Pop-SciDevang Mehta

Rewriting Our Food Supply

Pop-SciDevang Mehta
Rewriting Our Food Supply

How genome editing can revolutionise agriculture, if we let it.

I THE TECHNOLOGY

Scientists from Cornell University recently edited the genome of the Painted lady butterfly to discover the genetic basis of eye-spot formation on butterfly wings.

Scientists from Cornell University recently edited the genome of the Painted lady butterfly to discover the genetic basis of eye-spot formation on butterfly wings.

Genome editing is a simple idea: to purposefully make a targeted mutation in a particular region of the genome of an organism, usually a gene. This mutation (basically, a change in the gene’s DNA sequence) translates into a change in the protein derived from the gene and eventually manifests itself as a physical change in the organism. Over the last four years genome editing has become famous; it’s been talked about on every major news outlet, featured on at least one TED talk, covered by technology websites, and perhaps more importantly, on Buzzfeed. In the research community, genome editing has become a magnet for funding, publications and citations — the holy trinity of modern science. The reason for this popular interest in the idea is the recent development of CRISPR/Cas9, a simple technology that has made genome editing accessible to most biology laboratories the world over. In the four years since its first demonstration, CRISPR has been used to edit the genomes of human cells, various crops, insects, yeast, and even butterflies!

 

Before CRISPR, it was next to impossible to create a mutation in only a targeted gene, and with relative ease at that. It’s difficult to describe to non-specialists how much an advance CRISPR is over earlier genome editing techniques; it’s perhaps as much a leap in technology as the first internal combustion engine was over earlier attempts. Of course, all this talk of making targeted mutations raises the question of why we would want to do so in the first place?

Since the Human Genome Project-Read, biologists have learned a lot about the genetics behind human disease. We know for example that Huntington’s disease (an incurable genetic disorder) is caused by the presence of too many C-A-G bases in the DNA of the HTT gene. Or that sickle cell anaemia is caused by a single mutation from A->T in a gene involved in making haemoglobin (the protein that makes blood red). However, there’s little anyone can do about these (and many other) diseases, once acquired, apart from genetic counselling. Imagine the frustration biomedical scientists and doctors must feel—of knowing, in full, the cause of a disease and not being able to do anything about it. With CRISPR however, we could (eventually) figure out how to edit these genes and correct the disease-causing mutations. And this is just a small fraction of what genome editing enables us to do — I haven’t even mentioned cancer and viral disease.

Like with most new bioengineering techniques a lot of the press around CRISPR has focused on it’s potential to revolutionise medicine and personalised medicine. But while biomedical applications for gene editing are being furiously worked on by labs around the globe, they do remain a long way off.

A field I think will be more immediately changed by CRISPR and gene editing is agriculture — and this is what I will devote the rest of this article to discussing.

II NATURAL VARIATION

The story of genome editing in agriculture must begin with an account of natural genetic variation, and it’s limits. Most plant species have a lot of DNA in common ; a fact that seems obvious when you consider how many basic physiological functions, from photosynthesis to reproduction, different plant species share. (Actually most life-forms share quite a bit of DNA). However the same genes, even within the same plant species, sometimes differ; this variation can be as small as a single base-pair change or as large as the loss of an entire portion of the gene. Genes can also be present in single copies or more on the genome, or even absent entirely, representing another index of variation. What I’m trying to get at here is that while a lot of genes are conserved across and within plant species, a majority of them have small differences, or mutations. These mutations are largely the result of evolution and these differing versions of the same gene are called alleles. This allelic variation can change a gene’s function in myriad ways, from simply switching the gene off to changing what it does entirely.

The entire history of agriculture can be seen as the attempt to select for the most ‘desirable’ alleles, while excluding less desirable ones.

Usually, farmers and breeders do this in painstaking fashion — studying large populations of plants and making crossings until they obtain a plant that has a great combination of ‘good’ alleles for different genes. And of course, what’s good for one population, climate and ecosystem might be bad for the next, hence making the availability of genetic variation hugely important. 

III PRESERVING DIVERSITY

The presence of a vast store of allelic diversity which can be used to breed new crop varieties underpins all breeding efforts. In fact, without a lot of genetic variation there would be no benefit to be had from breeding at all. Fortunately, breeders and scientists have not been blind to the importance of genetic variation and lot of crop biodiversity has been preserved in seed-banks; around 1,300 seed-banks all over the world now store about 6 million different plant varieties. However, preserving diversity is not the same as utilising it. Breeders often use wild relatives of crops and older breeds as sources of new alleles but a lot of seed-bank material is left uncharacterised and unused.

Mari Tefre/Svalbard Globale frøhvelv.

Mari Tefre/Svalbard Globale frøhvelv.

A new initiative, DivSeek (led by scientists and biodiversity experts from 65 partner organisation across the world) seeks to change this. DivSeek wants to characterise the genetic material present in seed-banks at the genomic and phenotypic level and present this enormous store of data in an open-access online portal. This is massively ambitious, merely selecting which of the millions of varieties in seed banks to test is a project in itself. The project is also, I think, contingent upon a decrease in DNA-sequencing costs, automated pipelines for large-scale phenotyping and the willingness of farmers and breeders to share closely-held information. The initiative is brand new, very long-term, and has kicked off only recently, but its success could herald a new era of crop diversity.

IV CREATING DIVERSITY

Propaganda poster for Eisenhower’s Atoms for Peace Program. (National Archives)

Propaganda poster for Eisenhower’s Atoms for Peace Program. (National Archives)

A fact most of us do not know is that a lot of popular crop varieties used today originated from mutagenesis programs in the early- and mid-20th century; partly an offspring of nuclear technology research happening at the time and the US government’s Atoms for Peace program.

Mutagenesis for crop variety development basically involves causing mutations in seeds, either by X-Ray/gamma-ray irradiation or via the application of chemical mutagens. These mutagens induce breaks in the plant’s DNA and the repair of these DNA breaks results in the creation of new, mutant alleles, some of which might be present in other crops and some that are probably completely unique. Mutation via these techniques is, however, imprecise; they cause several million mutations in the genome of which only a couple might be desirable for breeding. The first products of mutagenesis must undergo selection and a series of matings to bring only the potentially beneficial allele(s) into existing crop varieties; a process that can take decades. Mutation breeding is thus both costly and takes a long time, but it does result in the creation of ‘new’ alleles and hence new genetic variation in crop species. Some of the (still) most widely used products of mutation breeding programs are the (now ubiquitous) dwarf wheat varieties that sparked the Green Revolution, dwarf rice varieties in California, virus resistant cocoa in Ghana and better-malting barley for beer and whiskey brewing in Europe.

Genome editing is, fundamentally, just another form of mutagenesis. The important distinction here is that while older mutagenesis techniques relied on random events, genome editing is precise and targeted, making the timescale from mutation to cropping significantly shorter.

V A NEW AGRICULTURE

Plant breeding is, even today, described in text-books as both an ‘art and a science’. This is because a lot of it still relies on the skill of the breeder to visually select plant varieties—the famous breeder’s eye. Conventional breeding also requires an incredible amount of time and resources since it uses a brute-force approach to discovering new crop traits and making new varieties. A lot of this is due to gaps in our knowledge of the underlying biology of several plant traits; gaps being filled by a dwindling pool of future plant biologists. And given the even greater lack of this knowledge in the past, breeders have done a fantastic job in creating crop diversity and increasing yields.

The history of plant breeding has been an exponential progression away from a ‘black box’ approach towards a more comprehensive understanding of what makes plants tick and how we can best utilise their unique biology. Our ancestors figured out that planting seeds from plants that had more fruits or less disease would give them better harvests the next season, but they remained blind to the biology of sex. Much later on, in the 17th century, we learned more about how plants reproduce and we started making artificial crosses. Soon after that came Darwin and Mendel, giving us both natural selection and the laws of genetics in the span of fifty years. And now, with the recent explosion of -omics technologies we can read a plant’s DNA, study how every gene responds to various conditions and predict how efficiently a plant can produce the biochemicals we eat them for. With genome editing this knowledge becomes ever more useful.

Once a breeder/scientist has identified a useful allele, using genome editing they will be able to move it into any plant variety or even any species almost immediately, without having to wait for successive generations. Going even further, genome editing could change the process of trait discovery itself. CRISPR based genome editing could be used to simultaneously edit every single gene in a plant’s genome (or even every single gene of a particular type, e.g. some R-genes which confer disease resistance), hence creating a wealth of new information and possibly discovering new beneficial alleles that could then be edited back into existing crop varieties. The true promise of CRISPR-based genome editing is, however, the ability to uncouple creating allele diversity from sexual reproduction.

Genome editing could, I think, enable a plug-and-play model of plant breeding.

The breeding pipeline of the future will, in my estimation, look akin to the modern assembly-line. Armed with data from thousands of research papers and initiatives like DivSeek, researchers will test out various combinations of alleles in model crop varieties by directly editing their genomes, guided perhaps by a degree of predictive mathematical modelling. After filtering down the number of alleles based on these results, scientists will run the edits again on a larger number of crop varieties, run field tests, and proceed directly to seed production. While a number of factors will alter this scheme (how the crop reproduces, for one), the biggest gain will be a reduction in the number of generations (possibly down to a single generation) until a variety is ready for testing. In other words, faster product development.

VI THE NEED OF THE HOUR

When have we ever had a world of plenty? The Irish Famine Memorial at Harvard University.

When have we ever had a world of plenty? The Irish Famine Memorial at Harvard University.

Students of plant immunity are familiar with the ‘zig-zag model’ of plant-pathogen co-evolution. The model describes an escalating arms-race between plants and the pests that attack them, many of which have shorter evolutionary time-scales than plants. The task of modern agriculture is just as uphill. The industry must feed an increasing human population, deal with the impacts of climate change: the increased occurrence of extreme weather phenomena in the short term and the longer term changes in the global environment, while also dealing with fast-evolving plant pests and it must do all this in a more sustainable manner.

Agriculture has of course, seen such threats off in the past, most famously when the Green Revolution took off and made Paul Ehrlich’s predictions seem irrelevant. That revolution was made possible only due to a host of new initiatives led by Nobel Peace Prize Winner Norman Borlaug, including new plant varieties and farm mechanisation.

Today we face the same challenges magnified, and standing still can only mean going backwards.

UNITS: Population- billions; Temperature- celsius; Yield- 10 tonnes/ha (cereals). For data sources, see footnotes

UNITS: Population- billions; Temperature- celsius; Yield- 10 tonnes/ha (cereals). For data sources, see footnotes

A lot of what I’ve discussed above has been said before, several times in fact—at the advent of every new agricultural technology: from crop hybridisation, genetic engineering to marker assisted selection. Two of these technologies were accepted, after some push-back, while genetic engineering still remains monopolised by a few large companies, rejected by a lot of nations, and a distant hope for many.

Which fate awaits genome editing?

VII BUT WAIT, IS IT A GMO?

GMO: Genetically Modified Organism.

I don’t know who originally coined this acronym, but it’s a scientifically vacuous concept. Technically ‘genetic modification’ is a fundamental aspect of evolution—sweet potato for instance, has had it’s genome naturally’ genetically modified by almost exactly the same method we use in the lab to make disease resistant crops.

However, on the regulatory front, the term GMO is used to define those plant varieties and those biotechnological processes that require assessment (for safety and ecological risk) by a government agency prior to release. The term GMO (or LMO, living modified organism) is also used in international treaties governing trade, for e.g the Convention on Biological Diversity.

This is probably the question I’ve been asked the most when talking about genome editing, and from a policy perspective it’s the question that will single-handedly determine its future in agriculture. (I don’t want to wade into the GMO regulation debate in this article and so I will assume that things on that front are not going to change in the foreseeable future, especially in Europe.)

To, to answer the original question: I don’t think so, for the simple reason that there is no way to tell the difference between an edited plant and a naturally occurring variant. The product of genome editing will not (usually) contain any transgenes (genes from other organisms, not normally occurring in the modified species) and there will, in all likelihood, be no trace of the method used to produce the edited crop variety. This poses a unique problem for regulators and interest groups that would like to consider the technology a form of genetic modification (i.e. subject to laws governing GMOs). How can regulation work when there is no way of telling which plant it applies to and which one it doesn’t? You could of course monitor breeding companies and labs or try to make it impossible to obtain the basic reagents required for genome editing (a difficult task), but do we as a society really want to police private breeding companies and public-sector scientists? Organisations such as Greenpeace, Friends of the Earth and the organic industry want products of genome editing to be labelled and regulated, but I haven’t seen a single proposal by them on how this regulation would be enforced.

Current regulatory status:

The US is revising it’s GMO regulations but the recent decision by the USDA to not regulate a genome edited mushroom leads me to believe that genome edited crops will largely be free of regulation in the US. In Europe, the European Commission is due to release it’s decision later this year. However, recent developments in Sweden and other EU countries hint at a similar outcome. For more, see this Nature News article.

On a more basic level, how is genome editing any different from mutagenesis? It’s performed using biochemicals (RNA and protein) which act in a more precise manner than UV irradiation or chemical mutagens; but the final product is exactly the same, a crop with a new allele. Now, you might consider mutagenesis to be genetic modification too. And you’d be right to do so, mutagenesis does cause a modification in the genetic material of the plant. But, importantly, countries make an exception for mutagenesis, for two reasons: a. it’s an inescapable part of modern agriculture (including that of the organic variety) and b. it too results in modifications that are impossible to distinguish from natural variation. So clearly we’re splitting hairs when we call the outcomes of one technique GMOs and that of another, not. One fact, however, that is obvious to us scientists is that the GMO/non-GMO distinction does not exist in the natural world.

Returning to our original question:

“Is it a GMO?” 

Technically, yes. (Just like several plants grown by organic farmers around the world).

“Does it matter?” 

Not really.

VII WHO WILL OWN THESE PLANTS?

Another question I often get asked when describing my current research project on making transgenic plants is: “Is it patented?”. A lot of the criticism directed at modern agriculture is aimed at the intellectual property protection of plant varieties; usually in the form of a statement like this one from Greenpeace:"Existing living organisms - plants and animals as well as their genes - are no-one’s invention and should therefore never be patented and put under private control." A fact this statement casually assumes is that crops and plants that we use today are ‘no-one’s inventions’. On the contrary, I hope I’ve shown above that agriculture is incredibly dependent on the skill and inventiveness of farmers, breeders and yes, modern biotechnology companies. Take a look at the picture alongside to see an example of how human ingenuity has created an agricultural system that’s able to feed more people every day.

Intellectual property rights are extremely important to the development of modern technologies and the IP landscape will play a huge role in the adoption of genome editing in agriculture. 

And now, a brief dive into the mundane world of intellectual property rights!

The inventor of a plant variety usually has two options to preserve her/his intellectual property: plant variety protection (PVP) or a patent (usually a utility patent in the US). Patents require a higher threshold of inventiveness and are used primarily by biotechnology companies seeking to protect their seeds based on the DNA sequence or trait that’s been introduced into the plant. PVP is used more by conventional breeders; it imposes less stringent criteria for inventiveness but also, I think, offers lesser protection in some respects. For example, patent protection does not allow farmers to replant seeds (the saved seed exemption) or breeders to use patented plants for creating new varieties (the breeder’s exemption) while a PVP has these two exemptions. The US, unlike most countries, allows patenting of bred plants and plant material, as well as methods of producing plant, if they meet the criteria of novelty and non-obviousness.

There’s clearly a demand for patenting! Conventional plant breeding patent applications (blue) and patents granted (red) in the EU. from NoPatentsOnSeeds, an initiative opposed to patenting of plants.

There’s clearly a demand for patenting! Conventional plant breeding patent applications (blue) and patents granted (red) in the EU. from NoPatentsOnSeeds, an initiative opposed to patenting of plants.

There’s clearly a demand for patenting! Conventional plant breeding patent applications (blue) and patents granted (red) in the EU. from NoPatentsOnSeeds, an initiative opposed to patenting of plants.

In Europe, conventional breeders mostly obtain PVP for their varieties since patents cannot be granted on an ‘essentially biological breeding process’. However, the situation is not as clear as that (see graph) and a recent decision by the European Patent Office (EPO)has upended this neat distinction by stating that though the process used to create conventionally bred varieties cannot be patented, the products of this process can be. In one instance, the EPO granted a patent to the Israeli Ministry of Agriculture for a conventionally bred drought-tolerant tomato. More recently, however, the European Commission has decided to step in and resolve the issue. It is at present working on a legally binding interpretation of existing directives that could prevent the patenting of bred varieties.

So as things stand in Europe, the products of genetic engineering can be patented while those of conventional breeding might not be. This presents an intriguing conundrum because, if regulators decide that genome editing is a non-GM technique, would its products still be patentable or would they only qualify for plant variety protection? On the other hand, if it is considered genetic modification, and hence patentable, how would a patent applicant prove that his product was unique (i.e. that there was no naturally occurring allele that matched his edited product)?

Another fascinating aspect to this is how patents affect the widespread adoption of certain products. Patents effectively give the inventor a monopoly on an invention for a certain amount of time (20 years in the US). This then prevents the adoption of genetically modified DNA into other plant varieties by other breeders (because the breeder’s exemptiondoes not apply to patented plants), unless, a breeding company acquire rights to these technologies from the patent-owner. But if genome edited plants were only eligible for PVP, the edited allele could (and probably would) be used widely by other breeders and farmers. However, this possibility is again contingent on an initial investment by some companies in developing and deploying the technology.

This poses the question: would industry make the economic investment required to get genome editing off the ground? And how would the patent landscape affect the adoption of the technology as a whole?

IX WHERE DOES THE MONEY COME FROM?

Every agricultural biotech company today is investing in genome editing for at least a few crops. In fact, a small US-based gene-editing company, Cibus is already planning to plant its edited herbicide tolerant oilseed rape this year. While this crop was developed with an older genome editing technique, it’s almost certain that new crops will rely on CRISPR based techniques. At the moment CRISPR patents are held by the Broad Institute at MIT and Harvard University (the Church and Liu labs), by DuPont, and three others, but this may change. As far as I can tell, DuPont and Caribou Biosciences (a UC-Berkeley spin-out) are, for now, the major players in agricultural CRISPR-based genome editing. The technology, though is developing rapidly and we will see progress and new techniques from other universities and companies too.

A key question here is, if patent protection is limited only to the technique and not the products, will there be any incentive for seed companies to invest in genome editing? Obviously, in the US, where these plants could be patented, the situation is different, but considering that ~40% of Monsanto’s (just one example) income is derived from markets outside the US, this is still a pertinent question. For companies outside the US (where in all likelihood, genome edited plants will not be patent-protected) this is even more crucial, will they be able to harness genome editing to create profit and better crops without patents on their products? PVP is probably a good idea in the current breeding landscape because generating a new variety from an existing one takes more than a decade, during which the original PVP holder can obtain returns. But if genome-editing has as much of an impact in reducing development time as I think it will, surely stronger IP protection is required to encourage innovation?

Perhaps it would be a mistake to exclude plants derived from breeding processes from patenting.

X FIRST STEPS

Some of the science I’ve discussed in this article is speculative, but a surprising amount isn’t. CRISPR based genome editing has been demonstrated in an astonishing variety of plants, from cereals like rice and wheat, in fruits like tomato, to vegetables like lettuce. Genome edited crops are also getting ever closer to the marketplace: both Cibus and DuPont are already conducting field experiments.

However, plant scientists still need to further develop the tools that could allow the development of the ‘plug-and-play’ model I envision above. The first step of rapid genome editing is transient genetic transformation and regeneration of a naked plant cell (protoplasts) and I don’t think enough scientific projects have focused on this basic tissue culture technology for many crops species. We also need to get better at predicting the outcomes of editing a particular gene or genomic region; something good genome scale models could provide. We need faster and more high-throughput phenotyping systems, single cell systems for testing immune response for example. We could stand to learn from the biomedical community here: where are the microfluidic cell culture systems for plant tissues? Human genome sequencing costs have fallen to the $1000/genome mark and are being driven down to even $100/genome. We need the same advances in plant genome sequencing, a faster too, given than many crop genomes are more complex than our own.

It’s also clear to me that truly widespread adoption of genome editing in agriculture depends greatly on how the technology is policed. As an advocate for a much greater role for genome editing in modern agriculture, I think the US is on the right track with both the regulatory and IP frameworks. The pending decisions from the European Commission are very important, because even though Europe is not the largest food-producing region in the world (13% of world cereal production), its regulatory frameworks often serve as a template for law-makers abroad. It also plays a major role in international treaty organisations such as the United Nations Food and Agriculture Organisation (FAO) and the World Intellectual Property Organisation (WIPO).

I’ve tried also tried to present here a moral case for encouraging new technologies in agriculture. It is an indisputable fact that we will need these technologies in order to raise yields and that even accounting for losses through wastage, we will need to increase yields to feed a growing population. At the same time with rising temperatures we need hardier crops and the ability to deploy them at a faster pace. And it is also true that the worst-hit from these stresses will be the weaker economies of the Global South, economies that cannot afford to subsidise agriculture as much as the developed world does.

To digress a bit: I recently attended a policy workshop at my university where we discussed the rise in solar and wind power globally. One point that came up was that this shift towards renewable energy is largely occurring due to the fact that there is now an economic incentive towards renewables. It seems that the impact of climate change rhetoric and talk of reducing energy consumption has been less effective than government actions to reduce adoption costs. Its also clear that technological solutions (cheaper photovoltaics and better batteries) have contributed enormously towards efforts at combating climate change.

I wonder if the same could hold true for modern agriculture? Perhaps advocates of a more sustainable agriculture should be more open to new technologies that could help, rather than clinging on to a less productivesystem. We have not reduced our energy consumption, but we have made energy generation more sustainable; it’s impossible to reduce food consumption but we can improve the efficiency with which we produce it.

 

Footnotes:

  • Population growth data was obtained from the World Population Prospects, 2015 revision provided by the United Nations.
  • Temperature estimates come from the IPCC projections under RCP2.6 (the most optimistic outcome).
  • Yield data is from FAOSTAT.

COI statement:

I do work with CRISPR-based genome editing technologies in plants, but it is just proof-of-concept research, primarily on model plants and a non-major crop, and very far away from market, if that even.