For your daily bread, give thanks to the latest genetic research

All flesh is grass, saith Isaiah. No grass contributes more to human flesh than the wheat that gives us our daily bread. Bread wheat feeds 30 percent of the human population and provides 20 percent of our calories. And bread wheat may be able to meet future challenges of feeding a hotter, drier, more populous world thanks to two major genetic research developments in just the last few days.

Last Friday, Science published a series of open-access papers describing the most detailed picture of the very complicated wheat genome so far.  On Sunday, Nature Biotechnology published an account of how Chinese researchers have used the latest gene-editing techniques to make bread wheat resistant to the fungal pathogen called powdery mildew, a major scourge of wheat growing.

The wheat genome sequence is a boon to plant breeders who want to bring to wheat not just disease resistance but other crucial traits such as the ability to withstand drought and pests.  The Chinese work gives hope that advanced gene editing techniques can yield improved wheats that are free of the stigma of GMOs and will not encounter consumer resistance.

These techniques — I wrote about the one called CRISPR and others here at GLP in February —are adaptations of naturally occurring genetic processes. In the wheat case, they did not involve traditional genetic engineering approaches such as inserting a foreign gene. They were gene deletions resembling conventional mutations.

In a Technology Review piece about the powdery mildew research, David Talbot quoted Xing-Wang Deng, who heads a joint research center for plant molecular genetics and agricultural biotech at Peking University and Yale. “And this could be considered as a nontransgenic technology, so that can be very significant. I hope the government would not consider this transgenic, because the end result is no different than a natural mutation.”

Give us this day the very complicated bread wheat genome              

The rice genome was sequenced as long ago as 2002, and the corn genome—maize—came along in 2009. Wheat is no less important for humanity than those two basic grains, but the wheat genome project has taken far longer. So why did the bread wheat genome project take so long? Because while good bread tastes like heaven, bread wheat’s DNA is hell to sequence. And the bread wheat genome project is not finished even yet.

The genetics of bread wheat, Triticum aestivum, are far more intricate than the genomes of those other indispensable grains. First of all, the wheat genome is gigantic—well over 100,000 genes, five times as many as H. sap‘s paltry 20,000 or so. That’s because wheat has been a more than usually promiscuous plant. That hybridization history has been revealed in the just-published research by a huge team known as the International Wheat Genome Sequencing Consortium.

Like many plants, bread wheat has more than the usual two sets of chromosomes, the diploid condition we animals are accustomed to.  As Jennifer Frazer explains at National Geographic, several hundred thousand years ago two diploid grass species, Triticum urartu and Aegilops speltoides, hybridized to produce emmer wheat, a tetraploid  (with four sets of chromosomes.)

Wild emmer has been found in a 20,000 year-old hunter-gatherer archaeological site near the Sea of Galilee, and domesticated emmers date back well over 10,000 years. In recent times emmer has been eaten mostly in Italy, where it is known as farro. In the US, farro has lately been resurrected as a trendy boutique food item, a crunchy cooked grain served on its own or as an ingredient in salads and soup.

But emmer is not bread wheat. Bread wheat is the result of another mating, this time between emmer and the grass Aegilops tauschii, a mating that is believed to have occurred at the dawn of agriculture about 10,000 years ago. This hybridization yielded Triticum aestivum, a hexaploid plant (with six sets of chromosomes.)

Wheat is the Habsburgs of the plant kingdom

To complicate matters further, A. tauschii itself appears to have been the result of the mating of emmer’s parents, T. urartu and Ae. speltoides. In a post at Scientific American, Frazer observed dryly that wheat’s family tree resembles the Habsburgs’ because of what it reveals about matings between close relatives. One scientist, she said, calls this revelation “shocking.”

More than 80 percent of bread wheat’s six sets of chromosomes consists of long strings of repeated sequences, particularly ferocious to sequence. Which is why the T. aestivum genome is still incomplete, still technically only a draft sequence. Researchers have finished the more-or-less final reference sequence on just a single chromosome, known as 3B. The plan is to finish the other 41 chromosomes within three years. In the draft, the genes are on the correct chromosomes in the correct order, but the huge sequences between the genes are not yet known.

The T. aestivum genome is also unusually redundant. Unlike most plants with multiple sets of chromosomes, where redundant genes are silenced, Frazer tells us that in bread wheat the same genes from all three sets of chromosomes continue to carry out the same functions. Many genes have also been duplicated.

A signal accomplishment of the Chinese work on making wheat resistant to powdery mildew is that the researchers were able to disable all three copies of the genes encoding proteins that repress defenses against the fungus. “This is very, very interesting; it is quite an accomplishment to knock out all three genes at the same time,” Deng said.

Bread wheat as a GMO?

Which brings us to prospects for making T. aestivum into a GMO. In contrast to other crops like corn, no significant amounts of genetically engineered wheat are grown anywhere. In a New York Times op-ed last February, Jason Lusk and Henry Miller say this is because short-sighted US wheat farmers resist GM varieties due to fear of higher seed prices and consumer resistance abroad that would damage the wheat export market.

Monsanto is developing an herbicide-resistant GM wheat that will be ready to market in a few years, they say. “But the federal government must first approve it, a process that has become mired in excessive, expensive and unscientific regulation that discriminates against this kind of genetic engineering,” Lusk and Miller complain.

They think the problem with consumer acceptance of GM wheat lies in the fact that wheat is grown largely for human consumption, whereas most corn goes for animal feed and ethanol. They argue that drought-resistance in particular is a trait wheat badly needs, especially because the US breadbasket lies mostly in the central plains over the Ogallala aquifer, which is rapidly being depleted.

Drought-resistance is obviously a most desirable quality to breed into wheat. Lack of water is a problem for much of the world far beyond the Ogallala aquifer, and agricultural land is only going to get drier as the planet gets hotter in the next decades. What is not clear is whether the biotechnology techniques Lusk and Miller speak of are the only way to achieve superior dryland wheat, or even the best way.

It may be significant that the agricultural scientists reporters interviewed about the wheat genome papers were excited because they thought this new information meant much-improved ways of bettering wheat with conventional plant breeding techniques. None of them mentioned engineering new wheats via foreign gene transfer or any other of the usual biotech forms of genetic modification.

The Chinese work on powdery mildew suggests that advanced gene editing techniques could contribute new traits to food crops in ways that mimic natural mutations. That may mean that CRISPR and other such editing approaches will create superior plants that can escape the label “GMO.”

Tabitha M. Powledge is a long-time science journalist and a contributing columnist for the Genetic Literacy Project. She also writes On Science Blogs  for the PLOS Blogs Network. Follow her @tamfecit. 

12 thoughts on “For your daily bread, give thanks to the latest genetic research”

    • @Mike—No. There is a popular myth that “ancient grains” are somehow more healthy or contain less gluten, but this is not the case:
      http://pubs.acs.org/doi/full/10.1021/jf305122s

      Interestingly, some ancient wheats found in an Egyptian tomb had higher levels of immune stimulating activity—relevant to people with celiac disease—than modern ones.

      Reply
      • Has actual prevalence increased, or is it diagnoses that have increased? A hundred years ago people were described as having delicate digestion but nobody knew what the problem was. People think diseases are new or suddenly increasing when the truth is, our understanding and ability to describe and detect them has increased. Particularly now that we don’t die of other more virulent diseases first.

        Reply
        • Hi battleshiphips, you raise some important points regarding how diseases are diagnosed. Part of the problem is the distinction between disease “prevalence” and “incidence”. (Simply stated, prevalence is the overall proportion of the population with a given disease at a particular time, while incidence is a measure of the rate of diagnosis over a given period).

          For a condition such as Autism Spectrum Disorder, there is no objective blood test, and diagnosis depends on a subjective medical assessment of symptoms. This is clearly very dependent on changing diagnostic criteria, plus changes in how many people are actually evaluated as candidates for the disease. It’s not surprising that the incidence of autism has increased recently, and is highly dependent on socio-economic factors.

          In contrast, celiac disease presents with a wide variety of symptoms, and only about 15% of the people with this disease in the U.S. been diagnosed. However, there is a quite reliable blood test, which means that large numbers of people, representing the whole population, can be evaluated. This test even works for blood samples that have been frozen for decades. The result is that we have reasonable confidence that the overall prevalence of celiac disease has increased substantially over the years (possibly reaching a plateau around 1990).

          (BTW This is distinct from the current ‘gluten-free’ food fad, which has been promoted by unscrupulous fringe “doctors”, celebrities, and people wishing to cash in on the fad).

          Reply
          • I wonder what the the effect of overall decreased mortality rates over the past century would have on the incident rates of less fatal diseases, especially those that are genetically related. It just seems obvious to me that as the incidence of highly virulent childhood diseases drops, the incident of less virulent diseases and conditions would increase because in the bad old days, people weakened by a chronic condition would be less likely to recover and survive to pass on the celiacs genes. Nobody ever seems to address this possibility.

          • @battleshiphips. A fascinating topic—the question of how our recent lifestyle changes might provide genetic selection pressure. This seems quite plausible to me, although I think it would take many generations to occur, together with consistent selection over a long period of time. The effect would also depend on how strong the selection pressure was (an extreme example would be a gene conferring resistance to Ebola infection in a population with repeated Ebola outbreaks). It’s also likely that this kind of selection would be most powerful in isolated communities, and much less likely to occur in the U.S., where this is a rapid mixing of populations.

            Other examples that seem plausible are short-sightedness (perhaps more relevant in ancient hunter-gatherer communities), and the size of the human birth canal. Humans are surprisingly malleable, and there is evidence that two traits—the ability to digest lactose in milk, and dark skin pigmentation—have evolved multiple times.

            Coming back to celiac disease, surprisingly, the major predisposing genes are extremely common, with about 30-40% of Americans susceptible, and there is no way this could have arisen in recent times. This implies that we need to look for a non-genetic factor in the recent rise of CD prevalence.

            On the other hand, there is evidence that historically there has been positive selection for some of the minor genes relating to CD, and these genes code for proteins related to infections of the gut. One hypothesis is that a hyper-responsive gut might have helped rid the intestines of pathogenic microbes, and hence increase survival.

  1. It won’t matter to the anti-GMO fanatics. Any dabbling with the genome of any crop other than “traditional” cross breeding will be considered GMO manipulation and the output will be given the “Frankenfood” designation.

    Reply
    • Why do they oppose science for coming up with a better way to improve our food than what we had before?

      Reply
      • I’m not sure, Jeremy. With new science, one should be conservative until it is well understood. But these people are fanatical luddites who hate science. Especially when it doesn’t satisfy their political agenda. And the period for being conservative with GMO foods is long gone.

        Reply
  2. Hats off to the writer for the lucidity with which she has described the science behind the new developments. Cross referencing with other blogs helps to add more value to the blog. Congratulations!

    Reply
  3. By one estimate, 50% of human protein intake come from wheat. This makes the world’s overall food supply highly vulnerable to plant diseases, pests and environmental stresses. Hexaploid wheat will probably be harder to engineer than other crops—both technically, and because of the widespread fear of GE technology, as Oldfart points out. Nevertheless, the availability of detailed genetic information will surely help future breeding programs.

    Incidentally, the thousands of genetic changes that have already occurred in the hexaploid genome of wheat (Hapsburgian, as Tabitha points out) is surely a ripe source of all kinds of “unintended consequences” of wheat breeding—anathema to many anti-GMO activists. Yet we are still comfortable consuming it. Ironically, improving the genome sequence further, by precise editing of a few nucleotides, for example, will almost certainly face major public opposition.

    Reply

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