements, differences in testing and interpretation, and the growing use of imported planting seed.

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. A positive GMO screening result can jeopardize acceptance of cotton into a particular textile supply chain and can trigger additional investigation. However, under USDA organic policy, inadvertent GMO presence does not by itself establish that the producer used an excluded method or violated organic certification requirements. Upstream seed testing is not an untested concept. Organic Cotton Accelerator protocols already recognize planting-seed testing before distribution as an important GMO control point.¹ Expanding that principle could give U.S. organic producers stronger documentation that the crop began with verified non-GMO planting material.

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 U.S. cotton seed companies may use internal quality-control standards to limit unintended GMO presence, GOTS does not establish a numeric GMO threshold for cotton. This creates uncertainty when a positive screening result is detected later in the textile supply chain. DNA-based GMO testing is most straightforward when biological material containing recoverable DNA is available, particularly planting seed and seed cotton. Mature cotton lint presents greater analytical limitations. Current testing protocols can screen cotton materials for GM-associated DNA, but a positive qualitative result does not by itself establish the percentage, source, or cause of GMO presence. This is particularly important in cotton-growing regions where organic and GMO cotton are produced in close proximity. Pollen movement, harvesting equipment, module handling, transportation, storage, and ginning all represent possible points where unintended GMO material may enter the supply chain. For that reason, the organic cotton industry needs standardized sampling procedures, laboratory methods, reporting practices, and interpretation guidelines that distinguish intentional use of excluded methods from inadvertent presence.

To address these challenges

A multi-faceted approach involving key industry stakeholders is essential. Here’s how we can move forward:

Establish Clear Planting-Seed Testing and Acceptance Standards

The organic cotton industry would benefit from a clearly defined planting-seed testing protocol that specifies sampling procedures, laboratory methods, reporting limits, and how results are interpreted. If numeric acceptance criteria are used, they should be scientifically justified, transparent, and applied consistently.

Improve Traceability Throughout the Supply Chain

Farmers, seed companies, ginners, certifiers, laboratories, textile manufacturers, researchers, and Extension specialists should work together to identify critical control points where unintended GMO material may enter the system. Clear documentation at each stage—from planting seed through harvest, transport, storage, ginning, and textile processing—would make investigations more meaningful and help determine where a problem may have occurred.

Develop Fair and Scientifically Defensible Interpretation Policies

Certification and textile programs should distinguish between intentional use of excluded methods and inadvertent GMO presence. Decisions should consider sampling methods, laboratory limitations, traceability records, seed documentation, and possible contamination pathways rather than relying on a single positive screening result alone. Upfront planting-seed testing could provide farmers and gins with stronger documentation and greater confidence throughout the supply chain.

Addressing Import Issues

The reliance on non-GMO cotton planting seed imported from other countries can help address seed availability, but it also introduces additional supply-chain and quality-control considerations. Imported planting seed should be subject to testing and documentation requirements comparable to those expected of domestically produced non-GMO seed. Standardized sampling, laboratory methods, and reporting would improve transparency, reduce uncertainty for growers and buyers, and help create a more consistent standard regardless of seed origin.

Conclusion

The organic cotton industry needs a system that protects organic integrity without holding farmers responsible for contamination pathways they cannot fully control. Standardized planting-seed testing, better traceability, consistent laboratory interpretation, and fair investigation procedures would strengthen confidence from the farm through the textile supply chain.

Organic Cotton Accelerator. 2024. Standard Operating Procedure for GMO Sampling and Testing. Organic Cotton Accelerator. ↩︎