The paper linked to in the "Here is a link that might be useful" box has 124 comments which the reader may find interesting.

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Other links that may be of interest:

http://healthticket.blogspot.com/2013/02/viral-gene-in-genetically-eng ineered.html

http://permaculturenews.org/2013/01/28/hazardous-virus-gene-discovered -in-gm-crops-after-20-years/

http://no2gm.com/category/gm-news/

In case anyone wants some information about "gene 6"...better/correctly known as "P6"...as it pertains to current discussion based on a study by the EFSA...

This is a very wide range of proteins found in virus encoding from HIV to mosaic virus...these proteins are also found in the smoke of burning meat and tobacco. It's a very wide range. In this case, one of the biggest dangers would be a chance encoding to re-invigorate the "dead" version of cauliflower mosaic virus (or P6 residues) that's very commonly used as a carrier string for DNA/RNA insertion that it's inserted into. This could lead to some allergy problems, too, even if it doesn't fully express the mosaic virus but still overlaps enough to express P6 proteins. P6 is a known allergen, though it's not one that everyone is sensitive to.

The expression of this gene is highly unlikely, though...and would be regulated to a single (or very small groups) of plants doing this replication rather than entire seed source or a field suddenly replicating mosaic virus or P6 residues. If it is the case that encoding suddenly made it large-scale available it would show up heavily in the research stage and it wouldn't make it out into the consumer market since it's showing inferior/bad genetic expression. One of the biggest parts of GMO research is tossing out 99%+ of everything you're actually trying to create because positive effects of expression aren't stable enough to sell it as seed...or it's showing "bad" expressions.

There's a lot of otherwise harmful viruses (to plants or humans) used to insert GMO traits for start/end points into a genetic change that are made inert (and distinctly different) from their original genetic package, but still contain large parts of what makes up the virus, itself. Viruses can easily carry genetic information and they're ideal vehicles for transferring it. The genetic carriers of the virus are merely vehicles. Once you change the "genetic package" inside a virus it's not even what you started with. The "guts" are changed dramatically. If you put a Dodge Neon engine in a Porsche very few people would still consider it a Porsche. That's the level of dramatic change in sequencing going on inside of these packages. You can take certain virus types, depending on what you're trying to achieve, and precisely insert genetic information with start/termination points into existing DNA/RNA...totally turning it's genetic information into something totally different in both makeup and application.

Btw, to those with P6 protein sensitivities...this would be a big deal. I'm not trying to knock the research at all. I'm just saying it's overlapping expression would most likely be contained to a very few plants in a field, not widespread. While genetic start/termination points are very good with insertion and replication once stable, nothing is perfect when you're exchanging genes...we see it even natural breeding. The major problem with this particular chain of insertion is the overlapping of the 2 sequences given as example in the paper and what could happen as a consequence of them being genetically linked so closely together...even if there's a very small chance of it happening as defined.

It's also worth mentioning we're talking a single virus carrier, not the 100s of types (or the 20-ish most commonly used) carriers. It would also be greatly influenced by the new information inserted, what was cut out, and where the start/termination points overlap (if there is any replication overlap). There's more than 1 way to insert genetic information into virus and the chances of overlap encoding or reversion is different depending on the type of method used.

The following is a quote from the link that indicates what they are concerned about:

"The Many Functions of Gene VI
Gene VI, like most plant viral genes, produces a protein that is multifunctional. It has four (so far) known roles in the viral infection cycle. The first is to participate in the assembly of virus particles. There is no current data to suggest this function has any implications for biosafety. The second known function is to suppress anti-pathogen defenses by inhibiting a general cellular system called RNA silencing (Haas et al. 2008). Thirdly, Gene VI has the highly unusual function of transactivating (described below) the long RNA (the 35S RNA) produced by CaMV (Park et al. 2001). Fourthly, unconnected to these other mechanisms, Gene VI has very recently been shown to make plants highly susceptible to a bacterial pathogen (Love et al. 2012). Gene VI does this by interfering with a common anti-pathogen defense mechanism possessed by plants. These latter three functions of Gene VI (and their risk implications) are explained further below:"

There's a very small chance of this happening in a plant as it is, and it's almost impossible for this to happen with a large amount of plants in a stand.

The particular virus + insertions have been in use for almost 20 years.

In order for a P6 allergen danger to manifest itself, which most people are not allergic to, it would have to happen in a plant which had a DNA replication error and happened to fix a P6 protein. A person who's susceptible to the allergy would also happen to ingest the mutated plant's grain...which would be a very small chance given how much grain is mixed with the rest of the crop or harvested grain in an elevator.

In order for the mutated plant to become susceptible to infections the same replication error (including a proofreading not correcting it) would have to happen and the plant would have to actually contract an illness. This would effect the plants and could effect the surrounding plants.

It's just something that's possible, but highly unlikely...and extremely rarely found to actually happen. The proximity of the gene insertion points gives a chance encoding of P6 a chance to happen via overlap.

Fwiw, the P6 replications found in the actual report are not even known allergens...though the P6 class of proteins include many allergens.

From the report...

"As no scientific literature has been reported on any allergenic properties of CaMV and no similarities have been shown to know allergens, it can be concluded that the P6 protein is most likely not an allergen. In addition, a toxin database was constructed, and no significant sequence similarity with the P35S variants was detected. These data suggest that the P35S variants do not contain ORFs that encode for proteins that have allergenic or toxic properties."

It's also worth mentioning that ORFs in a GMO insertion would also be a mutation because Open Reading Frames contain no genetic/DNA "stop" points so it continues to self-replicate. GMO insertions include specific start and termination points in order to precisely get a desired genetic string/chain into whatever it's being inserted into. If an insertion and mutation formed ORFs the chances of this P6 expression goes up, though, via sheer volume of replications without being stopped.

"Although the P35S overlaps partially with gene VI, the likelihood of unintended effects occurring will depend on whether the partial gene VI is transcribed. We believe that if P35S is embedded in a transformation construct with another gene cassette at its 5′ flank, it is unlikely that the partial gene VI will be transcribed. In contrast, when the P35S is inserted adjacent to plant genomic DNA, transcription from an endogenous plant promoter might take place and create a chimeric protein that contains part of P6. "

The chance that something can happen doesn't mean it will happen. For those that complain about GMO allergens this does open up an area to concentrate new research on, though the scientists themselves couldn't even replicate a known allergen in their forced experiments using unnatural forces to play with the DNA.

So then the chances are very rare then?

Talking about P6 proteins is like talking about "cars" or "trees"...there's many specific types that act in a different manner from each other even though they're all basically proteins...or cars...or trees.

There's a chance some people may be allergic to the types replicated, but given that they're not "known" to be allergenic it's doubtful enough that the researchers, themselves, believe the P6 produced aren't allergens. CaMV (Cauliflower mosaic virus) has existed a very long time and the whole study's effect is based around it's possible overlaps producing P6.

The following does refer to one of the points made in the link that I gave: "In order for the mutated plant to become susceptible to infections the same replication error (including a proofreading not correcting it) would have to happen and the plant would have to actually contract an illness. This would effect the plants and could effect the surrounding plants.

It's just something that's possible, but highly unlikely...and extremely rarely found to actually happen. The proximity of the gene insertion points gives a chance encoding of P6 a chance to happen via overlap."

Concerning whether something is "It's just something that's possible, but highly unlikely...and extremely rarely found to actually happen.".

What does history tell us?

When there was concern about plants developing resistance to glyphosate, the reply was: Citing agreement from university scientists, the company declared it “highly unlikely” that widespread use of Roundup Ready technology would lead to resistant weeds."
See the Google search below.

Even if it did happen to pass it's genetics in the wild, the negative aspect would have to be a sexually linked trait and that may not be in play here. I doubt it is, but I'm not sure...nor if it would be a dominate trait even if it is capable of being passed sexually. Either way we're talking about a small chance of a plant existing which would have to be on the very edge of a field and by chance pass it genetics to someone's saved seed. It becomes even less likely considering how few farmers save seed of most of these types of crops (corn, soy, cotton, etc) compared to buying fresh hybrid seed (GMO or non-GMO). It's a highly unlikely "perfect storm" situation.

GMO seed parents (and non-GMO hybrid seed parents) are very specific, tightly controlled, property...though regular non-GMO hybrid seed stock doesn't have patent control over gene sequences.

Weeds in the wild and insects in the wild go through many generations and changes in evolution. Every GMO and non-GMO hybrid seed is a bottleneck of specific genes.

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It is my understanding that one GM gene per plant is now "yesterdays news" and that stacked genes is now the "in thing". How much does this complicate the picture?
http://bch.cbd.int/onlineconferences/guidancedoc_ra_stackedgenes.shtml

We use a lot of "on the surface" scary virus/bacteria genetic material to make GMO insertions or create GMO "parts" for insertion. E-coli types are commonly used, though not any scary as the "flesh eating" E-coli type(s).

The plant virus in question in this insertion would be CaMV, which, if somehow invigorated wouldn't even effect corn/soy/cotton because this mosaic virus is plant specific to cauliflower, radish, cabbages, turnips, etc...plants that wouldn't even be growing this time of year.

That said, it would be an extremely low chance of a mutation creating the regeneration of the virus.

A GMO insertion can be thought of taking ABCDEFGHIJKL and turning it into ABCUVWXYZJKL. It's so dissimilar that the chances of it becoming what it once was is extremely low and would require some really extreme chance overlapping.

It's a lot more likely (though not very likely) that mutation + overlap would create the P6 proteins (or protein parts), not re-invigorate the virus, itself.

It's the cauliflower mosaic virus, and anyone who has eaten anything in the brassica family has already eaten the viral DNA ... every time you eat anything you eat its DNA and the DNA of all its viruses and bacteria.

I also gave links to several other papers which appear to have been ignored in this thread. Particularly,

http://permaculturenews.org/2013/01/28/hazardous-virus-gene-discovered -in-gm-crops-after-20-years

gives information which should be sufficient to negate the posted concerns in this thread about the complete virus being eated:
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Posted on Mon, Feb 25, 13 at 15:23

"OMG GMO!!!!! We're all gonna DIE!
It's the cauliflower mosaic virus, and anyone who has eaten anything in the brassica family has already eaten the viral DNA."
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Quotes from the link.
"It is of interest that the objections for ‘shredding’ the scientific paper of Podevin and du Jardin [1] and Latham and Wilson’s report [2] are exactly the ones used against us. The first objection is that humans have been eating the CaMV for millennia without ill effects; the second is that the CaMV 35S promoter is only active in plants and certainly not in animal or human cells.

Our rebuttal to the first objection is that the intact CaMV, consisting of the CaMV genome wrapped in its protein coat, is not infectious for human beings or for other non-susceptible animals and plants, as is well-known; for it is the coat that determines host susceptibility in the first instance. So eating the intact virus is of little consequence. However, the naked or free viral genomes (and parts thereof) are known to be more infectious and have a wider host-range than the intact virus. Furthermore, the synthetic CaMV 35S promoters are very different from the natural promoters, and are both much more aggressive as promoters driving inappropriate gene expression as well as more prone to fragment and recombine."

"The second objection ��" that CaMV 35S is not active in animals and human cells ��" is simply false as we discovered in the scientific literature dating back to 1989, and pointed this out in a third paper [6] (CaMV 35S promoter fragmentation hotspot confirmed, and it is active in animals). The CaMV 35S promoter was found to support high levels of reporter gene expression in mature Xenopus oocytes [7], and to give very efficient transcription in extracts of nuclei from HeLa cells (a human cell line) [8]."

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We're now talking about something totally different than what was initially brought up.

For over 20 years CaMV and it's promoters have been used for GMO insertion in agriculture plantings in the "real world" beyond the lab.

CaMV is no longer CaMV when GMO insertions are made. It's like ripping the engine out of a Porsche and replacing it with the engine from a Dodge Neon. It may have a Porsche shell, but that isn't a Porsche on the inside. There is no intact virus...just part of it...which is useless without the whole thing from an infection standpoint. We would be infecting plants with the initial virus every single time if that was the case. A partial expression of a gene isn't an expression of a gene. ABCDEFG isn't the same as ABCXYZG. Theorizing that that these genes would start splicing at exact points and randomly picking up new genetic insertions that would be infectious/re-invigorating is possible...about as possible as getting struck by lightning while dodging a meteor that was coming for you while you were on your way to cash in your $10m lottery ticket you just won.

Those objections from whoever you quoted also sounds like it came from someone who doesn't understand GMO or genetics. I'm really sure the person posting those objections has no idea what CaMV actually is/does. ...or they have some kind of agenda for spreading half-truths because this isn't "heavy" stuff in the world of GMO.

-edit- Okay, this is an ISIS article...she (Dr. Mae-Wan Ho) DOES know better, but she's trying to "do other things". She also believes AIDS isn't a real disease and it's an excuse for pharm companies to sell meds, btw. She's part of a very small minority of people/scientists who are rather sure we're going to see reversions of original virus/bacteria from parts of them merely existing...even though they're missing a lot of key information which makes them a new genetic package to begin with. The scientific community at large isn't a huge fan of her...and ISIS exists, mostly, because no one will publish her work.

"However, the naked or free viral genomes (and parts thereof) are known to be more infectious and have a wider host-range than the intact virus. "

This is true...but the guts aren't the virus, itself...it's the new genetic package that's "free." The "infection" that would be taking place is the whole point of GMO insertion...to pass that changed/inserted genetic information in a host plant.

CaMV carriers can infect almost ANY cells...human, plant, you name it. What matters is what's in the guts, not the fact it can be used in a carrier. What matters even more is that the host can actually do something with what's passed to it. This goes back to the early 1980s as far as practical use...especially in HUMAN insulin production (where most modern insulin comes from via GMO).

CaMV happens to be a great carrier for packaging any genetic packages.

H.Kuska comment. I started the thread and linked to a specific paper by Jonathan Latham and Allison Wilson . I have attempted to keep the conversation focused first on that paper and then later on the other links that I proved in my initial post . As far as I can determine, even the last post is only partially on the points that are in my initial links (and no references were presented). To keep this thread on track, If someone feels that they have points about my initial post, please put the material in quotes from the link that you are discussing. And please no personel attacks against others. If you want to discuss other subjects, please start your own thread.

I've been trying to explain this...

They're not taking all of the virus out and putting all fresh genetic code in...they're taking part of a virus's genetic code out and inserting new genetic information in.

It's no longer the same thing. It's genetically, uniquely different...both what it is and how it works.

Being 60-75-whatever% CaMV no longer makes it CaMV in practice. The insertions are made in order to pass along new genetic information.

If ABCDEFG encodes CaMV then ABCXYZG isn't going to ecode CaMV even though ABC+G still exists.

Our DNA contains much "junk data" along with the stuff that matters. When you restructure DNA in a matter such as GMO insertion you're putting new "data" that a plant/animal can "make sense" of along with turning old "useful data" into "junk data."

This isn't even the point of the paper at http://www.es.landesbioscience.com/journals/gmcrops/article/21406/?sho w_full_text=true

...what that paper was about I've covered above.

You seem to have questions raised by the article at permaculturenews...which was written by Dr. Ho from ISIS. The points she raised are simply things she's piggybacked on in order to write something totally different from the points raised by the initial study. Similar can be said by Dr. Mercola's points on that other blog link, only Dr. Mercola doesn't have the credentials that Dr. Ho has on the issue and probably doesn't fully grasp what's going on genetically. He tends to be a "jack of all trades" when it comes to subjects...and he's not the expert he asserts himself to be on as many subjects as he covers.

There's a lot of nothing being made over gene fragments (which isn't a new discovery) by Dr. Mercola and Dr. Ho and others...as if it was some kind of new "smoking gun" rather than something that is well known and matter of fact.

Also, what Jonathan Latham and Allison Wilson wrote isn't a scientific study...it's a "news report" from Independent Science News who (like Dr. Ho) run their own organization to publish their own news/views. If you look at some of the things they wrote, such as "When Gene VI is intentionally expressed in transgenic plants, it causes them to become chlorotic (yellow), to have growth deformities, and to have reduced fertility in a dose-dependent manner " then you'd see all these GMO crops in the field turning yellow and having growth deformities if this was more than an extremely low chance thing. They've taken a hodge-podge of other's work and pieced together an "article" backing up their point...some of which doesn't help show what they're trying to prove.

The important part (and actual focus) of the study concerns P6 overlap creation possibilities and I covered that above.

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H.Kuska comment. Please provide the quote where one of my cited papers states that it was CaMV in practice.

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The following quote was given: ""The gmo modifications utilize a virus to insert the new genes. Unfortunately, a significant fragment of the viral gene has been reported to stay in the gmo plant."

And then:
"I've been trying to explain this..."

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H.Kuska comment: Oh? I do not see the connection between your statements and that simple statement of fact that you have quoted. Is that an accurate statement or not. And if you feel that it is not accurate, please provide your references.

I've explained "The gmo modifications utilize a virus to insert the new genes. Unfortunately, a significant fragment of the viral gene has been reported to stay in the gmo plant." numerous times...recently in the post before hand.

I've also explained the point of the paper (the actual study) and chance encoding of P6.

As far as references go...I don't know. Textbooks, actual practice. Talk to someone besides me in the industry.

This is what I do for a living.

This is how GMO "happens." This is genetic interaction at a basic level of modification.

We can talk deletions and domains if you want...we're basically talking about "breaking a circle" at specific points of "important" initial genetic information and then deleting/inserting new genetic information in. It turns the old data into unreadable/unusable junk while the host knows what to do with the new information. It's like adding destructive noise to a voice message while also taking parts of the message out and inserting new voices in. It would be a very rare, next to impossible, thing to actually hear the initial message thanks to the tampering.

"nc-crn, your cut and paste from an earlier discussion is interesting, but it does not appear to address most of the concerns brought up in the main link that I gave ("The paper linked to in the "Here is a link that might be useful" box has 124 comments which the reader may find interesting.") .
The following is a quote from the link that indicates what they are concerned about: "The Many Functions of Gene VI
Gene VI, like most plant viral genes, produces a protein that is multifunctional. It has four (so far) known roles in the viral infection cycle. The first is to participate in the assembly of virus particles. There is no current data to suggest this function has any implications for biosafety. The second known function is to suppress anti-pathogen defenses by inhibiting a general cellular system called RNA silencing (Haas et al. 2008). Thirdly, Gene VI has the highly unusual function of transactivating (described below) the long RNA (the 35S RNA) produced by CaMV (Park et al. 2001). Fourthly, unconnected to these other mechanisms, Gene VI has very recently been shown to make plants highly susceptible to a bacterial pathogen (Love et al. 2012). Gene VI does this by interfering with a common anti-pathogen defense mechanism possessed by plants. These latter three functions of Gene VI (and their risk implications) are explained further below:"
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Please notice that they give scientific references. Have you any scientific references to refute their points and their references?

I've already told you I don't have a list of references to give you.

If you choose to not believe, that's up to you. The great thing about science is that it doesn't care about people's faith...it just is.

You're overlooking the fact that P6 expression is highly unlikely in the first place to concentrate on things it "might" do.

Reading the actual paper might fill in some blanks vs. the side-roads those blog/"news" postings are taking you on. Reading just the Discussion part of the paper says a lot about what you need to know without inserting fear and speculation.

"In conclusion, different P35S variants are in use to express proteins in transgenic plants. Here, we detailed the overlap of P35S with the coding sequence of gene VI. Our bioinformatic analyses indicated that no ORFs are present in the P35S that are similar to known toxic and allergenic proteins. Possible unintended effects that are linked to the use of extended versions of the P35S have been determined. The -343 variant, identified by Odell and colleagues, contains all of the necessary elements for full promoter activity and does not appear to result in the presence of an ORF with functional domains, rendering it and its related variants the most appropriate promoter variants for avoiding unintended effects."

-Reference...the actual report... =p

You may want to include a discussion of the following paper in your thread.

"Scientific assessment of publication by Podevin and du Jardin (2012)
24.01.2013

By request from the Norwegian Directorate for Nature Management, GenØk has written a scientific assessment of the publication by Podevin and du Jardin."

Of particular interest to me in your thread will be your discussion of the following:

"This approach ignores the potential availability of protein domains of toxins and allergens in the linear translated sequences. Domains are the functional portions of proteins and consist of at least 25 amino acids. If a domain search shows no hit against known toxic proteins, it should not be concluded that potential toxins might not be found in the future because the domain databases as collections of protein domains are constantly updated."

The original link stopped working, I upgraded it and will post it here:

http://www.genok.com/news_cms/2013/january/vitenskapelig-vurdering-av- publikasjon-fra-podevin-og-du-jardin-2012/181

It also shouldn't be concluded it should/could be found in the future.

P6 proteins are very old, very studied, proteins. There's tons of them.

I've also mentioned...quoting from some of my past posts...

"There's a chance some people may be allergic to the types replicated, but given that they're not "known" to be allergenic it's doubtful enough that the researchers, themselves, believe the P6 produced aren't allergens."

"The chance that something can happen doesn't mean it will happen. For those that complain about GMO allergens this does open up an area to concentrate new research on, though the scientists themselves couldn't even replicate a known allergen in their forced experiments using unnatural forces to play with the DNA."

If a company uses the shortest type of P35S insertion they can...you can lessen the chance of an overlap...and this is what's being done anyway. It is not the goal to blindly shoot huge strings of frames/genetics into existing genetic material hoping they stick. Precise start/end points as cleanly "taken" as possible is the goal. Aside from all of this, it would be rare for a "bad overlap" to actually happen in the first place.

What's probably more important is phenotype/genotype testing is done on everything before it's released into the market place to make sure everything is functioning as desired. The primary focus of this is to ensure a company isn't accidentally introducing something which can make the plant weak or otherwise faulty once a farmer puts a few thousand dollars worth of seed in the ground, but it easily identifies any other issues.

Putting together a GMO "package"/seed isn't as simple as "shoot some genes, breed, and done." 99%+ of all research plants put in the ground (non-consumer, research/development) are torn out as unsuccessful because it has undesired phenotype/genotype characteristics or the genetic insertion didn't "take". Some plants are doing what they're supposed to do, look like what they're supposed to look like, but once the transcriptions are looked at on a genetic level they show undesirable characteristics (such as possible inherit weaknesses to physical or disease issues via known genetic issues).

Could it happen? Yes. Is it likely to happen and hit the consumer? No. Does "no" mean it has a 100% chance of not happening? No.

If something does happen the GMO companies will have all the information needed to see what happened, what kind of insertion was made, what OFRs were used, etc.

As far as things to worry about in the GMO world, I would personally chalk this one up really low on the totem pole of worries.

No one's an expert on everything. Unless you're talking about changing plugs, changing the oil, or other general maintenance on a car...almost everything talked about cars is gonna go right over my head...especially if it's some kind of discussion about how to get the greatest energy exchange from a given fuel's combustion and the proper mechanical pathway to get there (for instance).

I'm trying to walk a line between being technical and not going too far over anyone's head. Just because the things I'm trying to explain in a less-profession-specific way sounds right in my head doesn't mean it translates well outside of my head.

Your opinion is "interesting", but other scientists opinions are "interesting" also. I have already pointed out the incorrect "opinions" about "Citing agreement from university scientists, the company declared it “highly unlikely” that widespread use of Roundup Ready technology would lead to resistant weeds."
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Here is the present (2012) "opinion" of the The European Food Safety Authority (EFSA). It is the keystone of European Union (EU) risk assessment regarding food and feed safety. In close collaboration with national authorities and in open consultation with its stakeholders, EFSA provides independent scientific advice and clear communication on existing and emerging risks.

"While addressing question two of the mandate, the EFSA GMO Panel compared the hazards associated with plants produced by cisgenesis and intragenesis with those obtained by either conventional plant breeding techniques or by transgenesis. The Panel concludes that similar hazards can be associated with cisgenic and conventionally bred plants, while novel hazards can be associated with intragenic and transgenic plants. The Panel is of the opinion that all of these breeding methods can produce variable frequencies and severities of unintended effects. The frequency of unintended changes may differ between breeding techniques and their occurrence cannot be predicted and needs to be assessed case by case. Independent of the breeding method, undesirable phenotypes are generally removed during selection and testing programmes by breeders. The risks to human and animal health and the environment will depend on exposure factors such as the extent to which the plant is cultivated and consumed."

http://www.efsa.europa.eu/en/efsajournal/pub/2561.htm