Comments on proposed revisions to USDA regulations -

7 C.F.R. PART 340

Environmental Impact Statement; Introduction of Genetically Engineered Organisms

Docket No. 03-031-2

Regulatory Analysis and Development

PPD, APHIS, Station 3C71

4700 River Road, Unit 118

Riverdale, Md. 20737-1238

Prepared by

Steven H. Strauss, Professor

Department of Forest Science

Oregon State University

Corvallis, OR 97331-5752 USA

Scott Merkle, Professor

School of Forest Resources

University of Georgia

Athens, GA 30602

Wayne Parrott

Department of Crop and Soil Sciences

University of Georgia

Athens, GA 30602

Co-signers are listed following the References

At issue is whether current regulations should be revised, and we believe they should. With respect to the question of the two "broad alternatives for study" in the EIS (p. 4), we strongly recommend against the alternative of "no change in the existing regulations." Although we believe that the previous regulatory system worked well for the first generation of biotech crops, it needs to be updated to reflect the knowledge and experience acquired over the past decade. In particular, we believe that the current regulatory system needlessly encumbers many kinds of GE research and commercial development with very low risk products, and that more discrimination is needed within the plant-made pharmaceutical and industrial feedstock crops (PMP/PMIPs). We applaud APHIS for its continuing efforts to update and customize its regulations in the light of its experiences and new knowledge and technology. Our goal with the comments is to propose a set of scientifically based regulations that protect health and the environment without undue burdens to research and development of transgenic crops.

Guiding Principles

1. Regulate scientifically valid risks, not perceived or precautionary risks. We recognize that different groups may regard the process of GE from fundamentally different ethical viewpoints, and may thus wish to impose regulations based on these beliefs rather than on consideration of the scientific benefits and risks of GE crops. However, numerous scientific panels have clearly stated that such a position is in fundamental disagreement with actual benefit and risk analyses. Two major National Research Council (1989, 2002) reports have stated that the product, not the process, is the main determinant of the benefits and safety of new crop varieties, and that traditional crop breeding, with its advanced methods of hybridization and many other methods, impose many of the same risks, and to the same degree, as GE crops. As such, risks are associated with the trait, not the process. Given nearly ten years of experience, a key goal of new APHIS regulations must be a focus on the scientific issues, not the method. GE crops that are similar in genes and/or traits modified should be treated the same as conventionally bred crops. If there is no novel risk, novel regulations are not warranted.

2. Regulation must be proportional to the risk involved, and risks should be considered in perspective. Science does not deliver certainty, but provides facts and defines paradigms to guide regulatory decision making. To assess whether certain kinds of GE crops warrant regulation, it is therefore essential to consider the level of uncertainty and risk in comparison to other common risks. A risk in one area may be cancelled out by lowered risks in other areas. For example, it is becoming increasingly clear that interspecific hybridization and related consequences of basic agricultural practice (breeding, use of exotic organisms, disturbance of environments to create new niches), can lead to new species or populations with novel forms of biotic and abiotic stress tolerances, and that these new forms can act as weeds of crops (e.g., Ellstrand 2003). For GE ecological risks to merit regulation, we expect that GE risks would need to be clearly higher than these documented, ongoing, and widespread risks that are inherent to agriculture. In addition, a new risk in one area may be cancelled out by lowered risks in other areas.

3. Conventional breeding and genomic diversity should be the reference point. Conventional plant breeding is essentially unregulated throughout the world, and has a history of predominant safety and effectiveness. It therefore has overwhelming social approval; there have been no significant calls to begin to regulate all new plant varieties for species under cultivation. Conventional breeding should therefore be the context for evaluating GE crop varieties. Where toxicological and environmental uncertainties fall within the realm of conventional breeding with its many variations (e.g., inter-species hybrids, mutagenesis, inbreeding, wild species crosses, cloning), similar kinds of principles should be followed for GE crops. Variation in regulation or structure of native (or functionally homologous) genes, or changes in gene/chromosome structure (e.g., duplications, deletions), are all common within and among wild relatives used in breeding programs. GE induced changes of this kind should therefore be exempt from regulation, or regulated at a lower level of scrutiny in those cases where new traits have the potential for tangible agronomic or toxicological impacts (e.g., novel types of herbicide tolerance that promote some forms of herbicide use or produce unusually high levels of native toxins that greatly exceed those in sexually accessible wild relatives. Note that our concern with GE herbicide-tolerant crops arises from the possible new uses of the agricultural chemicals in question, and not necessarily with the technological provenance of the plant itself).

In the end, the complexity and dynamism of plant genomes suggests that regulation of GE for alterations in genome structure and native expression are not warranted. Aside from the type of transgene used, the magnitude of GE change should be larger than naturally occurring changes to merit regulations that affect changes in DNA per se. The extensive variation in plant genomes in the absence of GE has been well documented in recent years. A summary of these is presented in Appendix I.

Responses to Specific Questions

The following information is intended to provide insights and direction for responding to the list of questions posed by APHIS.

1. Broadening regulatory scope beyond GE organisms that may pose plant pest risk to include GE plants that may pose noxious weed risks and GE organisms used for biocontrol. Do regulatory requirements for these organisms need to be established? What environmental considerations should influence this change in regulatory scope.


    Current field-testing and deregulation procedures, which include assessment for plant pest and weediness potential, have been sufficient to date.

    There is no scientific justification to a priori consider GE plants to have noxious weed potential, unless a transgene moves into a noxious weed species by crossing, e.g. herbicide tolerance moving from cultivated rice to red rice, which is a noxious weed

    Evidence shows that weediness is not controlled by single genes in nature (Gressel 2002; Hancock 2003) and that transgenes integrated into crop plants would be accompanied by linkage of crop genes as transgenes are putatively introgressed into wild relatives (Stewart et al 2003).

    As presented in this proposal, there is a problem with the definition provided for noxious weeds. They provide the definition from the Plant Protection Act, but omit the fact that not all weeds are noxious. Noxious weeds are a separate category listed under 7 CFR 360, found at

    In the absence of evidence that single genes have high potential to convert a weed or a crop into a noxious weed, regulatory oversight should not be broadened to include noxious weeds.

2. Defining specific risk-based categories for field testing that may include a) low risk products b) products with some or unknown noxious weed risk, sequences of unknown phenotypic function, containing a new unapproved PIP, and c) PMPs/PMIPs not intended for food/feed. What environmental factors should be considered in further delineating such requirements? What criteria should be used to establish the risk-based categories? Should certain low-risk categories be considered for exemption from permitting requirements? If so, what criteria should apply?


    We seek regulations that treat classes of GE organisms very differently based on the extent of familiarity with traits and gene functions, rather than the method of introduction or the life-form of the plant (i.e., annual vs. perennial crops, trees vs herbaceous plants). We believe that strict case-by-case consideration of every new GE crop defers important policy decisions that could be made for large classes of crops and traits. The establishment of classes based on scientific criteria (e.g., Strauss 2003a) would promote efficiency by enabling companies and regulators to focus on important issues associated with new traits, not the method of genetic change or unimportant linked genes or sequences.


    Below we suggest three specific classes based on scientific considerations for basic risk assignments (Strauss 2003b).


a.High risk Careful regulation of high-risk PMP/PMIP plants during field tests and commercial production where their transgene products that have a documented likelihood to cause significant harm to humans or the environment. Plants with a high ability to accumulate heavy metals or other environmental toxins might also be placed in this category, if their release could present a hazard for herbivores or their prey.


b.Moderate risk Relaxed but continued oversight for PMP/PMIP plants with novel products that have very low human and environmental toxicity, or are grown in non-food crops and have low non-target ecological effects (including, we expect, most plants used for phytoremediation). Continued oversight is also appropriate for plants with novel pest management traits such as herbicide tolerance and heterologous pest resistance genes. The moderate category should not be viewed as a permanent status, and transgenic varieties in this moderate risk class should be transferred to the high or the low risk category after a specific time period where ecological and/or toxicological studies have been carried out, as discussed below.


c. Low risk Exemptions or reduced regulatory oversight of low-risk GE organisms are warranted during field testing and commercial use where the imparted traits are functionally equivalent to those manipulated in conventional breeding, and where there are no novel biochemical or enzymatic functions imparted. In short, where GE brings about directed changes in expression of functionally homologous genes to achieve a commercially useful trait ("genomics-guided transgenes" according to Strauss 2003b). Where scientific considerations suggest that the modified traits are likely to be "domesticating" and thus retard spread into wild populations (e.g., sterility, dwarfism, seed retention, modified lignin), we believe that exemptions are warranted at the field-testing stage, and in most cases at the commercialization stage (assuming domestication genes do not directly impact endangered or threatened species). For cases where there is ambiguity, exemptions granted at the field-testing stage could be re-reviewed prior to commercial deregulation.


          To summarize factors to consider when assessing risk category should be:

                  a) Familiarity and nature of the trait

                  b) Functional homology of the genes employed to impart the new trait

c) Scale of the field trial or release, with widely grown crops and large field trials getting greater scrutiny (further discussion below)

d) Location of the field release; location matters. (e.g., corn in the middle of a cotton field in California should be treated differently than corn in the Midwest).


          Even within a given species, genomes are extremely fluid, and naturally contain many sequences of unknown function that are generated during normal breeding, mutation, and genome evolution (discussed further below). Similar kinds of sequences may be generated during transgene integration or transferred (e.g., from vector backbone DNA), during the process of GE and do not warrant regulation.

3. What environmental factors should be considered in distinguishing between these kinds of decisions? (i.e., Regulatory flexibility for commercialization of both unrestricted and continued regulatory oversight based on "minor unresolved risks.")


    Phenotypes– that is, traits, and their safety and behavior in the environment, not the method used to produce them, should be the main focus of regulation. This principle has been stated in National Research Council reports (1989, 2002), but has yet to be clearly translated into regulatory practice. GE can often produce very similar kinds of traits to conventional breeding, but using different mechanisms (e.g., increased pest resistance via up-regulation of an endogenous gene). In fact, because the mechanisms underlying conventional breeding, including complex genomic changes that can accompany hybridization (e.g., gene silencing via methylation, and chromosomal deletions and rearrangements) are generally not evaluated, they cannot be scrutinized to the same level as GE plants. Thus, it is likely that GE actually enables more precise risk consideration compared to conventional breeding, warranting similar or less, rather than more, regulation.

Environmental and toxicological issues will often be most strongly influenced by the trait rather than the genes, particularly as DNA and most encoded enzymes do not appear to pose threats. Examples of traits that are common both in conventional and GE programs include dwarfism, sterility, and altered chemical composition to favor industrial processing. Often, these traits "domesticate" (i.e., they add value but impair fitness in the wild). Where there is a strong theoretical reason, or data, to suggest that a trait will be neutral or domesticating, especially where wild non-GE populations are prevalent (discussed below), it should be exempt from regulation (Strauss 2003b). Sterile, dwarf, and low/weak lignin varieties are familiar examples. The recent NRC report on bioconfinement (2004) found that many GE traits will require no confinement; we believe that transgenes for domestication traits in plants are good examples of those where confinement is unwarranted for most species and geographies.


    Regulations should recognize the powerful buffering effect from extensive wild and cultivated non-GE populations that exist for many plants with extensive wild or cultivated relatives. In contrast to most annual agricultural crops, there are often extensive populations of wild relatives of some plant species that are grown in the USA. Examples include many grasses, berries, some orchard trees, and virtually all forest trees. These populations that act as reservoirs for gene flow, and for biological diversity (i.e., species that are ecologically dependent on the plants for food or habitat). Furthermore, a transgenic recipient will have to be competitive amongst wild genotypes that have had eons of evolution to fill niches. If not competitive, transgenes and linkage groups will be purged from population. For forest trees such as poplars and pines, gene flow from wild and current stands would be very likely to dwarf that of GE plantations by astronomical factors for the foreseeable future in all but the most isolated populations. In addition, due to their long life span, trees are replaced in forests and orchards only every several decades. This creates a very large lag time over which regulatory monitoring could take place and resultant decisions about extent of commercial use could be modified (e.g., relaxed or made more stringent depending on results of initial commercial uses). Thus, for many GE products, particularly those with genes that are likely to have neutral or negative effects on tree fitness in the wild, we believe that gene flow into wild populations is predominantly a biosafety benefit, rather than a detriment, as is sometimes assumed.


    For new crop varieties, transgenic or otherwise, regulatory structures should consider the many ecological scales on which environmental benefits of GE crops could be manifested, and on which the risks of GE crops can be mitigated. New crop varieties developed by any means have the potential to alter ecosystems in complex ways by changing plant structure, chemistry, and management. The impact of these changes will depend on the scale and pattern of use, and will necessarily be difficult to predict without some evidence from commercial use. It will also be important to make evaluations within the context of existing production systems, which are in most cases already dramatically modified from the wild ecosystems they replaced. It only would be in cases where the phenotypes are not similar to existing ones that monitoring and placement into the moderate or high risk categories would be warranted. Where there is a significant uncertainty about non-target effects (e.g., on endangered species), we recommend that APHIS issue provisional deregulations so that ecological factors could be studied on ecologically relevant scales. This might also motivate growers to include mitigation treatments in their initial evaluations, which could help to identify new doubly beneficial situations with respect to production and environment. An example might be use of herbicide-resistant crops to improve wildlife habitat and soil erosion via timed and directed herbicide applications. After an initial period of evaluation, APHIS could then restrict the scale of deployment, or remand further regulatory approval entirely, if environmental consequences are unacceptable.


          Additional allowances should be made for the use of risk-mitigation technology, such as tandem mitigation constructs (Al-Ahmad et al. 2004; Gressel 2002). Here a risky trait can be more than offset by transforming along with a domestication trait that reduces competitiveness under native conditions.

4. Are there changes that should be considered relative to environmental review of, and permit conditions for, genetically engineered plants that produce pharmaceutical and industrial compounds? Should the review process, permit conditions, and other requirements for non-food crops used for production of pharmaceutical and industrial compounds differ from those for food crops? How should results of a food safety evaluation affect the review, permit conditions, and other requirements for these types of plants? How should the lack of a completed food safety review affect the requirements for these types of plants?


    We do not believe that all industrial feedstock and pharma (PMP/PMIP) crops are necessarily a separate class of crops that require regulation, particularly where a similar phenotype could be obtained via conventional means. For the sake of illustration, consider a hypothetical corn variety engineered to produce ethanol more efficiently (e.g., by altering sugar content). That would make it a plant-made industrial product, since the product is intended to be used to produce ethanol, but the safety of the corn itself would not be changed.


    Novel PMP/PMIP traits not achievable by any other means should be regulated for the foreseeable future, but at widely differing levels of stringency, until their environmental, food and feed safety are better understood. This should promote public acceptance and adoption, accelerating delivery of the economic and humanitarian benefits they promise. As discussed by Peterson and Arntzen (2004): "Because of their specificity, lack of toxicity and therapeutic or disease-prevention capabilities, many pharmaceutical proteins that will be produced in plants will challenge our ability to define an environmental hazard. Simply because these proteins are in the environment does not necessarily make them environmental contaminants or human health hazards in the same way as we traditionally view chemical stressors." We agree, and therefore believe that regulations should be highly differentiated for different classes of PMP/PMIP crops, based on the level of risk from inadvertent consumption/contact by humans and animals. For example, common, rapidly digested, and highly specific antibodies might be treated with far less stringency than broad-spectrum, stable toxins, and the latter should be treated much more stringently than common, rapidly degraded, non-toxic proteins used in industrial processing. Data from laboratory and computer screens for digestibility and allergenicity should help to assign them to broad classes prior to significant environmental release. These classes would then also be the basis for different tolerance levels with respect to adventitious presence. If warranted due to the toxicological properties of the product in question, USDA should coordinate with EPA and FDA to establish acceptable, legal levels of adventitious presence for different classes of compounds based on such early assessments, which can be revised as toxicological data grow.


    Additional allowances towards relaxed regulation of PMP/PMIP crops should be made when:

      a)  The plant is not a food or feed crop, nor capable of crossing with a food or feed crop, or only inert materials are used as minor components in food (e.g., non nutritive fiber)

      b)  The crop is grown far outside of its normal area of production

      c)  The crop outcrosses at a very low level (e.g., usually below 1% in small grain cereals)

      d)  When the transgene is in the chloroplast genome or the transgenic plant is a female in a dioecious species

      e)  For hybrid crops, when the seed parent is male-sterile and the pollen donor is not transgenic

      f)   When genetic markers are used to easily distinguish the PMP/PMIP crops from their commercial counterparts– e.g., purple corn, black soybean, modified leaves in vegetative crops, etc, such that mixtures could be readily detected

      g)  When crops are engineered to be have complete (male and female) sexual sterility and can be vegetatively propagated

5. Is the regulation of nonviable material appropriate and, if so, in what cases should we regulate?


    We believe there should be exemption of non-viable GE plant materials from regulation, except where there is reason to expect that they will have distinctive ecological behaviors (e.g., high toxicity for long periods of time, as might occur with some high risk PMP/PMIP crops released in large quantities). These risks should be evaluated with respect to the very large variance in ecological toxicity and rates of degradation among plant species and varieties in relevant ecosystems. Regulation of all non-viable GE plant materials, because it would greatly increase the cost and legal risk of field trials, would make GE field research impossible for the large majority of crops.


    More specifically, small quantities of non-viable material should always be exempt. Large quantities of non viable material used as a pesticide, for example, should trigger regulatory investigations.

6. Confined production of PMPs/PMIPs: What should be the characteristics of this mechanism? To what extent should this mechanism be employed for commercial production of plants not intended for food or feed? What environmental considerations should influence the development of this mechanism?


    As long as a clear agreement is in place between the producer and APHIS that all production will take place in confined facilities (growth rooms, greenhouses, etc.), no additional regulations need be applied.

    In the case where PMP/PMIP crops are producing high-risk compounds, such that minimal tolerances cannot be established, APHIS might consider limiting their deployment to enclosed conditions, at least until data to the contrary can be provided.

7. Should APHIS establish a separate component within a revised regulatory system to address adventitious presence? Should the low-level occurrence be exempt from APHIS regulation? If so, what are the conditions under which the low level occurrence should be allowed? What environmental considerations would apply to establishment of such allowance?


    It has long been recognized that zero tolerance is virtually impossible to achieve. For this reason, certified seed is allowed to have a low level of foreign matter and seeds from other varieties or even other crops and some types of weeds. Likewise, the FDA/ORA filth standards allow for limited amounts of insect parts and rodent waste in food. As examples see CPG 7104.02, Sec 578.200 and CPG 7114.29, Sec 585.890 for cornmeal and tomato paste, respectively.


    Here, APHIS is advised to follow FDA recommendations as to whether trace ingredients must be labeled. The following is from The need to label:


“depends on whether the trace ingredient is present in a significant amount and has a function in the finished food. If a substance is an incidental additive and has no function or technical effect in the finished product, then it need not be declared on the label.”


    If the adventitious presence would not trigger the FDA labeling requirement, such adventitious presence should not be regulated.


    Any regulations for adventitious presence should not be more stringent than standards currently in place for certified seed or for the FDA/ORA filth standards.


    Under these criteria, low-level presence of transgenes and their products in foods should be exempted from APHIS regulations. In addition, there should be allowances for adventitious presence that are based on risks of specific classes of genes, and not on method (GE or not), with the classes as discussed above. These should include:


a) Unlimited presence of specific selectable marker and reporter genes, and vector DNA sequences, that are deemed safe and familiar in plants. Some of these might be redarded as GRAS (Generally Recognized as Safe) based on extensive experience over the last 10 years. The safety of reporter genes and vector DNA sequences will be discussed in Appendix II.


b) Order-of-magnitude limits that are proportional to biological risk categories (e.g., high-risk PMP/PMIP, moderate-risk PMP/PMIP).


c) Unlimited presence for low-risk transgenes that have been exempted, as discussed above (homologous gene modification, random modification).


    Our premise is that these deregulations would also need to be accompanied by legal allowances for adventitious presence of unlimited quantities of these DNA sequences and proteins in food crops. This would remove unnecessary obstacles to regulatory approval, reduce the risk of lawsuits from unintended gene dispersal common in crop systems, provide tools that help to track unintended movement of GE products, and promote the use of well known, carefully studied GE tools vs. newer, less well understood tools. The public safety value of the nptII gene for kanamycin resistance, in comparison to less well understood transgene removal methods (e.g., recombinase-based systems), was highlighted in a recent review by König (2003). He noted: "Only a limited number of methods for genetic modification of crops is currently available...[our] assessment finds that some of the new methods that are developed to replace or eliminate effective antibiotic resistance markers are less cost effective than previously established practices; [and] others raise new acceptance-related concerns...enforcement of the European Community law requiring the phasing out of transgenic crops developed with the nptII gene may well turn research on improvement of transformation methods into a bottleneck for innovation in plant biotechnology."


    The presence of transgenes in organic produce continues to be a point of contention, and the National Organic Program standards ( are too vague to provide for effective guidance. They read:


When we are considering drift issues, it is particularly important to remember that organic standards are process based. ... The presence of a detectable residue of a product of excluded methods alone does not necessarily constitute a violation of this regulation. As long as an organic operation has not used excluded methods and takes reasonable steps to avoid contact with the products of excluded methods as detailed in their approved organic system plan, the unintentional presence of the products of excluded methods should not affect the status of an organic product or operation.


          It is necessary to clarify what it means by “The presence of a detectable residue of a product of excluded methods alone does not necessarily constitute a violation of this regulation.” Therefore we recommend that “detectable residues” be quantified, and set a 5% tolerance threshold for the presence of excluded methods. The 5% figure is consistent with the threshold for the National Organic Program’s Organic Label requirements.

8. Should APHIS provide for expedited review or exemption from review of certain low risk genetically engineered commodities intended for importation that have received all necessary regulatory approvals in their country of origin and are not intended for propagation in the United States? What environmental considerations should be applied to determination of any such allowances?


    APHIS needs to be cognizant that materials not intended for release will be released anyway. Hence it is appropriate for imported materials to be placed in one of the three risk categories described previously. Those that fall in the moderate- or low-risk categories should be exempted from review; those in the high-risk category should not.

9. Should the regulation of other similar genetically engineered plants be consistent with the regulation of genetically engineered Arabidopsis spp.? Should the exemption from interstate movement restrictions apply only to those products that meet specific risk-based criteria? What should these criteria be? What species and/or traits should be considered for this exemption? What environmental factors should be considered?


    Arabidopsis thaliana, E. coli K-12, Saccharomyces cerevisiae, and Bacillus subtilis are currently exempted by APHIS from interstate movement restrictions because of familiarity and a history of safe use. Accordingly, we seek exemption from interstate movement restrictions of transgenic organisms that are low to moderate risk as defined above, or that could not establish in the environment without substantial human aid. This would greatly facilitate research and breeding with GE materials, and regulatory effort could then be focused on the more important issue of environmental releases, not contained shipments. Exemptions from regulation should include:

                  a)  All disarmed Agrobacterium strains

b)All Agrobacterium strains shipped in vitro under containment (unless they are under quarantine as pathogens)

c)All low to moderate risk transgenic plants as defined above (as seed, in soil, or in vitro), except for PMP/PMIP plants


    Because of their value and risk from theft or incorrect handling, moderate-to-high-risk PMP/PMIP plants should not be exempted.

10. What are other areas where APHIS might consider relieving regulatory requirements based on the low level of risk?


    Regulations need to be cognizant of the economic value and constraints of minor crops. There are a large number of minor crops with a great net social value that can benefit from GE. (Even a “major” crop destined for a very specialized use can be considered a “minor” crop). By their nature, minor crops are not grown on a sufficiently wide scale to pose serious, widespread environmental risks. Discussions with breeders, and the large reductions in the extent of field trials of minor crops in 2003 (J. White, pers. comm., 2004), suggest that large regulatory burdens before and after commercial use frequently preclude development. Many of these varieties are also produced by public-sector scientists operating on limited budgets. All special regulatory requirements should therefore be explicitly justified on scientific grounds with reference to conventional breeding in accordance with the recommended risk categories discussed above, or waived.


    APHIS should work with other federal agencies to broadly de-regulate GE tools for all of crop species where scientific knowledge and experience suggest a high level of safety. This should include:

            a.   Selectable marker and reporter genes used widely in transformation, as discussed in #7 above and in Appendix II.

            b.   Most Agrobacterium DNA, some of which is already known to be naturally present in plant genomes. For example, tobacco has genes from Agrobacterium rhizogenes (Harper et al. 2002).

            c.   DNA from plant viruses used as promoters/terminators or other functional elements, or when used in non-functional form to suppress viral genes (and thus impart disease resistance). Virus sequences by themselves do not appear to pose a hazard, and many have become incorporated into the genomes of plants. For example, plantain bananas contain the genome of the banana streak virus, rice contains sequences of the rice tungro bacilliform virus, and tomato has sequences from tobacco vein-clearing virus (Harper et al. 2002). Surely more evidence of such horizontal gene transfer will be discovered as sequencing of plant genomes proceeds.

            d.   General gene suppression methods such as antisense or RNAi (RNA interference) that are commonly used to modify gene expression. Its effects are similar to loss-of-function alleles common in wild populations, and to the widespread processes of microRNA inhibition of gene expression during development (Carrington and Ambros 2003). These mechanisms are also useful for inducing viral and bacterial pathogen resistance, and similar processes of viral resistance are known to occur in wild species.

            e.   Non-toxic proteins that are commonly used to modify development (e.g., barnase and barstar for tissue ablation, including sterility, present in deregulated male-sterile Brassica under tissue-specific promoters).


    Mutagenesis and pleiotropy should be explicitly de-regulated. The many intensive breeding methods routinely used (e.g., inter-species hybrids, mutagenesis, inbreeding, wide species crosses, polyploidy) produce abundant secondary (i.e., collateral) effects on gene structure and expression in plants (e.g., Song et al., 1995; Liu et al., 1998; Liu and Wendel 2000; Ozcan et al., 2001) that are routinely sorted through during conventional breeding. Loss-of-function alleles that may be generated by the GE process are common in breeding populations, and events such as transposon and retroviral movement caused by GE-associated mutagenesis are also common. In fact, we believe that breeders should be allowed to take advantage, rather than avoid, the mutagenesis that might be produced during GE to accelerate overall rate of improvement. In contrast, where novel proteins or pathways are inserted that could have specific toxicological consequences, these would logically continue to be studied as part of regulatory approval to ensure that the changes imparted did not exceed that considered safe and familiar in breeding programs. Accordingly, we suggest the following exemption of GE-associated genetic changes based on advances in genome and regulatory science:

                  a.   Mutagenesis or pleiotropic effects associated with gene transfer and in vitro culture,

                  b.   Random or directed transgene-imparted gain or loss of native gene expression.


These exemptions are warranted because similar variations commonly occur in wild populations or are generated via non-regulated breeding methods such as radiation/chemical mutagenesis, inbreeding, hybridization, and cloning. Again, the focus should be on product not process. These exemptions would be similar to those already in place for recombinant E. coli K12 and transgenic Arabidopsis, and would fit under NIH recombinant DNA Guidelines (Appendix C, Section III-F-6, which exempt "those [transgenic organisms] that do not present a risk to health or the environment."


    In keeping with the proposal for a multi-tiered permit system for field testing, regulations should vary widely in stringency, in both directions. Traits in the low-risk class, as discussed above, might be exempt from any regulatory oversight during field-testing. This would include "genomics-guided transgenes (Strauss 2003b)," and studies that examine how changes in homologous gene expression affect plant performance in the field. However, APHIS could nonetheless develop a BMP (best management practices) policy that would need to be agreed to by organizations seeking exemptions from requirements, that specifies how growers of GE plants for field research should monitor, make non viable, and dispose of plants after completion of field trials.


    Single-copy insertions should not be (effectively) mandatory. We believe that determinations of transgene, vector, and flanking sequences, and transgene expression and toxicological properties, should not be required for each insertion site prior to commercial use. Requirements for intensive characterization of insertion sites tend to de facto limit commercialization to single-copy events due to expense, and such single-copy events, as discussed elsewhere, are not always desirable. Stability of gene expression is weakly correlated with insert number, and examples of stable expression exist for both single- and multi-copy inserts. Some transgene loci act to silence one another, whereas others act additively to control the level of gene expression (e.g., Nap et al. 1997; Conner et al. 1998; Schmidt et al. 2004). Inserts on several chromosomes may be desirable when a high level of gene expression is needed, or when it is desired that most progeny inherit at least one copy of a transgene (e.g., of a biosafety promoting gene such as for semi-dwarfism).


    Event-specific regulation is not warranted. Based on the same logic as presented above with respect to copy number, the different types of mutagenesis produced by different gene transfer events do not require regulatory scrutiny. Event-specific regulation has tended to force breeders to choose one or a very few events early in the breeding process. This is a result of the anticipated cost of obtaining regulatory approval for all of them, and due to the complications of obtaining and complying with permits or notifications for each of them as they enter large-scale trials. However, because transgene expression and compatibility with specific genetic backgrounds can change during breeding, it is advantageous to delay event selection as long as possible so the best events are identified. It will also often be desirable to employ different events in different varieties that are grown for different product types or in different regions. In vegetatively propagated crops, where highly heterozygous GE clones are expected to be deployed, event-based regulation imposes a major burden for the development of diverse forms of GE varieties. Its likely result will be that fewer genotypes would be transformed and deployed than biologically and commercially desirable, reducing genetic diversity and thus the geographic scope over which GE could be applied.


          However, we are cognizant there are limited instances when event-specific regulations might not be sufficiently stringent. For example, one could envisage a transgene engineered into a fully domestic species being introgressed into a fully weedy species over time. As the rule is currently written, a deregulated herbicide-tolerant Brassica napus event is viewed the same (regulatory-wise) as the recipient B. napus x B. rapa hybrid and backcrossed progeny to B. rapa (Warwick et al 2003), although the genetic background has changed (different host species). Therefore, there needs to be flexibility in rules for the entity that should be regulated/deregulated.


    Conditional deregulation and post-commercialization monitoring may be advisable for some GE varieties. Because of the long time frames to obtain conclusive answers about performance, stability, and safety for some traits and crops (e.g. trees), we concur with APHIS' suggestion that permits should be granted for conditional commercial use in specific cases. In some instances this could be primarily for research purposes where the information needed exceeds that feasible under normal research projects (e.g., long-term evaluation of a tree variety with a new trait). Because conditional status could pose a large risk for businesses, it may preclude commercial development. The mode of monitoring, period of observation, and goals (thresholds) therefore will need to be very carefully considered on a case-by-case basis so that cost is reasonable, uncertainties in the process minimized, and scientific precision is maximized. To prevent regulatory oversight from continuing without cause, regulations might stipulate that monitoring ceases after a specific period (e.g., five years), and that a regulatory decision is reached or a specific extension granted where questions remain. Any decision to extend the period of post-commercial monitoring should be made only upon a demonstration by APHIS of a substantial need, should provide a mechanism for comment by the regulated entity prior to APHIS taking the decision, and should be subject to court challenge. It should also have explicit and measurable conditions under which further sale or planting would be prevented due to an unexpected consequence. To summarize, monitoring is appropriate when science-based questions remain unanswered. Monitoring is not a substitute for risk assessment or risk management.

11. What environmental considerations should be evaluated if APHIS were to move from prescriptive container requirements for shipment of genetically engineered organisms to performance-based container requirements, supplemented with guidance on ways to meet the performance standards?


    See answers under number 9 above. Anything that is safe enough to permit free interstate shipment is also safe enough to be exempt from any particular container requirements.

Appendix I

DNA behavior during breeding and evolution compared to rDNA

Plant genomes are incredibly variable and fluid. We now know that extensive variation in DNA content is normal within a species, that DNA movement and rearrangements are common and natural phenomena, and that individuals within a species can naturally have different numbers of genes in them, all without ill effects to the plant, to the environment, or to herbivores.

Perhaps the one natural aspect of plant genomes that most closely mimics transgenics is transposable elements moving in and out of genes, where they "can alter gene expression or serve as sites of chromosome breakage or rearrangement" (Wessler 2001), without substantial effects on plants or their nutritional safety. In addition, retrotransposons continuously insert themselves between genes (San Miguel et al., 1996). Because retrotransposon sequences are found in current EST databases, we know that their movement was not just a thing of the past, but something that continues to the present, and perhaps is likely to have resulted in evolutionary improvements in plant adaptation (e.g., Ceccarelli et al., 1997; Shirasu et al., 2000) and in breeding progress, as evidenced by the large differences in genome size within varieties of the same crop.

Varieties of the same crop differ greatly in the amounts of DNA they contain. For example, different varieties of maize can differ by as much as 42% in their DNA content; different varieties of chili pepper differ by 25%; and different soybean varieties differ by 12% (Graham et al. 1994; Mukherjee and Sharma 1990; Rayburn et al. 1989). This means that, for soybean, different varieties vary by over 100 million base pairs of DNA, dwarfing the few thousand base pairs that transgenes add to genomes.

Even different individuals of the same species differ by the number of transposon and retrotransposons they contain, a phenomenon vividly illustrated by Fu and Dooner (2002). As a result of a large number of deletions that are common in maize, they also found that different individuals within the same species do not even have to have the same number of genes. This finding has since been extended to another part of the maize genome (Song and Messing, 2003).

Repetitive DNA sequences (microsatellites) have a tendency to change in copy number (e.g., Lian et al., 2004), thus making them highly variable in plant populations and explaining their popularity as a molecular marker in plant breeding programs. Point mutations are also very common, as illustrated by the extensive single nucleotide polymorphisms ("SNPs") observed in plant genomes. Cytoplasmic male sterility, commonly used in breeding, can result from the creation of novel genes in the mitochondria, along with novel fertility restorer genes in the nucleus (Schnable and Wise 1998).

We also know that there has been extensive gain and loss of both organellar and nuclear genes in plants over evolution, and that genes can be transferred over wide phylogenetic distances. As discussed in point 4-3 above, horizontal gene transfer to plant genomes is common enough to not be considered as “unnatural” or dangerous. Besides the viral genomes already discussed, this includes transfer of Agrobacterium DNA to plant genomes (Harper et al. 2002), and transfer of genes between organellar genomes, and from organellar to nuclear genomes or the reverse (Adams et al. 2002; Cummings et al. 2003; Bergthorsson et al. 2003).

In the end, rDNA is actually better defined than breeding. It is already clear that different individuals within a species differ in their DNA and their genic content, and these differences are almost certainly exacerbated between species. Yet, large amounts of extraneous DNA can be brought in during the breeding process. For example, Young and Tanksley (1989) looked at tomato cultivars into which the Tm-2 gene had been introgressed, and found donor DNA left in modern tomato cultivars ranging from 4 to 51 cM long– enough for several genes to have come along from the donor species.

Appendix II

Safety of marker genes, reporter genes, and vector sequences.

          There is no evidence that selectable marker and reporter genes used widely in transformation (e.g., nptII, GFP, GUS, some herbicide tolerance genes) pose any risk. The product of nptII was classified as GRAS during the FlavrSavr approval (Redenbaugh et al., 1992) due to its safety (Fuchs et al., 1993). Strong arguments have been made for the safety of the GUS reporter gene by Gillissen et al. (1998). The same is true of GFP (Richards et al 2003), which seems to be an ecologically neutral marker (Stewart 2001).


          Bennett et al. (2004) recently made a strong general argument for the safety of virtually all antibiotic resistance genes in plants. They stated: "The Working Party finds that there are no objective scientific grounds to believe that bacterial AR [antibiotic resistance] genes will migrate from GM plants to bacteria to create new clinical problems….use of these genes in GM plant development cannot be seen as a serious or credible threat to human or animal health or to the environment." This view largely echoes that of Flavell et al. (1992) and the US FDA in their "Guidance for Industry" issued in 1998 (FDA 1998).


          As far as vector sequences go, Appendix I discusses the great amounts of DNA flux and sequence divergence that exist in plants. Against that background, the addition of background sequences is as effective as taking sand to the beach. We cannot find any scientifically valid reason for their regulation.


          A report by Kohli et al. (1999) found that the 35S promoter was hyper recombinogenic during the integration of the transgene into the genome, not after the fact. Subsequently, claims were made that the 35S promoter was unstable, prone to transfer and insertion into the DNA of other cells, thereby causing cancer in humans (Ho et al., 1999). The claims put forward in this un-refereed opinion piece were not based on scientific experimentation but were speculations based on certain pieces of information, along with a complete misinterpretation of the Kohli et al. (1999) reference. These claims have been subsequently extensively rebutted by the scientific community (e.g., news report by Hodgson 2000). The main thrust of the rebuttals was that this viral promoter is ubiquitous in nature. It has been estimated that about 14-25% of oilseed rape in the field is infected with cauliflower mosaic virus in the United Kingdom (Hardwick 1994); similar numbers have been estimated for cauliflower and cabbage. Historically, humans have been consuming cauliflower mosaic virus and its promoter at much higher levels than those in uninfected genetically engineered plants for decades, with no observable effects.


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Appendix III

Endorsed by:

The Society for In Vitro Biology

9315 Largo Drive West

Suite 255

Largo, MD 20774 USA

Additional co-signers

Herb S. Aldwinckle, Professor

Dept. of Plant Pathology

Cornell University - NYSAES

Geneva, NY 14456 USA

Fredy Altpeter, Assistant Professor

Agronomy Department

University of Florida, IFAS

Gainesville, FL32611

Roger N. Beachy, President

Donald Danforth Plant Science Center

St. Louis, Missouri 63132

Amy Brunner, Assistant Professor

Department of Forest Science

Oregon State University

Corvallis, OR 97331

Daniel R. Bush, Professor and Chair

Department of Biology

Colorado State University

Fort Collins, CO 80523

Victor B. Busov, Assistant Professor

Michigan Technological University

School of Forest Resource and Environmental Science

Houghton, MI 49931

Catherine Carter, Professor

Plant Science Department

South Dakota State University

Brookings SD 57007

Bruce Chassy, Professor and Executive Associate Director

of the Biotechnology Center

University of Illinois Urbana-Champaign

Urbana, IL 61801

Zong-Ming (Max) Cheng, Associate Professor

Department of Plant Sciences

University of Tennessee

Knoxville, TN 37996-4500

Vincent L. Chiang, Professor

Department of Forestry

North Carolina State University

Raleigh, NC 27695-7247

Thomas E. Clemente, Associate Professor

Dept. of Agronomy & Horticulture

University of Nebraska

Lincoln, NE 68588-0665

Glenn Collins, Professor

Department of Agronomy

University of Kentucky

Lexington, KY 40546

Violeta Colova, Associate Professor

CESTA, Center for Viticulture & Small Fruit Research

Florida A& M University

Tallahassee, FL 32317

John Davis, Associate Professor

School of Forest Resources and Conservation

University of Florida

Gainesville, FL 32611

Jeffrey Dean, Associate Professor

School of Forest Resources

University of Georgia

Athens, GA 30602

Richard A. Dixon, Director, Plant Biology Division

Samuel Roberts Noble Foundation

Ardmore, OK 73401

Sharon Lafferty Doty, Ph.D.

Research Assistant Professor

College of Forest Resources

University of Washington

Seattle, WA 98195-2100

David S. Douches, Professor

Department of Crop and Soil Sciences

Michigan State University

East Lansing, MI 48824

Nina Fedoroff, Willaman Professor of Life Sciences and Evan Pugh Professor

Huck Institute of the Life Sciences

Pennsylvania State University

University Park, PA 16802

John J. Finer, Professor,

Department of Horticulture and Crop Science

OARDC/The Ohio State University

Wooster, OH 44691 USA

Maria Gallo-Meagher, Associate Professor

Agronomy Department

University of Florida

Gainesville, FL 32611-0300

Barry Goldfarb

Associate Professor of Forestry

North Carolina State University

Raleigh, NC, USA 27695

Dennis J. Gray, Professor

Mid-Florida Research and Education Center

University of Florida

Apopka, FL 32703-8504

Jude W. Grosser, Professor

University of Florida Citrus Research and Education Center

Lake Alfred, FL 33850

Arron C. Guenzi , Professor

Dep. Plant & Soil Sciences

Oklahoma State University

Stillwater, OK 74078-6028

Mary Lou Guerinot, Professor

Dartmouth College

Hanover, NH 03755

President, American Society of Plant Biologists

Timothy C. Hall, Distinguished Professor and Director

Institute of Developmental and Molecular Biology

Texas A&M University

College Station, TX 77843-3155

Andrew Hopkins

Noble Foundation, Inc.

2510 Sam Noble Pkwy.

Ardmore, OK 73401

Heiddi Kaeppler, Associate Professor

Department of Agronomy

University of Wisconsin

Madison, WI 53706

James D. Kelly, Professor of Crop and Soil Sciences

370 Plant and Soil Science Building

Michigan State University

East Lansing, MI 48824

Edward G. Kirby, Professor

Department of Biological Sciences

Rutgers University

Newark, New Jersey 07102 USA

Schuyler S. Korban, Professor

Department of Natural Resources & Environmental Sciences

University of Illionis

Urbana, IL 61801

Peter R LaFayette, Research Scientist

Center for Applied Genetic Technologies

University of Georgia

Athens, GA 30602

William H.R.Langridge, Professor

Center for Molecular Biology and Gene Therapy

Department of Biochemistry and Microbiology

Loma Linda University

Loma Linda, CA. 92350

Peggy G. Lemaux, Ph.D.

Department of Plant and Microbial Biology

111 Koshland Hall

University of California

Berkeley, CA 94720

Baochun Li, PhD

Kentucky Tobacco Research and Development Center

University of Kentucky

Lexington, KY 40546-0236

Charles Maynard, Professor

SUNY College of Environmental Science and Forestry

Syracuse, NY 13210

Richard Meilan, Associate Professor

Department of Forestry and Natural Resources

Purdue University

West Lafayette, IN 47907-2061

Martina Newell-McGloughlin, Director

University of California Systemwide Biotechnology

University of California- Davis

Davis, CA 95616

Jerzy Nowak, Professor and Head,

Department of Horticulture

Virginia Polytechnic Institute and State University,

Blacksburg, VA 24061

Peggy Ozias-Akins, Professor

The University of Georgia, Tifton Campus

Department of Horticulture

Tifton, GA 31793-0748

Gary F. Peter, Associate Professor

Institute of Food and Agricultural Sciences

University of Florida

Gainesville, FL 32611

Gregory C. Phillips, Ph.D.

Dean of the College of Agriculture

Editor-in-Chief, In Vitro Plant

Arkansas State University

Arkansas State University, AR 72467-1080

Larry C. Purcell, Professor

Department of Crop, Soil, and Environmental Sciences

University of Arkansas

Fayetteville, Arkansas 72704

Rongda Qu, Associate Professor

Department of Crop Science

North Carolina State University

Raleigh, NC 27695-7620

Nancy Reichert, Professor

Dept. of Plant and Soil Sciences

Mississippi State University

Mississippi State, MS 39762

Suzanne Rogers, Associate Professor

Department of Bioscience

Salem International University

Salem, WV 26426

Pamela C. Ronald, Professor

Department of Plant Pathology

University of California, Davis

Davis CA 95616-8680 USA

Clayton Rugh, Assistant Professor

Department of Crop & Soil Sciences

Michigan State University

East Lansing, MI 48824-1325

Ronald G. Sederoff, Professor

Department of Forestry

North Carolina State University

Raleigh, NC, USA 27695

A. Mark Settles, Assistant Professor

Horticultural Sciences Department

University of Florida

Gainesville, FL 32611

Anthony Shelton, Professor

Department of Entomology, Cornell University
Professor and Associate Director of International Agriculture

Geneva NY 14456

Kenneth C. Sink, Professor

Department of Horticulture

Michigan State University

East Lansing, MI 48824

James E. Specht, Professor

Department of Agronomy and Horticulture

University of Nebraska-Lincoln

Lincoln, NE 68583-0915

C. Neal Stewart, Jr.

Professor and Racheff Chair of Excellence

University of Tennessee

Knoxville, TN 37996-4561 USA

Chuck Tauer, Professor

Department of Forestry

Oklahoma State University

Stillwater, OK 74078

Harold N. Trick

Department of Plant Pathology

Kansas State University

Manhattan KS 66506-5502

Chung-Jui Tsai, Associate Professor

School of Forest Resources and Environmental Science

Michigan Technological University

Houghton, MI 49931 USA

Allen Van Deynze, Ph.D.

Seed Biotechnology Center

University of California

Davis, CA, 95616

Indra K. Vasil

Graduate Research Professor Emeritus

University of Florida

Gainesville, Fl 32611

Lila O. Vodkin, Professor

Department of Crop Sciences

University of Illinois

Urbana, IL 61801

Zeng-yu Wang, Ph.D

Associate Scientist

Forage Improvement Division

The Noble Foundation

Ardmore, OK 73401

Pamela J. Weathers, Professor

Biology and Biotechnology

Worcester Polytechnic Institute

Worcester, MA 01609

Hazel Wetzstein, Professor

Department of Horticulture

University of Georgia

Athens, GA 30602

Jack Widholm, Professor

Department of Crop Sciences

University of Illinois

Urbana, IL 61801