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Down the Rabbit Hole: Crop science and GMOs – Karen Massel

Karen Massel is a Postdoctoral Research Fellow at the Centre for Crop Science at the University of Queensland, Australia. Massel’s expertise lie in the utilisation of CRISPR/Cas9 technologies for editing cereal crops in order to enhance their qualities and performance for the food industry. Massel is also a strong advocate for the use of biotechnology and genetically modified plants to create more sustainable food sources.

Please note the transcript has been edited for brevity and clarity.

FLG: Hello, everyone, and hello, Karen, thank you so much for joining me today as we go down the rabbit hole and explore some of the niche and unusual aspects of genomics. Today we’re going to talk about crop science with the lovely Karen, so if you could just introduce yourself and tell us what you do.

Karen: Thanks for having me. My name is Dr. Karen Massel, and I am a Canadian who did their PhD out here in beautiful Australia. So, I traded the snow for the sun! I started my PhD career developing genome editing systems in Sorghum bicolor, which is a relatively unknown crop but a really important one for food security – it feeds about half a billion people. I’m now working as a postdoctoral research fellow on this ARC (Australian Research Council) discovery project looking at drug tolerance in both sorghum and barley, which has been really exciting!

FLG: Let’s start off with the basics – what is crop science?

Karen: It’s a huge field – it is very interdisciplinary. At the end of the day, it’s all about studying plants that have really important economic and commercial uses. But this has to bring together so many different aspects of science. In crop science, we often talk about our G by E by M, which is genotype by environment by management. All three of these aspects need to be researched in order for us to really improve on crop production and understand how crops function. A lot of the time I am working on the G aspect, working on improving the genetics behind it and how that relates to the environment and management style. But you also bring in people who work on soil science understanding what is going on in the soil and all the nutrients. It involves plant breeders; you need people working on different types of weeds, you need pathologists working on all the different viruses and insects that are attacking your crop. Nowadays, with big data, we have got lots of bioinformatics and computer scientists, we have people modelling for different environmental conditions and different genotypes. It is a really big field of science to be a part of!

FLG: What are some of the applications of crop science?

Karen: At the end of the day, we are trying to produce more, or at least produce something different. People probably don’t realise exactly where their food is coming from, for example. But it’s all about generating different varieties that are being grown. So, when you go to the grocery store, it’s not just an apple, you’ve got all your different types of apples that you can now eat, and that’s all from plant breeding. Crops also have really big uses in the industry field as well, so we can make biofuels to try and get away from natural resources. And we use also use potato starch to stiffen collars! So, I think crops have really big uses. And also, I think understanding just how plants function within the natural word, the core biology of how do things function, is also really important, that is less applied, I guess.

FLG: What research are you and your team working on?

Karen: I have got my fingers in a lot of pies! I do have quite a few different things I’m working on. My main project right now is to work on CRISPR-Cas9 genome editing where we’re trying to manipulate a lot of these genes involved in how the plant grows. We’re trying to reduce how the carbon is organised in the plant and reduce biomass, which will then lead to more grain yields, especially under water stress, which is really important to produce more in some of these lands that are really difficult to grow plants on. I also work on a lot of traits that are involved more in reproduction. So, if we could try and make the plants have more flowers, which in turn would lead to more grain, we can try and boost yield that way. I also work on some really interesting projects where we are looking at the different types of pollen that we find throughout Australia, so we can try and have an allergy database that you can sense when things that cause your allergies are spiking. In Australia where it’s sunny all the time, we get allergies 365 days a year and it’s all from different plant species. So, I am part of this project where we’re studying the genetics of the pollen that we find in the air and hopefully, we can have an app so you know when you need to take your allergy medicine.

FLG: How have advanced technologies such as CRISPR improved manipulation?

Karen: CRISPR-Cas9 has really opened the doors for how we can do genetic engineering. I think it’s one thing to be able to put a foreign gene into another plant, but using that sort of technology, you can create really precise changes exactly where you want them to be. I mean we’re not finding that we are getting that much off-targeting, but I know when you talk to people in medical sciences, they are very freaked out about all the off-targets. But as you can imagine in a plant, no matter what sort of crop species you are working on, you are probably going to end up breeding with it anyway, which means you are removing a lot of that material outside of the region of the genome that you are manipulating. So, you don’t really care if there are off-target mutations because that part of the genome is not going to be in your final product anyway. I think working on plants, there’s a lot more potential for this sort of technology just by the nature of the work itself.

FLG: What other genomics tools have you applied?

Karen: There are so many genomic tools. Plant genetics are complicated. I think people underestimate how complex they can be. A lot of plant species haven’t even been fully genome sequenced just based on their complexity. The human genome is 3.2 gigabase pairs. Wheat, for example, is 14 and a half, and it’s a hexaploid which means in that jumble, for every gene there’s three different allelic copies and some of them can be so similar that it’s hard to know are they from the A, B or D genome. Then you got crops, like sugar cane, which are an alloploid, which means we don’t even know what ploidy level they are, and a lot of them will be 99% similar to each other. So, it’s really hard to even get some really great genetic data on some of these crop species because the ploidy level makes it complicated, and their sheer size makes it complicated. But it also means that because we can breed with crops and we can create populations, you can go back to the domesticated lines and all these wild cultivars. You can compare wild to domesticated and improved lines. We can get a lot of data about the evolution of these crops. You can use things like genomic selection for breeding practices and we use modelling. I think in the field of genetics, crop science is definitely a really interesting field where you can do a lot. Mostly just because you can grow 300 plants, cross them with whatever parents you want – no one cares when you’re working on plants! You have more potential to do QTL (quantitative trait loci) analysis and actually pinpoint the genetic basis of specific phenotypes.

FLG: Are they any attempts to sequence the genomes of plants and create a catalogue?

Karen: For sure! We can follow a lot of the cytogeny between different families. You can go to the sorghum genome and there a lot of online programmes where you can find its homologous gene in maize. You can see how the chromosomes have been rearranged throughout evolution. I read a paper recently published by some colleagues of mine where they do pan genomes. This means that you have your reference genome, which is fantastic when you can have it, but then when you go to sequence a different cultivar and if it’s not very related, it means that there’s all these regions that you can’t actually match to the reference genome. Pan genome then takes those parts into consideration. One of the issues with crossbreeding has been that throughout domestication, we have really limited the diversity of the genetic pools, which is why we are always trying to reintroduce diversity, because diversity is how we are able to adapt to different environments and pathogens. So, a lot of time we want to know those regions that have been lost in the domesticated lines from wild cultivars. So doing pan genome sequencing is one of the new things to be doing, especially for some really important crops.

FLG: What are some of the challenges working with crops?

Karen: It depends on what your research is specifically within the field. I know for myself, there are only a few main crops that people really invest a lot of money in, so there’s a lot of research focused on maize, or corn, wheat and barley. But these sorts of orphan crops, which we call them, do feed people. Everybody likes to go to the grocery store and see all of those different vegetables and all the different flours, like everyone wants the gluten-free alternatives, but I’m sure most people could not really think of what the gluten-free cereal is. What is that flour that they are eating? I would say that it is sometimes hard to get funding if you are not in the top five crop species to do the work and there’s just so much less known about a lot of these features. Crops are also complicated. You have to grow them. They all like their own temperature, their own humidity, their own nutrient profiles. Some of them are a bit more of a diva than the other ones.

FLG: Are these technologies being applied to the rest of the ecosystem, for example, microorganisms that affect crops?

Karen: For sure! Even as part of my PhD, I ended up doing some metagenomic sequencing of the bacteria that are in the root rhizosphere. Currently, I am focussed on the genetics aspect, but I work with a lot of physiologists who don’t particularly care what gene causes the traits; they’re looking at the entire trait and how that relates to the environment. There is a lot of push to try and improve photosynthesis, so that is light capture and involves some of the different types of light, the radiation and ground cover.

Looking at the environment is one of the main things to be considered and we are always trying. Agriculture has an enormous impact on the environment, in a bad way. When you talk about agriculture – I think cows get a bad rap. Everyone talks about the methane production – but the reality is that, actually, growing crops is a lot worse because nitrous oxide, which is from the denitrification of all our fertilisers that we’re applying, pollutes the airways a lot more. I think nitrous oxide is about 300 times more potent than carbon dioxide emissions. So, growing all this beautiful food for everyone to eat also damages the environment. So, reducing your meat intake is great, but if you’re going to make up for it by eating a lot more corn, you may not be doing as much good for the environment as you think you are. For most crops, we put so much money of nitrogen and phosphorus onto the soil, but crops can typically only take up about 30 to 50% of that fertiliser and the rest of that is either being denitrified into the air or is being polluted into our waterways, and that can cause algal blooms which can hurt lakes and waterways.

FLG: So the cows are taking the blame essentially!

Karen: Exactly we’re just hiding behind the cows!

FLG: How does crop science go from research into actual crop production? How do you work with other people in the chain?

Karen: That’s a good question! I would say a lot of the times our funding actually comes directly from companies. I work mostly on cereal crops – I’m working on grains – so most of our funding is from grain companies or breeding companies. They want solutions and they have their areas of expertise and we have ours, so we come together. There’s a lot of linkage projects and industry projects where we do receive funding directly from industry. A lot of people that I work with, they are always out in the field, and we work with farmers, so I think there’s actually quite a bit behind the scenes. At the end of day, I think people in crop science definitely need to consider an applied approach and you do want to see your research be useful. So, we’re always talking to farmers – what are the things they like about their varieties, what are the things they hope to change or improve upon – and you try to find a realistic way to help them. In the realm of plant science, it might get a lot less applied but definitely in the field of crop science, we have an applied endgame, so we do work very closely with industry.

FLG: What is considered as genetically modified and not?

Karen: This is a very complicated, I’m going to try to make it as simple as possible. But it is complicated because it’s also dependent on where you are and if it’s going to be used for cultivation or if you’re just importing it. Being genetically modified, I believe the term is just called this if it’s a living modified organism and that requires two different things. It means that there’s the combination of novel genetic material in the plant which, in theory, would also be breeding. But the second requirement is that it has to be introduced by modern biotechnology. So, a lot of the new breeding technologies like CRISPR are involved in that. So that basically means if I put in a foreign gene into the plant and I’ve changed the genome, that’s going to be GM no matter what. But with CRISPR, zinc finger nucleases and TALENs – these site-directed nuclease technologies, or SDNs – there are three different levels of that.

SDN 1 is when you just use your nuclease to create a double stranded break and then the plant is going to repair that all by itself using its own repair mechanism as it would if that happened naturally. That means that it’s basically the same thing as random mutagenesis. Maybe most people don’t know this, but one of the main breeding strategies before was to just chemically mutagenise the plant using chemicals or radiation and that would create hundreds to thousands of different random mutations. And you don’t even really screen for it or anything, you just grow the plants out in the field, and you find the phenotype that you’re hoping for and then you try to figure out what mutation caused that. This is sort of the same thing except I’ve gone in there with CRISPR, and I know exactly where I’ve done it, and I can show you what mutation has changed. Whereas the other breeding strategy was just completely random and that’s, of course, already being grown out on the field. So, you can imagine CRISPR technology, in this sense, is sort of equivalent to what’s already been done, and it’s really using the plants own repair mechanisms. And it would be indistinguishable from a crop that you have found out in the world once you have segregated away the CRISPR component that was required to make that transformation and the editing to occur.

Whereas SDNs 2 and 3, you are not allowing the plant to repair itself naturally; you’re forcing the edit to happen with a template. SDN 2, it’s a very small template – just an oligonucleotide that will help fix the gap, and that is usually under 7 nucleotides. Whereas SDM 3 is a large fragment, and often that is basically synonymous with just doing transformation with foreign genes; you are just putting in a KB (kilobase) worth of sequence. So of course, those two are more likely to be regulated as GM.

FLG: How are these crops currently regulated?

Karen: The beautiful thing is that it’s different basically everywhere, so it’s going to be complicated wherever you are. In Australia, where I’m at right now, SDN 1 which is just the natural you make a double stranded break using CRISPR and it fixes itself, that’s been deregulated; its non-GM, which is pretty fantastic. The issue is that Australia does a lot of exporting of things, and we’re not allowed to export it if the country that we want to export to does not agree with that regulation. So, farmers are, of course, a bit nervous to grow these sorts of crops, and I’m sure it’s the same in lot of countries. But for example, New Zealand has said, ‘No, they are GM all the time no matter what you’ve done. You’re using biotechnology; it’s a GM outcome. Don’t come near me’. The EU has sort of said the exact same thing – if the outcome is not from natural mating or recombination, it is GM. They have now changed that to include chemical mutagenesis; that’s now also viewed as GM, even though in the past that wasn’t the case.

There are a few countries in Europe that are outside of the EU that are okay with GM. But a lot of times they may be okay with it, but they have never actually approved a non-GM CRISPR-edited line, or they don’t cultivate them at all. The countries that are going for it would be Latin America (that isn’t a country but an enormous set of countries) they take up about 50% of the GM crop cultivation, so they’re very pro. It is confusing in Latin America; not all of them have said CRISPR is non-GM, but some of them have and they are trying, at the moment, to come up with a big document to explain it and have it be consistent across a lot of those countries. The US has said that CRISPR is okay, and they actually have almost 150 or something GM plant varieties that have been given a non-GM status and they’re growing, and you can buy them in supermarkets, such as the non-browning mushroom. It just has a gene knocked out in it, so it has much better shelf life. I think everybody would be happy at that, maybe not if they found out that it was CRISPR-edited, but for their fridge they’re happy to have a non-browning mushroom and things like that. Then in Canada and Japan they have also said that its non-GM. But between all these countries, even though they say it’s non-GM, they all have it written in their legal documents slightly differently and sometimes it’s a process-based thing, and other times it is a product-based way of regulating it.

Some countries, like the US, care how the CRISPR-Cas9 occurred (and that’s how the Australians do it). So, a template makes it GM, or, if there is no template, it’s non-GM. Whereas countries like Canada, it is all based on the product. So, they don’t care how it was created. As long as there’s a novel trait associated with that variety, it needs to go through the health Canada system and then they’ll decide how they’re going to regulate it from then on. Both have pros and cons. But I think, because of all the confusion, it is hard to be a farmer and you feel a bit nervous if you know you are going to export a lot of your grain.  

FLG: Why do think there is such hesitancy? Do you think this will change over time?

Karen: It is such a funny thing that people are so scared of biotechnology when it comes to their food, yet they are so happy to go for it when it comes to medicine. I’m sure that if people were using that technology that could cure baldness, people would be taking those pills right now! There would be no hesitation on it. But the second I tell you that I’ve created a mushroom that is non-browning from GM people freak out. I think a lot of that is we’ve had a lot of pretty good marketing campaigns against GM foods, and that’s mostly from people who are selling organic foods. I am not trying to hate on the organic industry, but no one has ever died from eating a GM crop, but people have died from eating organic crops, so I’d like to put that out there as a fact. Safety is an interesting subject matter, and I think most people just don’t realise that they’re already eating GM foods. A lot of different industries have actually got exemption, so the dairy industry, for example, they don’t have to mark anything as GM. But almost all the bacteria used to make cheeses is genetically modified. So, for example if you like cheese, you’re eating it. If you have ever eaten corn or have had any product that has corn syrup in it, I’m going to guess that it is genetically modified. I think 95% of the corn grown these days is GM. And you don’t have to always market that as a GM product.

At the end of the day, I think people just don’t understand what GMO really means and I don’t think they understand what DNA even is, to take it back a step further. I can understand when someone tells you that you are eating something that has a bacterial gene in it that that might sound a bit scary. An example would be golden rice, which is just a rice variety where people have inserted three different genes into it, and it means that it can now produce vitamin A. The rice is now golden in colour because it has carotenoids in it. That was developed because people in South America and stuff were suffering from river blindness, especially children, which happens when people have a vitamin A deficiency. They are literally trying to give sight to children and people are resistant to eat this golden rice plant or even cultivate it. Even though we eat vitamin A, and we need it, and we know about it, but the plant has a bacterial gene in it. I think people are scared of change and I don’t think they understand that mutations are happening all the time and DNA is in everything you are eating and it’s safe! I hope, like with any new technology, eventually it’ll come to a point where people accept that. I mean pasteurisation of milk, for example, people did not like the idea of that. Heating up the milk sounded too scary, but then you realised your milk would last three times as long – who wouldn’t want to do this? I think once we actually get some good non-GM products out there, such as non-browning mushroom and apples and such, hopefully we can prove that it’s not as scary as we once thought it was, and GM even as a whole isn’t as scary as it needs to be. I wish I understood why people were so scared; it would help me market it as not such a scary thing!

FLG: The effects of climate change are already having an effect on food production – what role do you think crop science will play?  

Karen: That is a great question, especially following on from our previous question. People are always hearing that climate change is affecting our food production and that’s most definitely true. I think a lot of times though, it’s not affecting us – we can still go to the grocery store and it’s full of food. So, we’re not really seeing that impact ourselves, which means why would I try some crazy new technology when I don’t feel the need to see it. I think, unfortunately, once things come about, when we start seeing our food prices rising because it is harder or if we can’t get our oranges in the middle of winter because the environment is playing a role on our food, I think then maybe people will start to consider GM crops as a potential way to combat these things. We’re seeing with climate change not only just longer summers, hotter summers, drier summers. But also, I was in Canada recently and I was shocked at how cold it was, and we have to deal with frost tolerance. The climate is just becoming less predictable, which makes it harder for farmers to know what to grow, when to plant and all the management aspects get really affected by it. And it’s hard to plan your G around the E, and then, how do you manage that? I work with some really great researchers who have some great prediction models, and we can try to use drones on farm management. But it’s definitely affecting crop production and we have to come up with solutions, and we have to do it sooner rather than later because there are countries that are suffering now. It will only get worse!

FLG: What do you think the future of crop science will look like?

Karen: As technology continues to improve, sequencing technology is already getting cheaper by the day, it seems, and now we’re moving on from even understanding genes to looking at epigenetic control. I work with some amazing researchers who are trying to study methylations patterns in genes, so instead of just knocking out a gene using CRISPR, maybe we just methylate promoter regions or remove cis-regulatory elements to tweak the expression levels rather than the actual presence or absence of a gene. And with big data, now we have so much more environmental data, so we can now have great datasets on what type of genetic varieties have been planted, what was the environment at the time, what were the yields like, and that can help us plan for next year, or for 100 years from now when you can look how the environmental trends are going. We are even using satellites and PhenoCams and unmanned vehicles and drones to help manage fields and look at weeds. That can help us to plan for fertilising and chemicals that go on the plants for pest control. Before you go, ‘Okay, the crops are not looking good. Let’s spray the whole field’, now by flying drones up and down, you can do a much more targeted approach, which means less chemicals, less fertilisers – better for the environment, better for everybody and much cheaper for farmers. I don’t know exactly what the future will hold, but I think as new technology comes about, we’re going to have a lot more engineering aspects coming in and working with big datasets will also be key. We need computer scientists, we need engineers. Not just a humble biologist, but we need to get even more interdisciplinary and bring in some experts from other fields.  

FLG: Thank you so much for joining me today, Karen. It has been interesting, and I hope this raises awareness of some of the great work being done in crop science.

Karen: Thank you so much for having me!

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