from the maybe-they-can-get-a-grant-from-starbucks dept.
When coffee leaf rust—which was first spotted in East Africa in the 1860s—made it to South America in the 1970s, Colombia's national coffee research center, Cenicafé, was already a decade into its rust resistance breeding program.
The rust, called roya in Spanish, is a fungus (Hemileia vastatrix) that is highly contagious due to airborne fungal spores. It affects different varieties, but the Arabica beans are especially susceptible. Rainy weather worsens the problem. The rust typically enters the coffee leaf via the stomata.
Their methods were traditional cross, breeding, planting, evaluating rust resistance, comparing taste and aroma. It was a long and arduous process, sometimes taking 25 years to develop a cultivar that was rust resistant. Still, Cenicafé succeeded with two cultivars, Colombia (in 1980) and Castillo (in 2005) that have been reasonably rust resistant.
Now ScienceMag is reporting that sequencing the genome of major Coffee families is shortening this development cycle by documenting those coffee genes that provide resistance. At the same time the sequencing of rust genes has identified those elements of its genome that are involved in gaining entry into the coffee leaf.
By selecting coffee for cross breeding with a map of the genome in hand, and analyzing the genome of the resultant plant, they can shorten the 25 year development cycle down to less than a year, without having to wait until the trees mature.
Unlike genetically modifying seed to tolerate pesticides, this method of selecting for the most resistant strains does not require the use of pesticides.
"Coffee farms the world over are still planting susceptible cultivars that increasingly require pesticides to fend off disease. This heavy application of pesticides is irresponsible", Álvaro Gaitán, a plant pathologist at Colombia's national coffee research center, says, "especially on small-holder farms like the ones dotting Colombia. "Every time you recommend the use of a pesticide you're exposing the farm family, too, because they live very close to these fields," he says. "And many of these coffee diseases are controlled by natural enemies of the fungus. You don't want to kill those off."
The US government will be offering a 5 million dollar aid package in partnership with Texas A&M Coffee Research Center to combat the fungus.
(Score: 0) by Anonymous Coward on Friday September 19 2014, @03:05PM
A programmer is a machine for transforming *GMO coffee* into code.
(Score: 1) by BananaPhone on Friday September 19 2014, @03:34PM
If Monsanto is involved, I don't want it.
Enslavement to GMO patents by a such an evil Corp is worse than the disease it prevents.
(Score: 3, Insightful) by Theophrastus on Friday September 19 2014, @03:49PM
This story supports at least two worthy notions:
(1) There really is no molecular difference (despite the dubious non-peer-reviewed "evidence" out there) between standard ancient cross-breeding and GMO techniques. It's just that the older technique will always take longer, often quite considerably longer. DNA fragments are either shifted directly, or one waits until that same event occurs randomly and hope you've captured it.
(2) If you're goal isn't to add value to your line of nasty (for 'nasty': anything with "-icide" suffix) chemical treatments, then GMO can be used to a positive result. It's just a technique; it can be used for 'good' or 'eeeeevil'. (yes... Monsanto and friends appear to prefer the latter)
(Score: 5, Interesting) by TK on Friday September 19 2014, @04:17PM
Exactly this. The only difference between this method of selective breeding and the old version is that you don't have to wait until the genes express themselves before you start the next round of breeding. You sequence the plants' genomes, find what you're looking for, then make a bunch of baby plants with your best picks. Rinse and repeat until you get the desired result.
As long as no one tries to patent the resulting plant, and there are enough competing varieties that we won't lose the entire world's supply when the next disease comes around, then I think this is a good thing.
Better coffee through science!
coffee++
The fleas have smaller fleas, upon their backs to bite them, and those fleas have lesser fleas, and so ad infinitum
(Score: 2) by opinionated_science on Friday September 19 2014, @06:39PM
Just to correct the narrative here. Selective breeding is by definition choosing a phenotype from a specific cross-breeding.
Genetically modified organisms can certainly achieve the same effect, this is not at all required.
The mechanism of recombination deliberately mixes up genetic regions, and this is NOT how GMO is acheived.
Hence, there are many things to be understood regarding regulation , but on the whole, splicing a single well characterised gene is probably a low risk.
My point is that it is not cut and dried - there are subtleties and we should be cautious when we seek to impose our desires on natural systems.
I'll buy happily GMO, but I'd like to know what they did...
(Score: 2) by tibman on Friday September 19 2014, @04:59PM
I think the key difference is that this wouldn't count as GMO if they are still cross-breeding. The genetics are checked to see if the desired traits have been passed down. But the DNA was not directly manipulated.
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(Score: 1, Insightful) by Anonymous Coward on Friday September 19 2014, @05:18PM
> I think the key difference is that this wouldn't count as GMO if they are still cross-breeding.
Compare this to what they did in Hawaii with papayas to make them resistant to the ringspot virus. [wikipedia.org] There are no naturally occurring strains of papaya that are resistant to ringspot. So instead of selective breeding, they went the transgenic route and implanted genes from the ringspot virus into the papaya genome. That is the kind of GMO that gets people worked up.
(Score: 2) by HiThere on Friday September 19 2014, @08:30PM
To be fair, it's more proper to characterize that as "The kind of GMO that increases the danger over simple crossbreeding".
For many people, myself among them, the primary reason to be against GMO is that it is acting to vest monopoly control over the food supply in a corporation. I will grant that its not there yet...but I *really* don't ever want it to get there.
Javascript is what you use to allow unknown third parties to run software you have no idea about on your computer.
(Score: 0) by Anonymous Coward on Friday September 19 2014, @09:28PM
The hawaiian papaya example doesn't fit that model.
The modification was done by the state university and the results are not controlled by any corporation.
It is true that the method of hybridization that created the new transgenic breeds was subject to patents owned by Monsanto, but the plants themselves are not.
https://noteasytobegreen.wordpress.com/2012/06/14/the-curious-case-of-the-transgenic-papaya/ [wordpress.com]
(Score: 2) by HiThere on Friday September 19 2014, @08:25PM
I don't think you're understanding the process. This has nothing to do with GMO.
If you want to move mosquito genes into a bat, you MUST use GMO techniques. If you just want to select from genes that are already present, there's no such requirement.
GMO techniques are more risky, have a higher failure rate, and have a chance of introducing some totally unexpected result. But they are, indeed, relatively fast. They are also of dubious safety...you need to test carefully for unexpected interactions, and even then you can be surprised, because you don't know what you need to look for.
OTOH, *both* techniques are usually safe. *Both* techniques and occasionally produce an unexpected result, which can be good but is more likely to be bad. However the GMO techniques, due to their wider range of possible changes, can produce worse catastrophes when something goes really wrong. (AFAIK, this has never happened. That doesn't mean it won't, it's a predictable consequence of the rarity of the use of GMO techniques and the rarity of the *really bad* result. ... Note that as a part of the definition a really bad result is one that isn't caught before the stuff goes on sale. Worse is one that isn't caught during the first decade.)
FWIW, such *really bad* things can also happen through pure natural selection. There's a fungus that infects a moth(?) that has the effect of killing off all female descendants....but increasing the number of male descendants. The moth, were it aware, would consider this a truly terrible result. The fungus, were *it* aware would feel the same way, as eventually the species that is is dependent on will go extinct through lack of females. We don't know how long the fungus has been spreading, but this must be a fairly recent mutation in the fungus, because it is otherwise well adapted to the moth.
(N.B.: The above anecdote is second hand to me, and I don't remember the original source. I think I may have encountered it in one of Stephan Jay Gould's books.)
The thing is, natural breeding rarely has this kind of large scale unexpected interaction. All the genes have been shuffling together for a long time. When you merge two strange sets, you need to EXPECT unexpected interactions. And it's really hard to look for unexpected interactions, because you don't know what to look for.
OTOH, in principle, and given enough time, one could add the mosquito gene to the bat (or was I going the other way). But you aren't talking about any small number of epochs. A billion years might be about right, provided you could keep the project properly directed.
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(Score: 2) by Yog-Yogguth on Friday September 19 2014, @08:34PM
One never¹ mixes kingdoms [wikipedia.org] and even mixing phyla can be difficult with classical cross-breeding while in GMO the whole point is the ability to do exactly that² or anything else you can imagine i.e. you are completely and utterly wrong.
¹ discussions on horizontal gene transfer [wikipedia.org] do not belong here and entirely misses the point: the more powerful the science the more careful one has to be, and GMO is as powerful as biology gets and as powerful as all of life ever gets (excluding making the jump to technological evolution as humans did). The stakes are at least on par with nuclear fission technology and much higher than that if one considers the accessibility, relative ease, and potential for unintentional damage.
² e.g. bacteria made to produce human proteins, insulin, etc. doesn't happen any other way than by mixing kingdoms.
Can be used for evil and good? Not so sure about that, certainly not under current conditions. There is some sort of threshold where the misuse of technology is not only easy but exciting and profitable (grants if nothing else), and where in addition the established best practices right from the start were superficial PR mainly concerned about not being too expensive (all GMO ought to be BSL-4 contained —not that it would seem to do any good in the US— but any non-GMO results could be “exported” given stringent enough purity control). Then add a debate filled with the usual uneducated noise where lots of people push their mostly worthless titles in front of them rather than anything resembling coherent arguments and where most of the opposition (who are right) doesn't actually know or understand or focus on why they're right.
No GMO (O is for organism) should be legal outside of laboratories and factories, containment breaks should invoke clear risks of capital punishment and full appropriation of entire companies (including top shareholders and any other assets they might own). That would fit the potential for accidental and inadvertent destruction that GMO carries and might alleviate a little of the rampant hubris.
The core problem? When people (and politicians) don't know shit or have no imagination of what can go wrong at all (the default state for all of us) they want to err towards “the middle” in order to be “reasonable” and never take a second to think through how often “the middle” is right about anything in a topic they know well. It would take time and effort and most people have neither through no fault of their own or anyone at all.
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(Score: 2) by buswolley on Friday September 19 2014, @04:39PM
(1) Great article submission. Interesting topic. Great framing for general discussion.
(2) The great danger in widely deploying GMO breeds is risk of spurring the evolution of fungii that can tolerate the new variety. The obvious method to ameliorate this threat is to also plant nonresistant varieties along side the resistant varieties of plants. I believe this has long been recommended practice, but one rarely followed; fewer resist and plants mean lower yield in the absence of an immediate threat. If others do but you don't, you enjoy an cost advantage. Therefore immediate incentives are lacking, and only after a threat is encountered will farmers act...by buying the newest variety ofvresistant plants from Monsanto.
subicular junctures
(Score: -1, Offtopic) by Anonymous Coward on Friday September 19 2014, @04:55PM
Well in the end 8 went to the inn. Grabbed a donkey with MTB pal in the in the Indian Summer. Besides even got a miniscule max IMHO from my dad
. in rese ting the TV to black and white. Really their should go home.
(Score: 1) by Arik on Friday September 19 2014, @05:03PM
You would be encouraging exactly what you want to avoid, by effectively culturing the fungi next to your resistant plants, you would be maximizing the opportunities for development of a new fungi strain that can eat them.
Better to clear anything that fungi might eat from as wide an area as possible around the new crop.
If laughter is the best medicine, who are the best doctors?
(Score: 2) by buswolley on Friday September 19 2014, @08:55PM
Planting varieties that the fungii you might be increasing the population of fungii overall, but any chance evolution to being able to eat the resistant plants is likely to be quickly diluted by the larger fungii gene pool existing on the non-resistant plants.
Was referring to this related story appearing earlier this year.
http://www.wired.com/2014/03/rootworm-resistance-bt-corn/ [wired.com]
subicular junctures
(Score: 5, Insightful) by sjames on Friday September 19 2014, @05:04PM
The GMO techniques so many object to are NOT in play here. This is regular cross breeding informed by gene sequencing. IMHO it's the right way to do it.
They do not extract genes from one organism and splice them into another. Instead, they sequence their breeding stock, and select the ones that have interesting genes. Then cross them the old fashioned way and sequence the results to select the ones that inherited all of the desired genes. By sequencing, they know where to focus before the plants even mature enough to breed further AND they can be sure which ones are interesting.
(Score: 2) by HiThere on Friday September 19 2014, @08:50PM
There's a problem here, though.
This is, indeed, the right way to do thinks when you *can* do things this way. But this depends on the needed genes already being present the genepool. Sometimes they aren't. And in that case GMO is the only viable approach.
The problem is that GMO introduces (well, significantly increases) the problem of "unknown unknowns". This is a low probability problem, but it's also a potentially high risk problem. (Bad results can be as bad as "species lethal" over time. This is unlikely, but it's happened in ordinary evolution.)
The problem with "unknown unknowns" is that you don't know how to look for them. So it's (nearly) always better to reduce them to the lowest feasible level. (You *can't* get rid of them.) The problem with them is that the results are almost always bad. (OTOH, occasionally, just occasionally, they are extremely positive.)
To take the example of the papays that you were mentioning above, how would you test that to ensure that when infected by an unexpected (particular) virus they didn't become hyper-contagious in a modified version of the ringnode fungus that would also infect sugar cane? It's a totally improbable result, so you'd be extremely unlikely to even consider looking for it. But it could have devastating economic impact. It clearly hasn't happened yet, but maybe that's just because the right strain of papaya hasn't been infected by the right virus around a sugar cane plant.
Well, that particular scenario is unlikely enough that it doesn't make sense to worry about it. But that class of scenario isn't that unlikely (though I'll grant that it's still unlikely). This class of event isn't much less likely than a new zoonosis event. And those seem to happen every year. (But consider the number of interactions between people and animals, and you'll realize just how unlikely each particular event was.)
So. As a scientific method I think GMO is quite a good thing. As a profit center I'm much less sanguine. Companies skimp on safety measures quite regularly, and this one has the possibility of being quite deadly. (And I'm also strongly opposed to ANY company being in a monopoly position WRT any major part of the food supply.)
Javascript is what you use to allow unknown third parties to run software you have no idea about on your computer.
(Score: 2) by sjames on Friday September 19 2014, @10:08PM
That's just the thing, if we can't make it happen through conventional cross breeding, the risk of irreversible harm is very high. I don't trust a for profit company with that level of responsibility. For scientific research, IF they also take measures to make the result non-viable outside the lab, it can be acceptable.
(Score: 2) by zafiro17 on Friday September 19 2014, @07:07PM
Great subject, and I'm thrilled/grateful to see some informed and scientific discussion around here. SN keeps getting better and better.
Coffee rust is a game changer in most coffee producing countries. I lived in one for about 5 years - Nicaragua, Central America - and when the coffee rust gets bad there is no harvest and people go hungry. There's a human element involved too, as bad management of coffee plantations has a lot to do with the spread of rust. But giving a little push in the direction of more resistant plants would be an economic game changer for many. Interesting article; thanks for posting it - I'll try to link from a couple of places including http://www.gotonicaragua.com/ [gotonicaragua.com] which follows subjects related to the country.
Dad always thought laughter was the best medicine, which I guess is why several of us died of tuberculosis - Jack Handey
(Score: 2, Interesting) by N3Roaster on Friday September 19 2014, @07:14PM
As a bit of side trivia and as an historical demonstration of just how serious this is, Sri Lanka (then Ceylon) used to be a coffee growing island until coffee rust wiped out the whole crop. It was after this that they switched to tea.
I am, however, sceptical of claims that the development cycle can meaningfully be reduced to less than a year because it's still important to know what kind of yield you can expect over a reasonable period. It usually takes at least 5 years (more like 5-10) before farmers figure out what they can expect of a given cultivar on their land (that's a general consideration moving varieties out of areas they are traditionally planted in). Coffee isn't something that you plant at the start of your season, harvest at the end, and start over with next year. That said, any improvement on development time is welcome.
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