Impact of USDA Regulations on the Use of Genetically Modified Plants as Biofuel Feedstocks (Part 2)

The previous entry of this blog listed the various permit applications and notifications that the U.S. Department of Agriculture (USDA) has received for the field use of genetically engineered plants and trees intended for use as biofuel feedstocks. These field test requests have been reviewed by the Biotechnology Regulatory Service (BRS) division of USDA’s Animal and Plant Health Inspection Service (APHIS) under USDA’s biotechnology regulations, found in 7 CFR Part 340 of the Code of Federal Regulations. In this entry, I’ll discuss the issues that have arisen in USDA’s review of those requests, particularly two applications from Arborgen and Syngenta requesting approval for activities beyond small-scale research,  and their possible implications for future applicants, and I’ll also make some general comments about the impact of the USDA regulations on development of transgenic biofuel feedstocks. 

Although the need to submit notifications or obtain permits from USDA can be seen as one more hurdle to be surmounted in the development of improved biofuel feedstocks, in reality the biotech regulation poses only a minor regulatory barrier at the early stages of product development. Agbiotech and seed companies have been living under this regulation for over 20 years, and they have found USDA APHIS easy to deal with, and that the agency’s Biotechnology Regulatory Services branch applies sound scientific principles to its review of notifications and permit applications. Many observers consider the USDA regulatory regime to be one of the reasons why the agricultural biotechnology industry has ultimately been successful in introducing into U.S. agricultural markets transgenic seeds for improved varieties of many important crop species, in that the regulations provided a predictable, scientifically-sound path to approvals of field tests and commercial use of engineered plants. 

That being said, the presence of the regulations does impose an added requirement on developers of transgenic energy crops that is not borne by companies using classical plant breeding or other traditional techniques to improve biofuel feedstocks. Notifications need to be submitted 30 days in advance of any planned outdoor planting of a transgenic plant, regardless of the size of the field plot, and permit applications must be submitted 120 days in advance (although in recent practice USDA has been approving many permit applications far quicker than this stated timeframe).  Although notifications require only a minimal amount of information, permit applications require compilation and submission of considerable data and information about the make-up of the plants to be tested, the size and location of the test plot and the procedures to be followed in the test, and consideration of the potential environmental impacts of the test. In addition, it is likely that, for the earliest field tests of any given transgenic variety, it will be necessary to prevent or control the release of pollen from the engineered plants, and possibly to ensure that the test plot is sufficiently isolated from growing regions of the same species as to make unwanted horizontal gene flow unlikely. Once a given variety has been used in the field after successfully navigating the regulatory process, not only will approval of subsequent permit applications become easier, but it should also be easier to prepare permit applications, since much of the needed information will already be in hand from the earlier applications. 

With the exception of familiar species such as corn and others, it is likely that most engineered biofuel crops will require permits for outdoor testing, rather than be allowed to proceed under notifications. Changes may come if USDA eventually issues new regulations based on the proposed revised rule that was published in 2008. Under that new proposal, notifications would be abolished in favor of a multi-tiered permit scheme, and presumably those field tests that qualified for notifications in the past would be subject to the least-stringent of the different tiers of permits. The impact of this change on transgenic energy crops is not clear, but given USDA’s interest in seeing “nontraditional” (e.g. industrial or pharmaceutical) uses of transgenic plants handled under permits rather than notifications, it may turn out that field uses of engineered energy crops will require one of the more stringent levels of permit. 

Although small-scale research field tests are more or less routinely reviewed and approved, the same may not be true of expanded field use, and is certainly not true when companies need to seek approvals for unlimited commercial use and sale of a given variety. The recent experiences of Arborgen, in its applications for large-scale testing of transgenic Eucalyptus, and Syngenta, in its petition to delist (i.e. deregulate) its amylase-expressing corn, may give some indication of what companies may face, particularly in the early days when USDA is still gaining familiarity with whatever issues may need to be addressed for the widespread use of transgenic energy crops. 

As described in the previous entry of this blog, Arborgen is a leading forestry biotechnology company that has been developing improved hardwood trees for use as energy crops, and which has received many APHIS permits for small-scale field tests of transgenic Eucalyptus engineered for this purpose. USDA’s recent decision to grant two particular ArborGen permit applications involved the company’s request to continue research on transgenic Eucalyptus trees that had already been planted at over two dozen sites under a prior APHIS permit (Number 08-039-102rm), to allow the planting of additional trees and to allow the transgenic Eucalyptus trees to flower at the various field site locations. These plants are a clone known as EH1 that was derived from a hybrid of Eucalyptus grandis x Eucalyptus urophylla and which have been genetically engineered with different constructs. The purpose of the these field tests is for ArborGen to assess the effectiveness over several years of growth of gene constructs which are intended to confer cold tolerance; to test the efficacy of a gene introduced to alter lignin biosynthesis; and to test the efficacy of a gene designed to alter fertility. This latter gene, barnase, is expressed to create male sterility, in order to limit possible gene flow from the transgenic trees. 

What distinguished these two permit applications from the many others that Arborgen has received over the years was the request to allow large numbers of the engineered trees to flower without the need for measures to restrict or prevent flowering. In most small-scale field trials of transgenic plants, it is necessary for the applicant to propose measures to prevent pollen set and/or flowering of the experimental plants, so as to prevent outcrossing and gene flow to native plants of the same or related species. Field trials of new varieties of trees usually need to be conducted over multiple years, and in order to accurately assess the performance of the trees over time, they must be permitted to maintain their normal lifestyle, which would include flowering, and so this request was a necessary step in Arborgen’s commercialization process. But because the request entailed allowing a large number of trees to flower at multiple field sites, APHIS decided to perform a full Environmental Assessment (EA) before deciding whether to issue the permits.  On June 3, 2009 APHIS announced the availability of a draft EA for public review and comment, but then on January 19, 2010 the Agency announced the availability of an amended EA that included consideration of one previously-unavailable document, at which time the review and comment period was extended until  February 18, 2010. In its decision on May 12, 2010 to grant the permits, APHIS made the final Environmental Assessment available to the public. 

The EA considered a broad range of potential issues and potential environmental impacts of the test, including those listed in the Table below. In spite of the male sterility engineered into the trees, the EA discussed the possibility for gene flow via pollen spreading from the trees, but concluded this was unlikely, given the male sterility of the trees, the expected limited range of pollen from  Eucalyptus, a tree which is ordinarily pollinated by insects rather than wind, and the fact that there are no native species of Eucalyptus in the United States and no established E. grandis populations in any location close to the proposed field tests. It seems clear that the chief concern, and the reason for compiling the EA before granting the permits, was the need to fully review the impact of allowing such a large number of trees to flower. Although this addresses a legitimate environmental issue, and it is certainly wise for other developers of engineered trees as biofuel feedstocks to consider this issue for their own activities, I’d stress that this concern is somewhat unique to perennial species, particularly trees, that will need to be grown over several years to reach maturity before harvesting for fuel use. For those energy crops that would be sown, grown and harvested during a single growing season (the way food crops and other agricultural commodities are typically grown), the issue of flowering over a multiple year lifespan may be less relevant, or even irrelevant. However, other issues may arise for annual species, especially food crops, used for biofuel production, as we’ll see in the Syngenta story. 

Table 1. Select Issues Considered in Arborgen Environmental Assessment. (Source: USDA Environmental Assessment)

  • Alteration in Susceptibility to Disease or Insects – Potential of the Eucalyptus to Harbor Plant Pests
  • Expression of the Gene Products, New Enzymes, or Changes to Plant Metabolism – Risk of the Gene Products on the Environment
  • Alteration in Weediness characteristics – Potential of the Engineered Eucalyptus to be Invasive
  • Possibility of Gene Flow Within the Field Test
  • Possibility of Gene Flow Outside of the Field Test
  • Possibility of Vegetative Propagation / Persistence Outside of the Field Test
  • Potential of the Eucalyptus in the Field Tests to Become an Invasive Species that Threatens Native Plant and Animal Communities
  • Transfer of Genetic Information to Organisms with which it Cannot Interbreed – Horizontal Gene Transfer to Other Organisms
  • Risks to Threatened and Endangered Species

As described in the previous entry, in 2005 Syngenta Seeds, a major multinational seed and agbiotech company, submitted a petition asking USDA for a determination of “nonregulated status” for a corn variety (known as “Event 3272”) genetically engineered to produce a microbial amylase enzyme that facilitates ethanol production by enhancing starch degradation in the preprocessing step. In this petition, Syngenta requested that APHIS make a determination that these corn plants should no longer be considered regulated articles under 7 CFR part 340. This petition process is the route under the regulations by which transgenic plants have been reviewed and cleared for widespread commercial use, and as of this writing, APHIS has approved 78 such “delisting” petitions for commercialization of engineered crop varieties. However, because Syngenta’s request would have led to the first determination of “nonregulated status” for an industrial use of a transgenic plant variety, APHIS conducted its review very carefully, and decided to prepare an Environmental Assessment before announcing its decision on the petition. 

APHIS published a notice in the Federal Register on November 19, 2008 announcing the availability of the Syngenta petition and a draft environmental assessment for public comment. APHIS solicited comments on the petition, on whether the engineered corn is likely to pose a plant pest risk, and on the draft EA. APHIS received over 13,000 comments on the petition, the draft EA, and the plant pest risk assessment by the close of the 60-day comment period, which ended on January 20, 2009, and in response to these comments, APHIS extended the comment period until July 6, 2009.  As of this writing APHIS has not announced any further decision on this petition. 

The EA itself addressed issues such as those shown in Table 2.  However, as explained in the June 4, 2009 Federal Register notice extending the comment period, there were several issues raised by commenters that APHIS felt justified further review. One issue was the appropriateness of the Agency’s determination that the amylase-expressing corn was not a plant pest – several comments argued that the alpha-amylase enzyme engineered into Event 3272 corn may cause damage (degradation of corn starch products) to manufactured or processed plant products if Event 3272 corn became inadvertently included in the manufacturing and processing of corn starch products. The commenters claimed that this type of damage comes within the definition of a plant pest (a position with which APHIS disagrees). Some of the commenters were also concerned about what they felt were specific food safety concerns, such as the potential for Event 3272 corn to be allergenic, as well as concerns surrounding the potential economic and manufacturing issues if Event 3272 corn were to become present in corn wet-milling processes. Comments were also received questioning the appropriateness for U.S. energy policy of using corn to produce ethanol, an issue with APHIS determined was outside their purview under the regulations. 

Table 2. Select Issues Considered in Syngenta Environmental Assessment. (Source: USDA Draft Environmental Assessment)

Management Considerations:

  • Corn Production
  • Cropping Practices
  • Impact to Other Specialty Corn Products
  • Ethanol Production

Public Health Considerations

  • Human Health
  • Worker Safety

Environmental Considerations

  • Gene Movement (Pollen flow)
  • Water Use in Ethanol Production
  • Effects on Animals
  • Effects on Plants
  • Effects on Soil

In my view, the major issues that USDA has faced in this review have all had to do with the fact that corn is a food crop. Some of the negative comments from the public have focused on the usual “food vs. fuel” arguments, with the commenters maintaining that it is not in the best interests of the U.S. to produce ethanol from a plant species that is so important for the nation’s and the world’s food supply. But other comments on the draft EA have followed familiar lines as has been seen in other applications for commercial use of engineered agricultural crops, including concerns over what is called “adventitious presence”.  This term refers to the inadvertent mixing of trace amounts of one type of seed, grain or food product with another, particularly when the first type of seed or grain is a genetically engineered plant or plant product. Many transgenic plant products are intended for a specialized use and often must be grown, harvested and transported separately from other varieties of the same species; in some cases the segregation is required because the transgenic variety has not been approved for food use. Although the harvested crop is segregated, some observers are concerned that the transgenic plant material could be accidentally mixed with nontransgenic material, or that nontransgenic corn could acquire the transgene through pollen-mediated gene flow. Some members of the public are concerned about the potential for such commingling and concerned that this could lead to contamination of the food supply with materials not approved for food use. This is an issue that has been known to agbiotech and seed companies for many years, and although the actual risks from low levels of commingling are likely to be minimal, strategies have been developed to isolate transgenic crops by a suitable distance from growing regions of nonmodified plants, to ensure segregation of harvested grain or seed, and also to reliably test food products for such inadvertent mixing. Although these issues were all addressed in the Draft EA, it may be that such issues have been the major reason Syngenta has not received its U.S. approval for commercial sale of Event 3272 corn. 

It is somewhat troublesome to the industry to think that this application, the first that would allow commercial sale and widespread production of a transgenic plant for a biofuel purpose, has been pending for almost 5 years without resolution. However, it has been a fairly consistent (although bothersome) trend in the history of biotechnology regulation that the earliest application(s) of any given type have taken far longer to approve than would become the norm for later applications. So to some extent, a lengthy review for the Syngenta petition was almost inevitable, and one can expect subsequent reviews to be quicker and more efficient. 

In addition, I think that many of the issues being considered in USDA’s review of the Syngenta petition are specific to any proposed use of a food crop, particularly one as economically important as corn, for an industrial purpose. Today, corn is the most abundant and most cost-effective feedstock for ethanol production in the U.S., but  most of the ethanol and biofuels industry see corn as a transition to “advanced biofuels” produced from cellulosic feedstocks and other non-food-use crops such as specialty grasses or trees. And so, while proposed commercial use of feedstocks like transgenic switchgrass, Jatropha or poplar would certainly require careful consideration of the possible environmental impacts, such proposals would most likely not engender any concerns over commingling, adventitious presence, or the alleged “contamination” of the food supply, and this alone could make agency review of the applications far more straightforward.   

Are there lessons that the industry can draw from this small (N=2) sample of lengthy regulatory reviews for expanded uses of transgenic biofuel species? I think there are, although some are fairly obvious and not at all surprising. For example: 

  • The earliest proposals under any relatively new regulation will always face the toughest scrutiny and, at least in the biotech world, often will undergo inordinately long review. However obvious this may be, it does argue that the companies that hope to be next in line behind Arborgen and Syngenta plan their proposals carefully, and devote sufficient attention to presubmission meetings and discussions with USDA APHIS staff (something that is always recommended for regulatory submissions of any kind).
  • The issues that have likely led to the length of these reviews were ones that could be predicted, yet are ones that might not affect every transgenic biofuel proposal. The concern in the Arborgen proposal about allowing large numbers of transgenic trees to flower at multiple locations would likely be applicable only to those energy crop species where multiple years of growth would be needed before the plants could be harvested for fuel use, and even for those crops, concern over this issue is likely to abate as more experience is gained with the field use of these transgenic species. And the concerns in the Syngenta review are likely to mostly be specific to the use of a food crop in biofuel production, and most other proposed transgenic biofuel crops would not need to address such issues.
  • Finally, although the nearly 25 years of experience we’ve had with the growth of transgenic plants in the open field, including tens of thousands of field tests worldwide, have made the regulatory path for small-scale testing quite straightforward, the same is not true for applications that go beyond limited-scale field tests. Some of these proposals do in fact pose environmental issues that regulatory agencies still must contend with, but these larger-scale proposals betray the fact that the small but vocal group of biotech opponents have not gone away, and in some places (like Europe) their impact is felt beyond their numbers, especially with regard to engineering of any food crop. Biofuel companies should count on the fact that there will always be opponents to any proposed large-scale or commercial use of transgenic plants, even for projects with clear environmental benefits or that address public policy imperatives. Although the concerns raised by such critics should not, in the end, be sufficient to derail any well-planned proposal, companies do need to take these concerns seriously and plan accordingly. 

D. Glass Associates, Inc. is a consulting company specializing in several fields of biotechnology. David Glass, Ph.D. is a veteran of nearly thirty years in the biotech industry, with expertise in industrial biotechnology regulatory affairs, patents, technology licensing, and market and technology assessments. This blog provides back-up and expanded content to complement a presentation Dr. Glass made at the EUEC 2010 conference on February 2, 2010 entitled “Prospects for the Use of Genetic Engineering in Biofuel Production.” The slides from that presentation, along with more information on D. Glass Associates’ regulatory affairs consulting capabilities, are available at or at

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  1. Bio-engineered trees tested | Technology Reviews

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