Press Release: The Genomic Signature of Crop-Wild Introgression in Maize

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Introgression or genetic exchange between crops and their wild relatives is of broad interest due to concern regarding the escape of transgenes from genetically engineered crops. Many fear the potential deleterious effects of such introgression including decreased fitness or diversity of wild relatives and/or the creation of “superweeds” that are resistant to the current arsenal of herbicides. But there is another side to crop-wild gene exchange. A paper published in the open-access journal PLoS Genetics this week reveals that crop-wild introgression is likely a longstanding and potentially beneficial phenomenon in some agroecosystems. Matthew Hufford, Jeffrey Ross-Ibarra and colleagues describe how introgression from wild relatives has shaped the genome of corn, potentially providing essential adaptations as it spread from a narrow center of domestication into novel environments.

Corn was domesticated in the lowlands of southwest Mexico ~10,000 years ago from a wild grass known as teosinte. A few thousand years later corn colonized the high altitudes of the Mexican Central Plateau. There, it came into contact with a different wild teosinte, one presumably well adapted to the new environment. Both corn and teosinte in the highlands have characteristics such as purple pigmentation and hairy stalks and leaves that are believed to help these plants tolerate the lower temperatures and higher ultra-violet radiation of the highlands. For some time, biologists have been stumped as to whether corn and teosinte obtained these highland adaptations independently or through introgression, with some arguing that the shared characteristics were a good example of maize genes escaping into the wild.

hufford.jpg

Through analysis of genetic markers from across the corn genome, Hufford and co-authors provide evidence that the shared characteristics of teosinte and highland corn are due to introgression, but with gene exchange occurring predominantly in one direction — from the wild teosinte into corn. Introgression was particularly common in regions of the genome previously linked to highland adaptation traits. When corn with and without introgression in these genomic regions was grown at low temperature, plants with teosinte introgression showed pigmentation and hairy leaves, consistent with highland adaptation, whereas those without introgression lacked these traits. These results suggest that the successful spread of corn to the highlands may have been enabled by gene exchange with highland teosinte.

In contrast, regions of the corn genome selected by early farmers during domestication appeared particularly resistant to introgression in either direction of gene flow, indicating continued selection against wild traits in corn as well as selection against corn genes in the wild teosinte.

In addition to corn, a number of crops have spread from small domestication centers into novel environments, often populated with locally-adapted wild relatives. The work by Hufford and coauthors suggests genomic data in other systems may reveal that introgression from wild relatives has provided crops with adaptations such as drought tolerance, acclimation to extreme temperature and disease resistance. Rather than focus solely on the biosafety aspects of crop-wild introgression, we can also begin to assess how crop-wild introgression may have contributed to — and continue to be harnessed for — crop improvement.

Reference: Hufford MB, Lubinksy P, Pyhäjärvi T, Devengenzo MT, Ellstrand NC, et al. (2013) The Genomic Signature of Crop-Wild Introgression in Maize. PLoS Genet 9(5): e1003477. doi:10.1371/journal.pgen.1003477

28 Comments

In contrast, regions of the corn genome selected by early farmers during domestication appeared particularly resistant to introgression in either direction of gene flow, indicating continued selection against wild traits in corn as well as selection against corn genes in the wild teosinte.

Does that mean that if early farmers had continuously selected for, say, fat kernels (or whatever), they could have forced enough of a divergence to discourage introgression?

Once again, the age of genomics has allowed for the detailed genetic analysis of evolutionary processes. In this case, the elucidation of a ten thousand year old experiment in selective breeding and artificial selection. This will make possible a more informed and genetically less naive approach to selective breeding in general and corn breeding in particular. It has now become apparent that evolutionary theory is essential to the modern way of life. Those who choose to remain ignorant will indeed be left behind.

But they’re still plants!

Doubt it. There’s enough inter-mating and sufficient recombination that I suspect it would be difficult to have prevented introgression completely. Certainly selection seems to have prevented introgression at some regions of the genome, however. When we look in the opposite direction, from maize to teosinte, we see ~10% of the teosinte genome is admixed with maize, in spite of selection against domestication genes and incompatibility loci.

fnxtr said:

In contrast, regions of the corn genome selected by early farmers during domestication appeared particularly resistant to introgression in either direction of gene flow, indicating continued selection against wild traits in corn as well as selection against corn genes in the wild teosinte.

Does that mean that if early farmers had continuously selected for, say, fat kernels (or whatever), they could have forced enough of a divergence to discourage introgression?

Breeding is simply an extremely well established method of genetically modifying crops.

Having said that, establishing best methods for the use of transgenic crops - a genetic modification method which is somewhat more radical - would be an extremely beneficial thing to do.

Current agricultural practices in developed countries have many unsustainable features. Scorned (by some) and ill-defined though it is, “organic” agriculture often features more sustainable practices (and much of the agriculture practiced in developing countries is involuntarily organic). However, although perfectly good for supplying certain types of crops in certain types of markets, organic methods alone might not be enough to produce needed quantities of major basic food crops.

Transgenic “GM” crops could bridge the gap, allowing more sustainable practices without compromising yields.

Unfortunately, and this is a case where other developed nations are as irrational as the US, there is a clash between two biased and unreasonable groups - affluent yuppie consumers who react hysterically to the word “genetic”, and self-interested corporations that resist any oversight while pushing their own transgenic products.

(Ironically, creationists should deny that “GM” crops can exist at all, but they don’t seem to.)

That’s just all too complex to happen without The Designer.

ID science done!

Glen Davidson

harold said:

(Ironically, creationists should deny that “GM” crops can exist at all, but they don’t seem to.)

Okay. I’ll bite. Why? It would seem to me to be an example of “Intelligent Design”. Monsanto scientists are “Intelligent” and they used “Design” to create the “GM” crops. Why should creationists deny this? Or, are you pointing out a possible distinction between Creationists and ID?

[ That’s two comments missing now. This is a connectivity test. Apologies again. ]

diogeneslamp0 said:

But they’re still plants!

And since AIG knows plants aren’t alive anyway, then anything that happens to them has nothing to do with the evolution of life!

Scott F said:

harold said:

(Ironically, creationists should deny that “GM” crops can exist at all, but they don’t seem to.)

Okay. I’ll bite. Why? It would seem to me to be an example of “Intelligent Design”. Monsanto scientists are “Intelligent” and they used “Design” to create the “GM” crops. Why should creationists deny this? Or, are you pointing out a possible distinction between Creationists and ID?

I’ll explain.

The hard way to understand evolution, which was the only available method up until about the 1960’s (coincidentally or not the time post-modern creationism exploded into view), is top down.

Not knowing the molecular basis of genetics, scientists nevertheless worked out classical/population genetics and developed the theory of evolution.

But now we know a great deal about molecular genetics.

Once you understand molecular genetics, you can easily see that it is impossible for life not to evolve, from the “bottom up”.

Essentially every time a nucleic acid genome replicates, there are mutations. The mutations which can occur are obviously constrained by the parent sequence, but the next generation is constrained by the new parent sequence, and so on. Inevitably, some mutations must impact phenotype. Anyone who denies this would need to provide a mechanism by which the chemical process of mutation could perfectly “know in advance” “exactly which” mutations would impact phenotype, would have to explain how a chemical process could stop itself, and would have to explain away all the extremely well known examples of mutations impacting phenotype. Arguing against what I have just pointed out would be exactly the equivalent of arguing that some ice cubes can decide not to melt at room temperature, because they can see in advance that melting would create some kind of outcome.

(You could, of course, argue that a deity actually permits or controls all chemical reactions, and could prevent an ice cube from melting if it felt like it, but that it nearly always chooses to let physics and chemistry run their course. That view is is more or less the “theistic evolution” view, which is fine with me and not at odds with what I have said about molecular genetics. What you can’t argue with consistency is that ice cubes routinely refuse to melt, or that random mutations in replicating DNA routinely “decide” whether or not to occur.)

Inevitably, if phenotype is impacted, some of the time the impacted phenotype must have a reproductive advantage or disadvantage in the given environment. Again, anyone who would deny this would have to explain how chemical reactions could know precisely, in advance, whether a mutation would impact phenotype, and then know how the phenotypic variation would impact stochastically expected reproductive rate in the near future environment. There is no magical reason why phenotype-impacting mutations would always be disadvantageous, in fact, it is nonsensical to claim that, because if that were true, probably all of life would be extinct now due to accumulation of deleterious mutations. I’ll also mention that the evolution of DNA repair pathways supports all of the obvious things I have just pointed out.

So molecular genetics expands and confirms the findings of classical/population genetics, and adds a huge amount of supporting evidence for the theory of evolution.

Therefore, to deny the theory of evolution with consistency, you must deny molecular genetics, which some creationists do (although others try to pretend they do not).

If you deny molecular genetics, then you deny that transgenic anything, including “GM” crops, can be generated.

Therefore, if you deny evolution, to be consistent, you must deny the existence of such crops.

(You could, of course, argue that a deity actually permits or controls all chemical reactions, and could prevent an ice cube from melting if it felt like it, but that it nearly always chooses to let physics and chemistry run their course. That view is is more or less the “theistic evolution” view, which is fine with me and not at odds with what I have said about molecular genetics. What you can’t argue with consistency is that ice cubes routinely refuse to melt, or that random mutations in replicating DNA routinely “decide” whether or not to occur.)

“Fine with me” not in the sense that it is what I believe - I am not religious - but in the sense that it’s not a view I’m interested in arguing against.

harold said:

Therefore, if you deny evolution, to be consistent, you must deny the existence of such crops.

Unfortunately, creationists are not constrained by the need for consistency. They can deny anything at all, whether it is consistent with other denials or not. And of course they think nothing of reaping the benefits of that which they so vehemently deny.

harold said:

harold said:

(Ironically, creationists should deny that “GM” crops can exist at all, but they don’t seem to.)

Scott F said:

Okay. I’ll bite. Why? It would seem to me to be an example of “Intelligent Design”. Monsanto scientists are “Intelligent” and they used “Design” to create the “GM” crops. Why should creationists deny this? Or, are you pointing out a possible distinction between Creationists and ID?

I’ll explain.

Okay. I see your point. First, however, I think this point is way too subtle. Were talking about “Creationists”, who (for the most part) don’t understand how genetics works, let alone how mutations work.

Second, a lot of your logic has already been rejected by Creationists, or actually used against Evolution. For example,

There is no magical reason why phenotype-impacting mutations would always be disadvantageous, in fact, it is nonsensical to claim that, because if that were true, probably all of life would be extinct now due to accumulation of deleterious mutations.

Yet, this is exactly the YEC argument (or one of their arguments). All mutations are disadvantageous, by definition (They’re mutations! Duh!), therefore life cannot be “old”, otherwise it would be extinct by now.

Inevitably, some mutations must impact phenotype. Anyone who denies this would need to provide a mechanism by which the chemical process of mutation could perfectly “know in advance” “exactly which” mutations would impact phenotype, would have to explain how a chemical process could stop itself, and would have to explain away all the extremely well known examples of mutations impacting phenotype. Arguing against what I have just pointed out would be exactly the equivalent of arguing that some ice cubes can decide not to melt at room temperature, because they can see in advance that melting would create some kind of outcome.

(You could, of course, argue that a deity actually permits or controls all chemical reactions, and could prevent an ice cube from melting if it felt like it, but that it nearly always chooses to let physics and chemistry run their course. That view is is more or less the “theistic evolution” view, which is fine with me and not at odds with what I have said about molecular genetics. What you can’t argue with consistency is that ice cubes routinely refuse to melt, or that random mutations in replicating DNA routinely “decide” whether or not to occur.)

It’s Poe’s law. No parody of Creationism is too extreme. You say this like it’s impossible, or ridiculous, or inconsistent; and I agree. Yet, Ray Martinez believes exactly this point. His “mechanism” is “intelligence”, which is outside the physical realm.

Therefore, to deny the theory of evolution with consistency, you must deny molecular genetics, which some creationists do (although others try to pretend they do not).

If you deny molecular genetics, then you deny that transgenic anything, including “GM” crops, can be generated.

Therefore, if you deny evolution, to be consistent, you must deny the existence of such crops.

You’re conclusion doesn’t follow. You left out “God” or the “Intelligent Designer”.

Consistency isn’t the Creationist’s strong point.

“If you deny evolution, to be consistent, you must deny the existence of such crops, or invoke “Poof” or invoke “Intelligence”.”

Remember the DI’s contention. Anytime you stick “intelligence” anywhere in the equation, all logic and consistency are magically erased. “Intelligence” is that magical discontinuity in logical reasoning. Humans “intelligently” made GM crops. Therefore, Jesus.

Sigh… It’s like trying to reason with a bag of water balloons.

harold said:

(You could, of course, argue that a deity actually permits or controls all chemical reactions, and could prevent an ice cube from melting if it felt like it, but that it nearly always chooses to let physics and chemistry run their course. That view is is more or less the “theistic evolution” view, which is fine with me and not at odds with what I have said about molecular genetics. What you can’t argue with consistency is that ice cubes routinely refuse to melt, or that random mutations in replicating DNA routinely “decide” whether or not to occur.)

“Fine with me” not in the sense that it is what I believe - I am not religious - but in the sense that it’s not a view I’m interested in arguing against.

I don’t think most people have a problem allowing for “theistic evolution”. “Strong” atheists (like “phhht”) would argue that it isn’t necessary, there is no physical mechanism to support it, and no statistical gap for it to fill, but at least it isn’t in denial of existing science.

[ If I may be indulged, three attempts at this comment have disappeared. I will trying breaking it into pieces, and see what happens. ]

[ Piece #1 of 3 ]

harold said:

Breeding is simply an extremely well established method of genetically modifying crops.

Breeding is an extremely effective means of “Natural Selection”. Breeding is limited to using “natural” variation or mutations.

[ Piece #3 of 3 ]

Do “we” (the scientific community) even have the ability (today) to discern such bio feedback responses at that level of granularity? It would seem to me that the genetic and behavioral variability (what people eat, where we get our food, how health changes are reported, etc) at the national or regional level would prevent any detailed analysis of the effects of a specific crop gene on the human population, unless there were some invasive and massive public health initiative to gather and track the necessary data, even assuming we knew what data to gather and track.

One possibility that might justify the conspiracy is that there might be some simple and specific test for some biological “marker” in the population, which is easy to identify (non-invasively and in aggregate), and highly correlated with the proposed genetic modification. But from what little I can (being outside the “scientific community”), this seems highly unlikely. While the genetic diagnostic abilities I see reported here and in the popular press are indeed impressive compared to just 10 or 20 years ago, it seems we are still at the very rudimentary stages of being able to attribute specific effects to specific genetic causes, let alone to intentionally manipulate those effects.

[ Humph! Odd. Simply removing two pairs of “italics” HTML tags allowed the comment to go through, even though it passed the “Preview” button just fine. Apologies for the “meta” comments. Carry on. ]

[ Nuts! It disappeared again. ]

[ Piece #2a of 3 ]

harold said:

Unfortunately, and this is a case where other developed nations are as irrational as the US, there is a clash between two biased and unreasonable groups - affluent yuppie consumers who react hysterically to the word “genetic”, and self-interested corporations that resist any oversight while pushing their own transgenic products.

[ Piece #2b of 3 ]

The argument that I’ve heard most recently is that Monsanto (for example) closely monitors public health records, and “dials up” or “dials back” certain specific modifications to some gene in some seed crop on a sub-decadal cycle, in response to changes in (say) the prevalence of autism or food allergies. Somewhat like what tobacco companies did with scientific data, back in the day. You just can’t trust them trans-nationals.

[ Piece #2c of 3 ]

While I’m willing to believe that there may be unintended human physiological consequences to various genetic modifications of crops, I’m skeptical of such conspiracy theories. While I’m willing to admit that such conspiracies are possible (after all, the tobacco companies did manipulate the science), I’m even more skeptical that such science can even be performed at the level of detail required for such a grand “GM” conspiracy. But I lack the biological background to make such judgements.

[ The comment is now complete, if somewhat scattered. Again, my apologies for this. I couldn’t leave well enough alone. I still don’t have an explanation for why “Piece #2b of 3” consistently failed to appear. ]

Jeffrey Ross-Ibarra said:

(snip)There’s enough inter-mating and sufficient recombination that I suspect it would be difficult to have prevented introgression completely. Certainly selection seems to have prevented introgression at some regions of the genome, however. (snip)

That’s what I was rather clumsily trying to ask. :-) Thanks.

DS said:

harold said:

Therefore, if you deny evolution, to be consistent, you must deny the existence of such crops.

Unfortunately, creationists are not constrained by the need for consistency. They can deny anything at all, whether it is consistent with other denials or not. And of course they think nothing of reaping the benefits of that which they so vehemently deny.

This is also a reply to Scott F.

Needless to say, I completely agree that creationists are inconsistent. The only consistency is “say anything to deny evolution, even if what you say right now contradicts what you said a minute ago”. But my point was not that creationists will or do deny the existence of GM crops, rather, my point is that this is just another example of the fact that, while they deny science verbally, they implicitly accept its findings with their behavior. Other examples include use of computers, use of stairs or elevators instead of jumping out of high windows, etc.

Scott F said:

[ Piece #2b of 3 ]

The argument that I’ve heard most recently is that Monsanto (for example) closely monitors public health records, and “dials up” or “dials back” certain specific modifications to some gene in some seed crop on a sub-decadal cycle, in response to changes in (say) the prevalence of autism or food allergies. Somewhat like what tobacco companies did with scientific data, back in the day. You just can’t trust them trans-nationals.

This is a very implausible sounding conspiracy theory.

What cigarette companies did was nothing of the sort. All they ever did was deny and distort the evidence linking cigarettes to disease (while simultaneously marketing ostensibly “lighter” or “healthier” versions, thus contradicting themselves, even though the “healthier” versions aren’t even “healthier”). Cigarette companies behaved exactly as creationists and climate change denialists - “say anything to deny the science, even if you contradict yourself”.

I think it’s important to differentiate between the behavior of Monsanto, and the concept of GM crops overall, though. One is a private corporation with a reputation for somewhat ruthless behavior in terms of both currying government favor and dealing with customers and competitors. The other is a science-based technological advance that might allow higher food production with far more sustainable techniques.

We live in a society with fairly good control of infectious disease and acute environmental toxins like lead etc, and fairly good emergency treatment for common emergent cardiovascular conditions - at least that’s true for now, assuming some sort of “bipartisan austerity package” doesn’t destroy all of that. Meanwhile, some multifactorial conditions like obesity are increasing, and others, such as autism and autoimmune/allergic conditions, are either much more increasingly recognized, or increasing. There is a fair amount of public concern, bordering on hysteria, in certain segments of the affluent community, about these conditions. Unfortunately, this concern often expresses itself as a preference for fake expertise rather than real expertise. I can understand why someone would say “modern medicine can’t perfectly deal with my particular problem”. That’s often true. Why this leads to the conclusion that “some obviously self-serving ‘healer’ who operates with no oversight and doesn’t care about feedback or evidence is better” is a mystery to me.

Nevertheless, at a broader level, the concern is valid. If autism, for example, is either going up or being increasingly recognized, that does lead, logically, to the question of which it is, and how to best prevent or manage what we call autism (with the caveat the some people who carry an autism spectrum diagnosis deny needing any type of medical management, and they are perfectly right that it is their own business whether they want it or not).

The epidemiology of complex, chronic diseases is poorly understood, and I personally think it’s valuable to acknowledge that, and not dismiss all concerns. That doesn’t mean that conspiracy theories, crackpots, fraudulent quacks, and so on should be treated with kid gloves, but it does mean that we shouldn’t be too dismissive of peoples’ concerns, either.

We live in a society with fairly good control of infectious disease …

p.t.?

About the subject of GM crops and autism, etc. I had done some online searches on the topic, and I must say it appears to me that scientists do not yet have a strong case either way. There is now a consensus that the rates of reported autism spectrum disorders have risen to as high as 1 in 50 (in the US), but researchers do not have a clear consensus about whether that is a real increase, or due to increased screening and sensitivity to diagnosing autism, or a bit of both. So whatever side you are on about the increase in autism it seems you can refer to sources that support your view. Lots of web sites say there is an increase, but these tend to be have a non-objective tone, and they cite the causes as correlating with vaccinations or GM crops. The anti-vaccers are still very much alive, sadly. As to a link to GM crops, there are anectodal ‘reports of reports’ of a study finding that animals raised on GM crops develop behavioral problems and intestinal problems. A common side effect of autism is intestinal problems, especially due to eating foods that happen to be more likely laced with GM ingredients. If this was an actual controlled animal study, and is reproduced, then that may be suspicious, but again the cites touting this are not vetted sites that report on science based medicine. What is puzzling too is I have yet to find peer reviewed research that has looked into this issue, which is strange since it is well known and should be looked at.

If Monsanto actually knew the relation between Roundup Ready seeds and autism well enough to “dial it back”, then they could go into the autism detection/correction business and/or collect a few Nobel Prizes in Medicine. Sorry, this is pure conspiracy theorizing.

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