Talking Biotech Podcast 373

Dr. Philippa Borrill, Genes Controlling Plant Size
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Kevin Folta: [00:00:00] Hi everybody, and welcome to this week's Talking Biotech podcast by Colabra. Now, when we think about growing plants, or especially in an agricultural context, we automatically think that bigger plants or bigger trees would be better, right? More stuff. But is that always the case? And there's a lot of advantages to compact growth.

So dwarfing genes have been a massive contributor to food production. Something like billions of people have been fed by dwarf varieties or genes that control size when incorporated into things like wheat and rice. But genes that affect that elongation growth sometimes have problematic secondary effects, things like less flowering or maybe lower yields.

So alternative genes that control plant stature are of incredibly important interest to agriculture and basic science. So today's guest discovered just that, [00:01:00] and her results were published in the November 23rd, 2022 issue of the Proceedings of the National Academy of Sciences or P N A s, a really nice journal.

I. So today we'll talk to Dr. Philipa Borrill. She's a group leader in the Department of Crop Genetics at the John and the Center in Norwich, uk. Welcome to the podcast, Dr. Borrill. 

Philipa Borrill: Thank you. I'm got to be 

Kevin Folta: here today. I'm glad you're here too because this is a topic that I'd like to cover for a long time, and your recent paper talks about this idea.

A new way to create a dwarf plant. And I always thought this was a cool topic because I think most of the audience doesn't appreciate why dwarf plants are important and, and the different ways to make it happen. We automatically think we want plants to be big and tall and stature and, and vigorous, but what's the advantage of being a dwarf plant or a semi d.

Philipa Borrill: So when we think about shopping for food, which most of it comes from plants, then it's a particular part of the [00:02:00] plant that we're eating. So in the case of fruits or grains like rice or wheat, then we're eating the fruit of the plant. And if we grow a really big plant, then we have a lot of parts of the plant we're not gonna eat like the stems or the leaves, for example.

So if we have a dwarf plan that has kind of shorter stem, but it still makes the same size grains, then that could be quite an advantage for, for us as consumers. . 

Kevin Folta: So why is that an advantage for us as a consumer to have a, a shorter stem? You know, if we're just eating the same grain? 

Philipa Borrill: The advantages you can in the same amount of area make more grain because, for example, for wheat which is a major cereal crop, then if the plants are really tall, which they have been historically, then they often suffer from lodging so they can fall over in high winds.

And that means it's really hard to harvest the grain. So although the plant could make the same amount of grain, a lot of it's lost into the soil. So if we have a, a dwarf plant, then it's less likely to fall over and we can harvest all of the grain. 

Kevin Folta: That makes a lot of sense. Is there also a question of, of investing in [00:03:00] that biomass that's not really used, you know, you're making this tall plant, or is that just expansion in water?

Or is it actually more stuff that's creating that taller plant? 

Philipa Borrill: Yeah, exactly. So there's more stuff is used to make the stems and the leaves and the plants that we don't need. So by reallocating where the the, the stuff that makes up the plant, so the carbon inside the plant, then you can send more of it into the harvested part of the plant.

In these dwarf. 

Kevin Folta: Yeah, I, I don't think people ever really think about this, but Okay. Let's talk about what are some of the plant species where dwarfing is really important to production? 

Philipa Borrill: Yeah, so I think two really key examples are wheat and rice. So they're generally around the world grown in semi dwarf varieties nowadays but also other.

Crops like fruit trees are often grown as dwarf varieties because you can fit more trees per orchard then and have a higher fruit production. 

Kevin Folta: Yeah, that's a really good example. I, I grow fruit trees and always put them on semi [00:04:00] dwarfing rootstocks because we can fit more trees and, and you don't get these massive 30, 50 feet tall trees that require, you know mountain climbing gear to go harvest fruit.

So really important for, for horticultural production too. But the big place this made an impact was in the Green Revolution. And so why was dwarfing so important to build into these key food staple crops? 

Philipa Borrill: Yeah, so it was really a, a major challenge in the kind of middle part of the 20th century to increase food production, to be able to feed the growing population of the world.

Billions of people depend on staple crops like wheat and rice. So we had to come up with some ways to improve the amount of wheat or rice grains that could be produced on the same amount for area. And as you said, the green revolution, which happened in from the 1960s onwards, made a huge difference to the amount of.

Production that was possible per area. And a key part of this was the introduction of these assembled warf varieties of wheat and, and rice that could, were were [00:05:00] shorter, so more of their fixed carbon was allocated into the grain and it was easier to harvest because they didn't fall over. So that was a really key part.

Plus, with these semi dwarf varieties, you can apply a much more fertilizer, so produce higher yields because you have better inputs without running the risk of the plants 

Kevin Folta: lodging. Yeah, this is really an important point. This was work done by Norman bolo and, and colleagues and really was revolutionary I, and really can be blamed for feeding a billion people.

And, and some of these places like Pakistan, Mexico India, where. There was food shortage, and certainly, if you call it food insecurity would be an understatement. And so this idea of dwarfing really fed billions of people. 

Philipa Borrill: Exactly, and I think Norman Boag was awarded the Nobel Prize for Peace for this work.

Kevin Folta: Yeah. That was and well deserved and I, it goes under everybody's radar. I'm surprised more people aren't aware of, of who he is and what he did because of this [00:06:00] tremendous contribution. But what are the ways, so we start talking about mechanism. What are the different ways that dwarfing usually is conferred?

So what, what, what happens genetically to get a dwarf? 

Philipa Borrill: Yeah. So these semial varieties of wheat and rice that were introduced in the Green Revolution generally affect a particular plant hormone. So they have a genetic change in them that alters either the synthesis or the signaling related to GI Relic acid, which.

Growth hormone that promotes growth in plants. So these particular lines have a mutation in genes related to Gire. And, and therefore don't grow as, as tall. 

Kevin Folta: Yeah. So let, let's just touch on GI Relic acid just a little bit. So this is, as you said, a plant hormone that causes this elongation growth.

And so, Dwarf varieties are just ones that either can't make the hormone or are insensitive. Or are insensitive, so they either can't make it or can't perceive it, and so they, [00:07:00] they tend to stay short. But are there other problems when you upset GI Relic, acid sensitivity or production? 

Philipa Borrill: Yeah. So these plants, they, they generally look reasonably similar to the kind of conventional taller varieties.

But they do have some potential drawbacks. So, one particular one is that this change to GI Relic acid means that the plant is shorter, but also at all stages, the plant's life. So we, we actually want this to happen at maturity so that when the plants are developing their grain and then we're about to harvest them, that they're shorter, they're less prone to lodging.

But also even at seeding stage, you see differences in wheat. And this is a problem where for seedling emergence from the soil, so if you sew the wheat, Seeds deeper underground because you want them to be able to access some groundwater, for example, in a drought prone region. Then wheat lines that are semi dwarf may never emerge from the soil, and that causes a huge problem for crop production.

Kevin Folta: Yeah, it's a huge problem. , no, no crop, no production, right? Yeah. Yes, . [00:08:00] So we're speaking with Dr. Philip Abor. She's in the Department of Crop Genetics at John in center in the uk. And this is The Talking Biotech podcast by Col Labra. And we'll be back in just a moment. And now we're back on the Talking Biotech Podcast by Col Labra, and we're speaking with Dr.

Philip Bore. She's at the John Inness Center, and we're talking about dwarfing and why it's important in plants and some of her work that indicates there are new mechanisms to create a dwarf plant that are really kind of surprising. So what are some of the alternative networks that could control D? 

Philipa Borrill: So in wheat, the conventional dwarfing gene that was used was one that makes the plants insensitive to the GI Relic acid.

So the plants can't sense gires, so they don't elongate like they would normally. So in wheat, when we've been talking about alternative dwarfing genes, so options that we can use that aren't the standard conventional gene often. [00:09:00] We haven't known about what mechanism underlies these alternative dwarfing genes.

But in recent years, a couple of genes giving these alternative dwarfing phenotypes have been cloned. And these turn out to be involved in making giren to start with, which is exactly the mechanism that was used in the rice semi wolff varieties coming from the Green Revolution. Kind of con continuing this GI Relic acid.

Kevin Folta: Yeah, and, and I guess the thing that comes to mind to me is what, how do you know that you have a dwarfing situation where something just isn't elongating or just a plant that is just pathetically ill and just doesn't want to grow? 

Philipa Borrill: Yeah, so I think that's a, obviously a really key question because you don't want to just grow a sick plant that's never gonna get very big and be very useful for agriculture.

The semi door varieties, they generally have similar size leaves and other organs, so it's mainly the height that's affected rather than, Other organ size. There might be some small effects on the grain size, depending [00:10:00] on the exact genetic background and the particular dwarfing gene that's being used.

But in general, these plants develop at a similar rate to the tool plants that they're compared with. But then they just kind of over time just don't. Gas hole. 

Kevin Folta: Yeah, and I, I guess I asked the question like a, like a geneticist and a molecular biologist and not like a wheat farmer, that if the plant produces wheat, who cares what's wrong with it?

And, and you know, that's, that's, I work with a lot of farmers and I'm learning very quickly that if it works and it's, it is broken. It's fine as long as it works. So your recent paper talks about this gene called R H T 13, and this would be a gene that if we looked at it by structure and you know what kind of gene it belongs to, a normal gene family.

That's pretty well understood. It doesn't seem like it would have some kind of roll end dwarfing. So what, what kind of protein does it en. Yeah, 

Philipa Borrill: that's exactly right. So the RHT 13 gene encodes an N B L R R protein, [00:11:00] which is a nucleotide binding leucine rich repeat protein. And this type of gene is usually thought of to be associated with disease responses.

So if a plant's exposed to a pathogen or a pest then these nbl R genes act or proteins act as sensors to detect the disease coming in onto the plant. 

Kevin Folta: And do we have an idea of how many of these there are in a plant like wheat? 

Philipa Borrill: So there are probably hundreds to thousands of these individual NBL r genes in the wheat genome.

Kevin Folta: And so this one, does it seem that it has somehow specialized either in, does, is it still play a role in disease or is this strictly maybe playing a role in cell expansion somehow? 

Philipa Borrill: So we don't really know the answer to that question. That's a topic of ongoing research. We have some hints. It might be also still involved in disease resistance, but we think what's unique about this particular NBL or R gene is the allol that causes the dwarfing phenotype has a mutation in it.

So there's one single [00:12:00] change to the immuno acid sequence that gives it this effect on the height of the. 

Kevin Folta: Yeah, so it's a mutation in the normal gene. So the gene is, is normally required for correct vigorous growth and it's this mutation that causes the dwarfing effect. Do I have that correct? 

Philipa Borrill: Current hypothesis is more that normally the gene is kind of usually present as an inactive protein.

And then if it senses the disease then it would react and cause downstream signaling to respond to that disease. But in the mutant version that we've identified, then the protein is always switched on. So it's an auto active protein. And this means that it's kind of triggering different downstream signaling pathways when maybe it shouldn't be.

And that means that resources are perhaps, We distributed that would normally used be used for growth. And that causes the reduction in height. That's our, our current 

Kevin Folta: hypothesis. Ah, very good. And is this conserved across plants? I mean, do you, is there a possibility that we can make another dwarfing rootstock that doesn't have a gire problem?

Philipa Borrill: Yeah, I think it's possible. So it's known in other plant [00:13:00] species that these auto active mv l r genes, which would be like RHT 13 can cause this kind of reduction in growth because they're auto active, but often those genes are associated with some penalties. So the auto activity causes necrosis, so like small spots of cell death.

So on the leaves you'd see like brown flex. Which isn't a desired trait in a, a crop species, but what's unique about the RHT 13 all is that we didn't observe any of these necrotic flex. We don't know the molecular reason for why we don't see that, but it gives us kind of a way in to try and understand that.

And then potentially we can engineer auto active. And are genes that would be suitable to use also in other crop species. 

Kevin Folta: Yeah, this is pretty exciting stuff. So it, it really gives you another opportunity and potentially a new tool to be able to use something like gene editing, like crispr whatever, to engineer virtually any crop to have this auto active pro, to have this pro protein that doesn't [00:14:00] build in the penalty.

Other dwarfing genes. So does that seem like the long term goal of the project? Yeah, 

Philipa Borrill: I think that is the, the long term goal. So we'd like to understand kind of in the wider setting how the RHT 13 gene operates in weeks. So in different genetic backgrounds, different environments, and then also to start transferring this knowledge into other crops.

Kevin Folta: And so once you create the mutation using something like gene editing in, say, a major grain like wheated or rice, can you then just use traditional breeding to introduce it to new lines? 

Philipa Borrill: Yeah, definitely. So you can use conventional breeding crossing your, your edited line to other varieties of that crop.

And I think that's a bit of a long process, so it takes time to cross them and then go down the generations to make sure you. Get the rest of the genetic background suitable. So you need to stack other traits like disease resistance or yield components. But yeah, that will definitely be one way to introduce that benefit to a whole range of different cultivars.

Kevin Folta: I, I [00:15:00] guess maybe the last question is, you know, we've been selecting dwarf varieties of lots of different plants for a long time, and do you think that well, Has RHT 13 shown up as being the causal mutation in any other dwarfs or is it potentially that the plants that have been affected just haven't been sequenced yet?

Philipa Borrill: I'm not sure. So I think that that particular mutation we've seen in the RHT 13 wheat is perhaps unique to wheat. And what's also interesting is this gene isn't found in all wheat cultivars, even the the version that doesn't cause warings. So the yeah, so, so it might be that it kind of took a special combination of circumstances.

So this particular wheat cultivar that had this specific N B R R gene and then chemical mu genesis was done on that vir to try to make new traits that breeders could select. So this. Particular gene and the particular mutation we've seen, I think could be quite unique to this wheat line.

Kevin Folta: So what's next for the project? 

Philipa Borrill: So [00:16:00] next in the project is going to be trying to understandable more about the agronomic benefits of the RHT 13 allele by growing it in wider field Trials in the range are different environments and genetic backgrounds, but also drilling down into the molecular me. So I mentioned earlier, we don't know why the RHT 13 all doesn't incur these penalties of things like necrotic spots on the leaves.

And so we'd really like to understand how does the signaling downstream of the RHT 13 gene work and, and what that can tell us for applying this. Method into other 

Kevin Folta: crops. The thing I don't understand is that, you know, people have been selecting for dwarf wheat varieties for a long time, and wheat breeders have even used genomic selection and new breeding tools to be able to identify the causal mutations in dwarf wheat.

So what was it that allowed this to be detected now? 

Philipa Borrill: Yeah, so this all for RHT 13 has been known for decades, but it's only recently we got the tools to be able to identify the precise gene underlying [00:17:00] RHT 13. And one reason is that our reference genome that we usually use in wheat research is called Chinese Spring.

And this was fully sequenced in 2018. But when we looked in Chinese Spring, this gene's not actually present. So that really held up the research for quite some time. But more recently, a pan genome project has published multiple weak genome sequences and we were fortunate that one of those sequences does contain the RHT 13 gene.

So that was really the enabling technology to be able to clone this gene. 

Kevin Folta: Ah, really good. So a big score for Pan Genome Research . Exactly. Well, Dr. Phillipa bore, thank you very much for joining me on the podcast today. It was really informative and it helps me and other people understand this really important plant trait of not growing so big.

So thank you very much for joining me. Thank you, and to everybody else who's listening, thank you very much for listening to The Talking Biotech podcast. Join us every week to talk to experts in agriculture and in medicine, plant [00:18:00] science and conservation. Because we're learning more and more about the nuts and bolts that make up biology and how they're being applied.

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