Plant Genome Editing for Sustainable Agriculture with Evan Groover

On this episode of The Climate Biotech Podcast, Paul Reginato is joined by Evan Groover, a plant synthetic biologist and postdoctoral fellow in Mary Gehring's lab at the Whitehead Institute at MIT. His work spans CRISPR tool development, engineering photosynthesis, plant epigenetics, and making plant genome editing accessible beyond the well-funded incumbents that have historically dominated the field.

Evan grew up in Northern California in what he calls the epicenter of the non-GMO movement, and studied music seriously before finding his way to plant biology. He came into the field just as regulators began distinguishing gene-edited plants from transgenic ones, a shift that opened modern editing tools to a much wider set of crops and researchers. During his PhD at UC Berkeley at the Innovative Genomics Institute, Evan built a screening system in sorghum protoplasts capable of testing roughly 30,000 CRISPR edits at once, targeting the promoters of three photosynthesis genes to find the smallest possible edits that could increase their expression – a process that would take months or years and many acres of land to perform in the field. 

One of Evan's core points is that flowering plants – which account for nearly all crops – share most of their genes, and much of what distinguishes one species or variety from another sits in the regulatory DNA sequences that control when and where those genes are expressed. That has implications for how we improve crops. Traditional breeding selects variation that already exists in crops, but genome editing can introduce small but novel changes in regulatory sequences that access phenotypic space that no living plant currently occupies. In his current postdoc, Evan is extending this thinking into epigenetics, asking how much crop performance is shaped by chemical modifications to DNA that exist outside of the sequence itself. 

Listen to learn how genome editing can be a powerful tool for agriculture with regulatory acceptance, and why improving photosynthesis is a promising lever for sustainable agriculture and potentially carbon removal.

Transcript

A New Era For Plant Editing

Speaker 1 0:03

Now that this sort of floodgate has been opened about allowing genome engineering, the question that we ask is how can we use genome engineering within the confines of what has been deregulated to improve photosynthesis and allow more agricultural opportunities for carbon sequestration, or at least just improving photosynthesis and ultimately yield in crop plants.

Speaker 0:26

Welcome to the Climate Biotech podcast, where we explore the most important problems in climate and environmental biotechnology and how we can solve them. I'm Paul Reginato, co-founder of HomeWorld Collective. Together, we have agency to build technologies that enable a brighter future for all life on Earth. I'm thrilled to welcome Evan Groover here for a discussion about climate biotech. Evan is a plant synthetic biologist working on plant genome engineering as a postdoctoral fellow in Mary Gering's lab at the Whitehead Institute at MIT. He received his PhD from UC Berkeley, where he worked at the Innovative Genomics Institute in the labs of David Savage and Brian Staskowitz, developing new CRISPR cast gene editing tools for plants and applying them to improve photosynthetic efficiency and nutritional quality in grain sorghum. His research spans development of CRISPR tools for a range of crops, trait engineering for carbon dioxide removal, yield, and disease resistance, and the fundamental science of plant epigenomics. A central thread of his work is making plant genome editing accessible beyond the well-funded incumbents that have historically dominated the field. He's a National Association of Plant Breeders Borlog Scholar and an instructor for the African Plant Breeding Academy's CRISPR course. Evan, welcome.

Speaker 1 1:48

Thanks, Paul. Really happy to be here.

Speaker 1:50

Glad to have you here, Evan. I think we met what was it, like 2021, when I was just starting to get into the full breadth of climate biotech, and we were recommended to chat. I think it was our friend David Ding said, You gotta chat with Evan Groover, he's gonna blow your mind about plant science. And indeed you did. And I'm so glad that we're still chatting today. Excellent, likewise. So, Evan, let's start with your background.

From Music To Plant Science

Speaker 2:20

Where did you grow up? How did you get here? Did you always know you'd be working on plant biotech and agriculture?

Speaker 1 2:26

I grew up in Northern California, which I think is a place that disposes one to the outdoors. So I grew up backpacking and bird watching and gardening quite a bit, and always had a pretty innate love of nature, but outside of some early aptitude in the physical sciences, did have no idea how to become a plant biotechnologist, much less a scientist. I studied music through most of my adolescence and early adulthood very seriously. And then over the years, this sort of early interest in natural things, especially plants and animals, blossomed now into a career in in plant science. I tell people that I still pinch myself though. I think I've had so many interests in my life, and I feel lucky to have found one in plant biology that I really love, but it was never a sure fit from the beginning.

Speaker 3:14

Very cool. I love that background in music. I also share a background in music, which is music is just such a great joy in life. But we are here today to talk about for much of the discussion, plant genome editing and different

Gene Editing Versus Transgenic GMOs

Speaker 3:28

facets of it. And so why don't we start just by defining that? What is genome editing and how does it differ from transgenics?

Speaker 1 3:36

One of the other kind of quirky things about growing up in Northern California and specifically the Bay Area is that I was raised in the epicenter of the non-GMO movement. So, you know, a lot of people in my family and friends had this very ardent belief, and this all came to a head in 2013 with the first march against Monsanto, that agriculture and the industrialization and large-scale sort of commercialization of agricultural processes was this harbinger of doom, and that we should all be acutely concerned about this transpiring. And so I kind of grew up died in the wool, sort of East Bay kid, and really afraid of these technologies, at least in as much as they were available to me at the time or I was aware of them. And this was in the era of GMOs. And so this is a GMO or a transgenic plant is defined by taking DNA or some oligonucleotide from one organism and putting it into the other. So, you know, people talk about putting salmon DNA in a tomato or something. But around the early 2010s, with the advent of CRISPR and some of the decades before that, there existed a whole different suite of technologies that we now define as genome editing technologies. And so genome editing, as most of us know, involves the precise manipulation of DNA bases in a host organism. And a gene-edited plant is differentiated from a transgenic plant on the basis of looking like something that could have happened in nature. So when we evaluate, our government regulators evaluate whether a plant is gene-edited, they look specifically at the DNA constitution of that plant and decide are the deletions, substitutions, or short insertions that have been introduced into that DNA sequence something that could have happened in nature and not something that is far afield or only available because of biotechnology. And if so, happily over the past five years or so, they've decided that those plants will be exempt from the traditional GMO label. And so we've entered into this new era in sort of the dawn of CRISPR, wherein we have this very large-scale ability to use gene editing to improve our crops, besides all of its medical and therapeutic applications. And there's a new regulatory paradigm that demarcates a strong distinction between GM plants and GE plants, genome-engineered plants.

Why Breeding Still Runs Agriculture

Speaker 5:53

Got it. And one thing I've seen stressed across your work is also the importance of combining genome editing with more traditional plant breeding. So maybe you could explain that as well. What is plant breeding and why does it need to combine with genome editing for some of the applications we'll talk about?

Speaker 1 6:10

Yeah, I think plant breeding is perhaps one of the oldest, if not the oldest, project of human society, at least the one that we live in. Over the past 15 to 10,000 years, our ancestors have been meticulously breeding crops intentionally as to improve their agricultural traits. And this is all under the umbrella of plant breeding. And in the modern era, we've really benefited from this. The evidence of that is the huge human global population that we have. But it also is a very sophisticated sort of industry and technological scientific industry inside of plant breeding that we continue to improve and refine the crops that we grow for food. And so a lot of foundational discoveries in genetics and just quantitative genetics, population genetics owe their origins to plant breeding. But a lot of biologists that I talk to, especially molecular biologists and genomicists like me, are surprised at just the sheer scale and capital expenditure of plant breeding. We still spend hundreds of billions of dollars a year distributed across the world continuing to improve crops through crosses, sexual crosses, and selection. And this is still the incumbent paradigm of how crops get improved. And so when I talk to people about gene editing, I think it's really important to emphasize that any biotechnological improvement of a crop need be integrated with this existing incumbent paradigm of plant breeding simply because the breeders think about things that we don't think about in the laboratory, things like the genetic background that might be optimal for a certain environment, or the environmental conditions that might influence how a trait manifests. And so there's a lot of really specific and I would say critical derived knowledge in agriculture that is cordoned off in the domain of breeding. I think the challenge for this next generation of plant biologists will be to reconcile these two domains of more molecular genomic-based biology with this more classic model of crop improvement through selection.

Speaker 8:05

There's one other thing I wanted to highlight that we talked about in a previous conversation, which was this sense in which breeding in throughout history has maybe unintentionally reduced diversity. And genome editing maybe gives us an opportunity to reintroduce some of that diversity and have diversity while also having breeding. Maybe you could explain some of that.

Speaker 1 8:31

Yeah, it's such a fascinating thing to think about. And really one of the great joys of being a plant biologist is that every crop is a little bit different, right? And a lot of that difference is attributable to these ancient events in the domestication history of a specific plant. But we can see that in certain crops, and take sorghum, for example, crop that I worked on in my PhD. Sorghum is very closely related to maize, which we is the basically the most popular grass grown for food on the entire earth. And maize is basically corn. Corn, of course, yeah. And compared to corn, is relatively less diverse. There have been significant bottlenecks in its evolutionary history. And as a result of that, we have less useful variation that we can select on when we're breeding it. Now, of course, CRISPR and gene editing at large is an incredible tool for introducing diversity. And so pushing the phenotypic potential of sorghum outside of anything that could have existed in the entire suite of germplasm that we have on hand as a species. And so I think what's really fascinating to me about living in the era of genomics and gene editing is that we can really reinvestigate these hard limits that we assume that plants have and that there exist opportunities to push plants to do things that would have never been possible by the traditional genetics that we've relied on for their improvement.

Speaker 9:49

I'd love to expand on what sorghum is and why it's important. And maybe we can bring in some of your work with the African Plant Breeding Academy for that. Because for many years during your time at IGI at UC Berkeley, you were working also as an instructor for African Plant Breeding Academy, APBA. And so maybe you can tell us about APBA and what applications of plant genome editing you're trying to enable there and how sorghum fits in.

Orphan Crops And CRISPR Training

Speaker 1 10:16

I have been fortunate, as you mentioned, to work with a lot of really world-class institutions and organizations working on the forefront of fighting malnutrition and food insecurity in the developing world. But yeah, the long story short of it is that during my PhD, I was fortunate to work with some of the seminal figures in gene editing and developing tools for editing crops. And in about 2023, we received the call to get involved with an organization called the African Orphan Crops Consortium, which is a sort of a long-standing NGO on the continent of Africa that is doing capacity building mostly for breeders. So they have had a course now called the African Plant Breeding Academy Breeding Course. They've trained to date over 150 breeders from over 28 countries in mostly the African continent. And they've really set up this really strong network of breeders that are trained in the contemporary practices of crop breeding and are integrated with their regional jurisdictions, whether it be the private or public seed industries of their respective countries. And the opportunity that we seized, and this was with my my colleagues Nicholas Caravolius and Dave Savage from UC Berkeley and many others from UC Davis, the University of Illinois, and elsewhere, was to build a CRISPR course that would integrate with this network of breeders and allow the sort of accelerated improvement of orphan crops, i.e., staple crops that feed typically tens of millions of people, but are relatively ununderimproved or unimproved compared to crops like corn or rice, for example. So I'm talking about things like cassava and teff and tree tomato, sorghum, of course, finger millet, crops that are totally indispensable to the lives and livelihoods of many, but don't really have many of the agronomic benefits that we appreciate in our domestic markets. And so it's been a really incredible opportunity to work with senior scientists from all over the African continent. Our CRISPR course has now trained 31 scientists from 11 different countries, and they've returned to their home countries to integrate with that network of breeders where the rubber really hits the road and introduce new traits that might be interesting for improving and preserving the sort of the breadbasket of Africa.

Speaker 12:30

Fascinating and beautiful.

Photosynthesis For Carbon Drawdown

Speaker 12:32

So another application that you've worked on is the use of gene editing in photosynthesis improvement, which has a lot of broad utility. And you recently published a review paper on the potential of plant genome engineering in carbon sequestration and CDR. And so we've talked in the past on this podcast about CDR and why it's so important that we develop ways to remove CO2 from the atmosphere. Or maybe you can tell us more about how you see photosynthesis and the enhancement of photosynthesis playing a role in CDR and also its its general importance. And then maybe we can dive into some of the details around that. So we've published this piece.

Speaker 1 13:17

This was co-authored with my talented colleague Flora Wong at UC Berkeley. Basically describing a few ways that we might improve plants that they could scalably capture carbon dioxide. And now this was, I would say, majorly prompted by the creation of voluntary carbon markets, especially here in the US. But what our central premise is, and it actually gets back to this question of phenotypic limits, it's that when we look at all of the crops that we grow for food, and then some of the plants that we don't even grow for food, things that we haven't domesticated or improved, we see that there is a huge variation in how efficient they are at doing photosynthesis. So capturing light and carbon dioxide and turning it into biomass. Some of this is contingencies because of the domestication process, like I mentioned earlier. And others just have to do with the sort of the physiological or environmental constraints that a plant might be living in. But what we can learn after decades of molecular biology and hundreds of years of plant physiological studies is that plants are suboptimal at photosynthesis, and that growing them at scale with improved photosynthesis by way of genome engineering might be a way that we could take a lot of carbon out of the air quite quickly. And I would say importantly, and maybe this is my bias, but it doesn't require us to develop a bunch of new technical fact faculties like other industries that are seeking to tackle the same problem because we are quite sophisticated at growing plants across almost all the environments of the earth. And we know plants like sorghum, for example, that are able to grow in relatively inhospitable, almost inerrable environments that would allow us to be able to seize on these CDR opportunities in relatively suboptimal land for agriculture.

Speaker 15:02

And so when we think about photosynthesis and its role in agriculture, whether we are cultivating plants for food or potentially for materials and forestry, or potentially also for carbon drawdown, why is photosynthesis a focus for that? Of course, photosynthesis is the mechanism by which carbon is fixed using energy from the sunlight, but why focus on photosynthesis as an optimization factor?

Speaker 1 15:32

Yeah, it's a really good and reasonable question because I think if we inspect how agriculture works right now, crop plants take a lot of carbon out of the air, and almost all of that carbon is eventually respired back into the atmosphere. A lot of agricultural schemes, at least in our sort of late industrial era, are net emissive or drawdown. Depending on how you describe it. We see that by improving photosynthesis, it improves the economics of growing crops for bespoke carbon sequestration, but it also gives us new avenues to improve food and to improve the general sort of carbon sequestration capacities of agricultural plants, which are occupying an increasable, increasingly large portion of the earth's surface. And so we think that not only can this the improvement of photosynthesis potentially open up new opportunities and sort of new markets in the space of carbon drawdown, but it can also improve and intensify the efficiency by which we grow food in the places that we already grow food. And hopefully the sort of the second-order effect of that is that we don't have to deforest or raise as much land to convert it into agricultural land.

Speaker 16:42

And so if you're improving photosynthesis, essentially you're improving the rate at which carbon is fixed into plants and the plants are going to grow faster. In the review paper, you offer a lot of different ways that we can improve photosynthesis. And it seems like a theme there is that there are actually a lot of ways that we know we can improve photosynthesis that we have learned through past research that aren't yet implemented. And so is that the case? And and if so, why aren't they implemented? And why do you think we need a we need genome editing for that?

unknown 17:26

Yeah.

Speaker 1 17:26

I'll break it down. So I think in most science fields you're standing on the shoulders of giants. But then those specific giants that that I I hope I'm standing on in some capacity are those people who, for about four decades now, have been doing transgenic experiments on photosynthesis and demonstrating that there are various rate limits distributed across the photosynthetic physiology. These have to do with the specific harvest of light or the specific sort of constitution of the carbon sequestration apparatus, but also the sort of the downstream processes of carbon sequestration that turn captured carbon into sugars and ultimately biomass. We have observed that by transgenic overexpression, typically, of some of these rate limiting factors, we can empirically improve the rate of biomass assimilation in a plant, and that typically those yields in biomass aren't really accessible through traditional breeding. So I should say this is not an uncontroversial field of biology, because people that breed plants are typically quite skeptical of our results because they assume that the limits of photosynthesis or of yield sort of deposition in a plant are hard-coded by the genome and that there's no optimality outside of what could be achieved through heterosis and careful crosses. But I think there's a strong body of evidence to suggest that by simply tweaking the expression and stoichiometry of various photosynthetic pathways, we can improve carbon assimilation ultimately, either through different routes of the photosynthetic apparatus. And that really one way to do this is with transgenics. But as we've seen over the history of plant biotechnology, transgenics are very hard to get to market. They're quite expensive to commercialize for both practical and regulatory reasons, and they're inaccessible to a huge swath of the seed industry and also the academic market, especially because of the high costs associated with commercialization. And so now that this sort of floodgate has been opened about allowing genome engineering, the question that we ask is how can we use genome engineering within the confines of what has been deregulated to improve photosynthesis and allow more agricultural opportunities for carbon sequestration or at least just improving photosynthesis and ultimately yield in crop plants?

Speaker 19:47

The way that it's framed in the paper, there's this equation that I found really useful for getting my head around what the different inefficiencies are in photosynthesis that could be improved, which is basically just an equation that describes how well light energy is converted into or how well light energy is used to actually fix carbon and generate yield. And so it it basically is it's the energy of light multiplied by these different efficiency factors. And each efficiency factor reduces the amount of light energy that you're actually using for yield. And so maybe we could walk through each of those efficiency factors and just talk a little bit about how you could make an improvement on some of those efficiencies. And also I'm curious why you think evolution hasn't figured this out itself. But anyway, let's start with, or maybe we can yeah, overview what these efficiencies are and then go into it each

The Monteith Equation Explained

Speaker 20:46

one.

Speaker 1 20:46

But yeah, the the equation that you're describing, I think it's called the Montiith equation, and it's a canonical equation that's used in photosynthesis studies. It basically discretizes all the various faculties of light capture and processing. And so it basically gives you some sort of quantitative estimate about how efficient a plant is of like capturing all of the sunlight that falls on a field and ultimately turning that into energy and then biomass. And the way the equation is broken down is that the this like ultimate yield potential is, I guess, can be described in terms of how much energy or light falls on a field. And of course, that's kind of subject to the environment. So we think about that less, right? That some corn growing in Minnesota might not get as much sun as it does in Tucson, but that's just the way that it is. And then the next term is the light interception efficiency. So that's how good the plant, as it stands, is at just dispersing itself and ensuring that a lot of that light is captured and that the full spectrum of energy that it's receiving from the sun is used usefully towards energy harvest. The next term is conversion. So this is like radiation use efficiency. So it's how of that light that is able. To hit a leaf, how useful is it to the plant's photosystems and the chemical apparatuses they use to capture that light? Notably, plants have great disparities in how well they are able to convert light for a bunch of physiological contingencies. And then the final term is has to do with some people call it the harvest index, but really it has to do with the efficiency of partitioning. And see if you're able to capture that light in accordance with some amount of CO2, how good are you at turning it into roots and stems and leaves as compared to something that might be radily respired back into the atmosphere? And so there's a lot of intrigue here about the sort of the fundamental metabolic wiring of the plant that would probably be relatively interpretable by people that work on strain engineering or metabolic flux, for example. And so if we take these terms of interception, conversion, and partitioning as they stand, and this is getting to your point about evolution, we can see across plants that there's actually huge disparities in their efficiencies at these basically three steps. The best example, I think, of humans doing their job really well is that we have bred plants to have incredibly high light interception efficiencies. So if you see a cornfield at the peak of the summer, you'll see that there isn't an ounce of space that's being wasted in that field, because we have bred plants to sufficiently spread their leaves as to account for all of the incident solar radiation that would fall in their proximity. Where there's really great opportunities for improvement, it's in the actually the capture, the harvest of that light, and then the conversion of it into chemical energy. And we see that across not just plants, but also photosynthetic bacteria and eukaryotic algae, there's actually a bunch of evolutionary innovations that can improve these terms significantly, but they haven't really made it all the way into crops. And no one crop is really optimal in all of the faculties that sort of contribute to this total yield efficiency. And so there's a lot of opportunity here to do, I guess you could say phylogenomic or comparative phylogenetic studies about how we could improve photosynthesis. But I think the approach that I would say I am descended from is really considering the quantitative yield of chemical energy of a plant from first principles and trying to surmise where are the real sort of choke points in the processes that allow for the capture and implementation of that solar energy. And when we do that, and again, this sort of gets back to decades of molecular biology research, we can really elevate these targets for improving the physiology of the plant that now we can see in the scientific literature are actually quite effective at improving carbon capture and light harvest at large.

Speaker 24:58

And so what would be an example of a mechanism that we know through transgenic studies that does reliably increase photosynthetic efficiency that we might be able to use gene editing to to access more readily in a way that could actually be brought into implementation?

Speaker 1 25:18

So there's all these genes, right? That we know they might be rate limiting. We can empirically prove that when we transgenically overexpress them, that we can actually improve carbon assimilation. One of my favorites is a gene called RAF1, which is one of uh sort of rubisco's chaperone proteins. So hopefully we have some rubisco heads in the chat. And in plants, RAF1 is pretty indispensable for the folding and the localization and the active to activity of Rubisco. But we see that the chaperone is typically produced substoichiometrically to the Rubisco holo complex in general. And we know that when we increase the expression of RAF1 in certain plants, we can actually just get more carbon assimilation and improve various faculties of photosynthesis. And so take RAF one as an example. We want to turn up this gene, but we can't just slap a strong promoter in front of RAF one, because that will have essentially been a transgenic event. And so the question that we really ask, and this sort of maybe alludes to some of my other work, is how can we modulate the expression of a gene like RAF 1 with the smallest possible edit to the genome? The answer that we arrive at is that the manipulation of cis-regulatory DNA, so things like promoters, introns, and untranslated regions, is the most effective way that we can do this. And that the modulation of gene expression through small cisgenic, we call them, edits, is a really effective way to do this, tune the photosynthetic apparatus and tune the quantitative traits that it sort of begets. But the real question that we pose in the piece, and one that I think should be a source of great scientific interest, and it certainly is in domains of agriculture, is how do we know where to edit? If we want to change the expression of a gene, how can we predict where the optimal site to edit is? And are there ways that we can accelerate the process of genomic discovery to be able to induce a quantitative phenotype without having to screen tens of hundreds or hundreds of acres of edited plants?

Speaker 27:24

The Climate Biotech Podcast is powered by Homeworld Collective, a 501c3 nonprofit unlocking biotech solutions for planetary health by fostering community, building knowledge, and directly supporting early stage research. We are always looking to connect with scientists, innovators, and funders who want to accelerate progress in this space, whether in our current program areas of critical minerals and greenhouse gas removal or in other application areas. If that's you, reach out to us at hello at homeworld.bio. So this is now starting to get into some of the work that you did in your PhD, right? And so let's talk about the work that you did on new ways of making and screening genome edits.

Fast CRISPR Screens In Sorghum Cells

Speaker 28:08

And maybe you can also just tell us a bit more why this is so important in plants, relating to their life cycle, and because plant biology is notoriously difficult because plants are so slow growing, right?

Speaker 1 28:20

So let me set the stage, Paul, because I I live in Cambridge and you live in the Bay Area, and we both live in places where it's really hard to do an agricultural field trial. Now, let's say that you wanted to improve the expression of a gene, like RAF1. In the paper that you're mentioning from last year, which was co-authored by our aforementioned friend, David Ding. We took three genes in the photosynthesis synthetic apparatus that we thought we'd really like to turn up in sorghum. So they were RAF1. They were a gene called PSBS, which is an accessory protein to one of the photosystems. And then this gene, Cetoheptalose 1-7 bisphosphatase, which for again the strain engineering heads is a rate-limiting metabolic step in the Calvin-Benson cycle. And we said we want to find the minimal edit in the promoters of these genes that can allow us to overexpress them relative to their unedited plant. And so we stood up a large functional genomic screening system in primary cells, i.e. protoplasts, wherein we could isolate millions of cells at a time from the leaves of immature sorghum plants, and then test just about every possible CRISPR permutation to their promoters. In doing so, we were able to screen, I think the number was like 30,000 different CRISPR-type edits in these cells, and eventually find edits that translated to improved expression of the genes that we were interested in. And I would say a lot of this is forthcoming, but we hope that we can evidence in the near future that this also translates to improved photosynthesis in an edited plan. And so essentially what we did is create a system to screen many types of CRISPR edits in about two days, and effectively replace a process that might have taken, I don't know, months or years had it been performed in a field, and needless to say, but tens or hundreds of acres and thousands of man hours to actually make and screen all these edited plants. And the necessity for this, and maybe this is what your question evokes, is that actually transforming plants, actually making edited plants is still very challenging in a lot of species, and especially in species like sorghum, where we have relatively fewer resources and less of a community that's working on genetic problems. And so not only would it be very infrastructurally intensive, like I mentioned, to do the incumbent paradigm of breeding with all of these different editors, but it might just not be technically possible given the certain sets of tools. So I think I'm very animated right now by people that are seeking to build more transient screening systems in plants and de-risking and characterizing the existing ones that we already have. I think it's going to give us incredible tools, not just for functional genomic improvement of crops, but also for training models that can predictively tell us how to perform gene editing experiments. But I'm also quite heartened to see incredible progress right now in the plant tissue culture space. I wouldn't want to pose it like we're racing each other, but I do think that there's great work to do on a couple frontiers that are going to allow us to more scalably evaluate the effects of gene edits and in doing so gain more sort of inference about what is the optimal way to genome engineer.

Speaker 31:39

And for folks who are maybe more familiar with human cell biology, like this would be something like a single cell screen, right?

Speaker 1 31:48

I think what people are surprised to learn is that prennoplasts are much more fickle than human primary cells. They can't divide readily in tissue. They're, I would say, onerous. I just finished my PhD, so yeah, I will say they're very onerous to harvest. And they're they're not maybe as amenable to a lot of the same sorting, sequencing, and screening techniques that we use in other organisms, like in metazones or human cells. So it's definitely less of a mature field doing single cell screens in plants. I think there's great potential there. But I think we're always going to be threading a needle where you can have the largest, biggest, baddest screen of all time, but you need to make sure that your screen is going to actually recapitulate what you're going to get in the plant. And so really trying to decipher what the confines are of your screening system in advance, I think is really important. And I'm heartened to see a lot of great biologists working on that problem right now.

Speaker 32:42

Very cool. Also, I'm I can't help but chuckle at the largest, biggest, baddest screen.

Speaker 1 32:48

Yeah.

Speaker 32:49

Can't wait to read the next paper that screens more. Okay, let's move on to some of your current work.

Epigenetics As A Crop Lever

Speaker 32:55

Now we just spoke about your PhD work. So you've recently begun a postdoc with Mary Gehring at MIT's Whitehead Institute. And there you're diving into some of the fundamental science on plant epigenetics and how it connects to phenotype. So I'd love for you to share a little bit about what you're working on, what some of the biggest mysteries in plant epigenetics and phenotype today.

Speaker 1 33:19

Yeah, so maybe I can blow your mind now with assuredly be a kind of a controversial statement. But so plant, flowering plants at large, the angiosperm clade, right? They've been on land maybe 200, 150 years. They all have just about the same genes. So we look at a soy plant, a maize plant, corn plant, pardon, a sorghum plant, they all have the similar sets of tools in their genome for constructing phenotype and diversifying across the evolutionary time. What's really diverged as this clade of plants has proliferated all around the world is how they express their genes. And so we can appreciate when we look at, and this is maybe one of the best understood sort of archaic domestication domestication of maize in Central and South America, that a lot of the genetic sort of attributes that we were selecting on weren't actually selecting on different genes, but it was selecting on different cisregulatory DNA. So we weren't necessarily changing this tiny Teocente weed into a corn plant by picking different genes. We were picking different allelic variants in promoters, enhancers, and introns. And so this sort of gives you a baseline that probably one of the most interesting levers that we have for improving and just generally, I would say, adapting plants to our changing climate is just changing how gene expression programs work. And so in my PhD, I really focused on cis regulatory DNA. I think apparently, and quite empirically, we can see that cis regulatory DNA is super important for changing gene expression. But there are other contributors to this black box between the molecular state and phenotype. And in plants, a lot of it has to do with what we label as epigenetics, but really what we're talking about with epigenetics is things like methylation, histone occupancy, and constitution and chromatin state. And one really fascinating molecular attribute of plants is that they have these really unique and independently derived mechanisms for epigenetic regulation. And so my current advisor, Mary Gehring, has been at the forefront of this field for her entire career in science, characterizing how epigenetics, these states that are not encoded in the genome, but are manifestly and sometimes heritably important for phenotype, are encoded and how they work. And really the big question that I have as a postdoc is what contribution do these epigenetic states have to crop phenotypes? And how much phenotypic potential are we leaving on the table, so to speak, by not accounting for epigenetic information? And I think this is all coming into a head in the era of AI, where we're getting all of this data about genomics and about various, I guess you could say, ohmic measurements of plants, and ultimately realizing that they have typically only sparse or sometimes relatively wimpy correlation with the actual quantitative phenotypes that we're trying to measure. And so my hope, my hypothesis as a fellow is that by manipulating epigenetics itself, the way that DNA is structured and organized inside of the cell, we can find a new angle for improving crop phenotypes. And super importantly, I mentioned that CRISPR and gene editing is becoming deregulated globally right now, but there are many countries that are holding out, most significantly the European Union, which is making small but relatively slow progress at deregulating genome engineering. And so what if we could be using epigenome engineering in those jurisdictions where more sequence-based biotechnological approaches aren't allowed to improve plants? I think that's a really exciting prospect. But I think we have a lot of figure of work to do to figure out just how influential any one epigenetic regulatory layer could be.

Speaker 37:14

Very cool. And I want to, there was a lot packed in there, so I want to try and summarize it. And you can tell me if I do a good job. What I actually learned from you, I remember on our first call years ago, you told me about this phenotypic plasticity of plants. And so this is like most plants, many plants have the same set of genes, but these different have different regulation of those genes, right? And you talked about cis-regulatory elements, which are like enhancers, promoters, introns, DNA sequences that are located close to the gene and are involved in regulating how that gene is expressed. Those are like causing different genes to be expressed differently across different plants, which gives rise to a lot of different phenotypes. And now you're saying, okay, in addition to cis regulatory elements playing such a role in this fantastic plasticity of plants, we also have epigenetics, which are these non-DNA sequence factors that affect regulation, which you mentioned methylation, histones. For those who aren't familiar with what those are, these are modifications to the DNA that don't change the DNA sequence, but change the way that the DNA is structured and expressed. And so you're saying that this is like in a whole other frontier of where we get plant phenotypic plasticity that could be an additional toolkit in how we optimize plants for the benefit of humanity and the planet, and also could also be amenable to different regulatory environments that might be more stringent.

Speaker 1 39:01

I think plants are really one of the domains of life that we know of where there actually is strong evidence of transgenerational epigenetic inheritance. This is to say that if your parent experienced some adverse event in their life, that could actually be chemically transmitted to you, the progeny of that parent. And so there's an interesting sort of Lamarckian tinge to this entire pursuit. But I think it's uncontroversial to say that epigenetics are an incredibly important contributor to plant phenotype, but it is less well-defined how quantitely influential they are on any one phenotype. And so I think there remains a lot of good work to be done there. And for someone like me that cares about changing gene expression and accounting for how sequence translates into phenotype, it's really the big great black box of what happens in between the genome and the organism in its morphogenic potential. But to your point, yeah, plants are quite phenotypically plastic and really inspiring subjects to be using to study epigenetics as a fundamental phenomenon in biology.

Speaker 40:11

Very cool. And what was the controversial part of what you said?

Speaker 1 40:16

There are people in plant biology, and again, I don't mean to throw breeders under the bus again here, but I think there are people that are skeptical about the contribution and the heritability of epigenetic information to phenotype. There are people that either say epigenetics doesn't have a huge bearing on grain yield in corn, or they say you can modify all you want, the methyls, the methyl cytosines in this genome, but they're ultimately going to revert and they don't have a huge bearing. And so I think the great work of epigenetics in the modern era, especially now that we have great tools for sequencing, understanding, measuring epigenetic information, is trying to understand how much epigenetics is a great mover inside of the cell versus just a correlate to what has already been encoded by the genome and its accessory proteins.

Speaker 41:07

Got it. Very cool. And and an area of disagreement or controversy is always an area where, especially in science, where there's progress to be made. And so very cool that you're taking that question on. And so I have one more question for you before we move on to the rapid-fire questions that we ask all our guests.

What To Work On Next

Speaker 41:28

So for folks who are early working in some of the spaces that you've talked about, whether it be genome editing or applications of genome editing or plant epigenomics, if folks are looking for actionable ways to contribute, what are some actionable problems that people could start working on right now that you would recommend folks consider if they're moving into this space?

Speaker 1 41:54

One of the incredible things about working at plant biology is that it's just such an interdisciplinary field that you're asked to span the breadth of agroecology to physiology to cell biology to genomics. And any plant breeder or plant biologist is typically well-versed across all of those disciplines, at least as much as it abets their breeding program or their research. So this is to say it's a really big tent. And if you're excited about working in plants, there's probably a place that suits your disciplinary interest. But I think the problem that we have right now, to say it plainly, is just that we have to grow enough food to feed our burgeoning human population and also adapt our agricultural systems to a climate that is quickly changing in most parts of the world. And so I think working on fundamental problems in, I would say, crop physiology is always going to be the highest leverage thing for a lot of these problems, just adapting specific crops to certain environments, reducing the amount of inputs, especially nitrogen fertilizer for certain plants, improving the yield, agronomic utility, and pathogen resistance of various plants has immense use in fighting food insecurity. But I also don't think that this should be limited by my imagination. I think there's one of the things that we sought to evoke in this recent review on photosynthesis that we discussed is that we should really be asking ourselves, how far can we push certain plants right now with regards to their phenotypic potential? And maybe we can get plants to do new things like capture carbon, bioremediate different environments, mine for trace minerals, create therapeutics or other uses in biomanufacture. And I think some of the most exciting opportunities really do exist on the fringes. When we account for the natural history of our earth, we can see that we've changed it a lot. We humans have, by way of introducing agriculture and various other anthropogenic activities. And projects like reviving or de extincting threatened. Extinct species of plants, for example, that were previously huge contributors to our terrestrial ecologies. The American chestnut comes to mind. That's a really exciting thing. There are plenty of crop plants that in some places are on the verge of extinction. I'm thinking of banana, citrus, cacao. There's major problems to be solved in just fortifying our agricultural ecosystems and our natural spaces against the scourge of global million of beetles and bugs and fungus that come from having an international economy. And so there's plenty of fascinating things to work on, but I think the central one that I am animated by and have been animated by over my career is adapting our food systems that they can feed enough people. And the negative externalities of that feeding are limited as it comes to threatening biodiversity.

Speaker 44:55

Wow. There is a lot of work to do. And one of the things that probably the thing that encourages me most in these times of facing so many problems is how many people really do want to work on them and are smart and passionate and are looking for ways to contribute to a better world. So I look forward to seeing people work on all this stuff. Okay, so we are at a point now where we ask these rapid-fire questions. These are pretty fun questions that have just revealed some nice nuggets over many of our episodes, and I'd love to hear your answers to them. So the first one is what is a single book, paper, art piece, or idea that blew your mind and shaped your development as a scientist?

Speaker 1 45:39

Do I owe my scientific career to a lot of artists and writers? The one that always comes to mind first is maybe it's not a specific piece, but the extended collection of Hilma of Kleint, the great early 20th century painter. She's well known for her sort of abstract paintings, but she was quite an accomplished, I would say, natural historian and botanical illustrator. And yeah, I think the depth at which she describes plants in her native landscape is always a real touch point for me when I think about what the role of a plant biologist is, not just to be a an incisive scientific mind, but also to be an advocate and a champion of the of the utility, aesthetic qualities, and just innate spiritedness of plants. And so that's been a constant source of inspiration, especially at my lowest experimental moments.

Speaker 46:34

Beautiful. Okay, what is a great line of advice that a mentor has given you?

Speaker 1 46:39

This is perennial advice that I've received many times in my career. I will attribute it to my mentor, Rita Mum, who's the director of the African Plant Breeding Academy. But it's to talk to breeders, especially if you're a plant biologist. I think if if you if you work in any sort of ecological or applied plant science, I think it really behooves you to understand the system by which we make food right now. And so talking to people across the distributed supply chain of agriculture, whether they're seed companies, breeders, farmers, is really the ingress that is most effective at trying to understand what is needed. And right now there are many things that are needed, and a lot of those needs are going unmet in in agriculture. So yeah, trying to talk to maybe I should say talk to a farmer, but I think I always get the most out of talking to breeders.

Speaker 47:32

Cool. Okay, if you had a magic wand to get more attention or resources into one part of biology, and it can't be what you work on, what would it be?

Speaker 1 47:42

I have a few things, but the main one, I think the biggest umbrella I can cast is agroecology. So I think we we know that the way we farm is destructive to many aspects of our biodiversity. We see problems with eutrophication, other negative externalities of industrial farming. We don't have good longitudinal studies to be able to predicate that that sort of intuition that we have. And so a great example, very germane to the topic of conversation in this podcast, is that we don't really have a lot of awesome longitudinal studies on soil carbon. What how when we farm, what are we doing to the carbon that exists in soil? And there are there any sort of gold standard measurements or just methodologies that we can use to study that at scale? And so I think that if I were running an NGO or something, I would probably want to give it all to agroecologists that we're trying to understand the effects of agriculture, that we might minimize the negative effects of agriculture.

Speaker 48:38

Cool. Okay, give us a hot take. What's one view you hold related to climate and environmental biotechnology that you think some others in the field might disagree with?

Speaker 1 48:50

I'm a real genome editing acolyte. I I think it it it has a lot of potential to solve really big problems, but I don't think any of those problems will be solved, or at least maybe not the right problems will be solved unless we really work much more interdisciplinarily in in plant science. I think that especially in my time working on CDR, I was very much edified to be working with not just plant molecular biologists like me, but soil scientists and ecologists, breeders, people that understood the downstream impacts of whatever CRISPR added I was interested in that day. And so I think that trying to build coalitions that sort of bridge all of the disciplinary gaps in agriculture is really the only way that we're going to get ourselves out of this thing. And I'm really emphatically supportive of any efforts that can bring people together just to discuss how we can synergistically approach problems in agriculture and food.

Speaker 49:55

Okay, last question. What is one aspect of personal development that you would encourage biotechnologists to spend more time on?

Speaker 1 50:03

But I will say that one thing that I have spent time on that has I found very personally meaningful in biotech is just reading the deep history of my field. So I think I've been fortunate to be a plant biologist. We can read back through the 19th and 20th centuries what plant breeders were doing as it became a field and achieved massive global scale. And so reading people like Borlog and Vavilov and Goldschmidt and all these sort of early names in plant biology have been really important lessons for me in understanding the conceptual framework on which I do my science. And I think a lot of people would benefit from doing the same. Now, this might not apply equally to all fields. If if you work on phage biology, you can't read that back deep into the archives. And I don't think Pliny the Elder was writing about phage in any specific terms, but at least in plant science and in ecological sciences, there's a very long intellectual history that we can claim. And there's so many gems to discover if you take the time to read deeply in into the past. So I would really recommend that practice, and I do to the people that I train.

Final Thoughts And Ways To Connect

Speaker 51:16

All right, Evan, we have reached the end of our time together here today. This has been a very interesting conversation. I'm super grateful to you for taking the time to come and share your perspectives. So thank you so much. And I look forward to the next time we can kick it.

Speaker 1 51:30

Yeah, likewise, Paul. Thank you.

Speaker 51:33

Thanks for tuning in. I hope this has been educational and inspirational for you as you navigate your own journey to bring the best of biology into planet scale solutions. I'll be back soon with another conversation. In the meantime, you can stay in touch with Homeworld on LinkedIn, X, or Blue Sky. Huge thanks to our producer Dave Clark, along with Paul Himmelstein, Caleb Sims Austin, and Ricardo Sarcosa for making these episodes possible. Until next time, I'm Paul Reginov, and this is the Climate Climatech Podcast.