Dr Michele Ragot: Technologies for all: Bringing new crops to the forefront

Dr  Michele Ragot: Technologies for all: Bringing new crops to the forefront

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[ Music ] >> Hello, good afternoon. Good morning. Good evening. Welcome to the International Plant Breeding Series organized by NC State.

And happy that you could join us again as -- all Thursday -- this past Thursday. Please tell us where you're joining from in the chat session and post your questions in the Q&A session. We have today Dr. Michel Ragot talking about technologies for all and bringing new crops into the forefront. Michel is right now the Managing Director of Nouvelle France Genetics and which is a plant breeding and technology consulting company. And he's also the Chief Business Officer at DELTAGee, which is a database decision making support company for plant breeders.

Previously, he worked in different roles at Syngenta and legacy companies, from horticultural crops to field crops, and local and global programs. He graduated; he did his Ph.D. here at NC State. So welcome back, Michel, virtually.

He grew up in western France. And one of the things that you may want to know about Michel, he's an aficionado of one of the somehow not well-known cars here in the U.S., the Citroen 2CV and the relatives of it. But it's great to talk about cars with -- that type of cars with Michel.

Michel, thank you so much for accepting the invitation for talking to us, and we look forward to your presentation. I'm going to stop sharing so you can start sharing your presentation. >> Hello. Are you seeing my presentation? >> Not yet, but -- >> Not yet. Let me share that screen.

>> Yep, it's good. >> There we go. It's coming.

>> Okay. Yeah. We can see. Good luck. >> I know.

Well, thank you, Carlos, for the introduction. It's actually nice to somehow be back at NC State. It's a place where I've had some of the best years of my life. It was quite an experience to come as a French student, international student to NC State, and spend a few years there and do a PhD.

So I will now jump into the presentation. Can I move things down? Yes. Also, I will talk about Technologies for All: Bringing New Crops to the Forefront. I'm actually very interested in small marginal crops and breeding for those crops.

I will first give you a very quick introduction about who I am and why I'm speaking here. So I've had about 30 years of experience in Plant Breeding Innovation. Starting with Masters in France at AgroParisTech, Ph.D. at NC State. And then number of jobs with Syngenta and Syngenta, Legacy companies. Moved into independent consulting role a few years back with Nouvelle France Genetics, that's based out of Minnesota, in the U.S..

And we really work on all crops and provide assistance from strategic development to specific projects, training. Everything that's really around breeding and really the interface between breeding and technologies, which is something I'm very passionate about and have tremendous experience in. And more recently established a company is called DELTAGee, which really mission is to provide some platforms for decision making at critical points in the plant breeding processes. So going beyond just that analysis and really understanding the processes and helping make a bit more informed database decisions.

And mixing, understanding of genetics, plant breeding, and mathematics and computation. I think it's actually a very interesting time to be involved in plant breeding. There's so many opportunities, so many new crops to be bred, and that's what I'm going to try to talk a little bit about today.

What is a new crop? I also talk about new trait potentially or, you know, an orphan crop. These are crops that haven't been bred much or at all. If you look at the diagram, you see that, you know, the Global R&D Spend on crops is focusing very much on two crops, maize, and soybeans. There's some investment other major field crops. On the non-field crops, tomato is the one that gets some level of investment, and then everything else shares, you know, the 10% of the total R&D Spend. Which means not much for anyone and some essentially get nothing.

So that recreates, you know, what some people call orphan crops. I'd rather call them, you know, new crops or opportunity crops. There are crops or traits also with, you know, very small volumes in terms of potential seed markets, like the traditional seed companies are often not very interested in working with those crops. And there are also crops with, you know, potentially with significant volumes, but low value in terms of potential seed markets and this is, you know, some of the crops that are high volumes in developing countries where the breeding is, you know, breeding investments or not at the level where there should be given the volume of those crops. So a few example of, you know, new crops or orphan crops, some there are used, you know, as food or food ingredients.

Many of them used for ingredients, and you know, some things like, you know, are high beta-glucan oats. There's, you know, red radish, something I've been working on recently that is used as food coloring. Some example, I'll just mention that little later biofortified maize. Stevia is also a very interesting crop that is, you know, food ingredients that hasn't received much attention in terms of breeding.

There are some crops are used for as pharmaceutical ingredients, you know, opium poppy. Crop protection ingredients where we're talking about biologicals, pyrethrum is one of them but there's more. And this is something that is definitely growing in terms of the interest for agriculture and the markets. And then industrial ingredients, for textiles, for, you know, other types of industries.

So, you know, flax, hemp, indigo as a dye. So there's a number of crops that have very clear applications and uses, but they're really not [inaudible] where investments have been minimal. When I talk about plant breeding, I like to bring the genetic gain equation, because this is really how progress has to be made in plant breeding. And that plant breeding, that genetic gain equation shows very clearly the levels of plant breeding, the levels of genetic gain.

What are the levels that have to be actioned to achieve genetic gain? And I think it's always very, very important whenever one does anything in plant breeding to think about, you know, how does that impact any of the levels of genetic gain equation? So those levels are selection intensity, selection accuracy, genetic variance, and the duration of a cycle. And when we talk -- when we think about, you know, new crops, crops that don't have much of history of breeding and limited investments, you know, we can really get, you know, what does that imply to be working on a new crop in terms of those levels of genetic gain? So if we think about, you know, selection intensity. It's being able to essentially select, you know, individuals from a larger pool. And, you know, the more intensity, the more selection pressure, the better, the higher genetic gain. So what that means, it means, when you're thinking about going into breeding a new crop, it means that you really need to have the minimum level of investment in terms of, you know, volumes of materials that you'll be looking at, to really be able to replace significant and sufficient selection intensity to results in genetic gain.

So that's something that's very important, you know, there needs to be a minimum investment. What that minimum investment is, I don't know. Specifically, it's a case-by-case analysis that needs to be done. But again, conceptually, there needs to be a minimum investment. And if you're below that minimum investment essentially, you might be just spinning your wheels in the air with no impact on genetic gain down the road. When we look at another level of genetic gain, selection accuracy, what does that mean? It means that the more accurate you're able to make selections, the more progress you will make.

And the more accurate means, you know, that means essentially, the relationship between what you see and what really happens, you know, is what you see really the genetic basis of the traits you're selecting for, or is it not? So two elements to think of when, you know, moving into breeding of a new crop about selection accuracy, it's going to be easier to make progress for simple traits and for complex ones, because simple traits are, you know, that's why they're called, simple traits, and that's why complex traits are called complex. Ones, some are simple, also are complex, and the simpler traits are generally simpler to measure and simpler to select than the complex ones. So you know, focusing on simple traits or, potentially, you know, simple components of complex traits.

And when you're looking and thinking about new crops that really haven't been bred very much, essentially, they have either a very short or almost an existing breeding history. You know, they're likely to contain large effects, either favorable or deleterious alleles. And selection for those favorable alleles or against those deleterious alleles will be very effective.

And so those are simple components of maybe, you know, moderately complex traits. So again, an ideal one going into new crops, maybe trying to, you know, how much progress can you make by working with simple traits, if that's something that can be done, then you're very likely to achieve a significant genetic gain. And also, second point from the selection, accuracy level of genetic gain. It's the fact that high-quality phenotyping data will result in significant gains. So this is important for anyone who does breeding. It's very important when you go into a new breeding program.

Make sure you regenerate high-quality phenotypic data. This is really a prerequisite to being successful. And there are tools today, actually, they're available. And I will mention that later to really help generate very high-quality phenotypic data.

Next, level genetic variance. You know, it goes without saying, but it goes better with saying. It is mandatory to have access to some sufficient genetic diversity. And when you think about genetic diversity, I like to think about genetic diversity in two dimensions.

I like to think about genetic diversity in the allelic dimension. But I also like to think about genetic diversity, the recombination dimension. So the allelic dimension means just getting access to material.

And recombination, that recombination dimension means generating breeding populations that allow you to sample enough recombination. So, you know, if you're working, and that kind of gets back to the first point on selection intensity, which is, you know, you need a minimum investment in terms of size, of volume of material you will be looking at. And, you know, you need to look at enough allelic diversity and enough new recommendations of those alleles that you have in your program to be able to achieve progress. So something very important to keep in mind.

And then the last level, years per cycle. I would say, you know, when you're moving into a new crop that hasn't been bred very much, I think what you're most interested in is achieving gain. And I would say that speed is nice to have, but it's probably not your highest priority. You know, if you don't get the numerator of that equation, be positive no matter what you do on the denominator. It's not going to have much impact on delta G, okay, on the rate of change.

So speed is nice to have, but it should not be at the expense of gain per cycle, at least at the beginning of an essentially new crop breeding endeavor. Okay. So before launching breeding for new crops, what should you check? You should check your ability to access germplasm.

You know, there's IP around germplasm. There's the convention on biological diversity. There's Nagoya Protocol. Those are important things to think of. If you can't access germplasm, you won't be able to have genetic diversity, and that genetic gain equation is going to all go down to zero. You need to be able to check the suitability of -- you know.

You should check the suitability of existing germplasm in varieties for your product objective, you know, trait performance in target environments. You know, before again, getting into breeding, if there's something out there that meets your requirements, then there's no need to go into breed. So that's something that really needs to be checked. So you're just putting, getting, whatever germplasm you can get your hands on, evaluate it, measure the traits you're interested in and divide the ones you're interested in and see how that works. Don't just go into breeding without that check, you know, it's really the low-hanging fruit, you know.

But check it out, and if there's a low-hanging fruit, just pick it up. You also want to check the availability of, you know, non-genetic alternatives, agricultural practices, processing, et cetera. Again, I'm not trying to deter you from getting into plant breeding. But if you don't have to, well, you know, then don't make it complex.

If it can be simple, you know, so check alternatives. And also, the last thing would be, you know, to check your ability to measure your target trait. If you can't measure a trait, you won't be able to make progress on that trait. So this is something that's very important, and sometimes it's something that may need to be worked out before actually embarking into the breeding or at least as you create, you know, the diversity material. So this is four points.

Very important to check before going into breeding. If those are all checked and green, then you're all ready to go into setting up a breeding program for your new crop. This graph comes from a paper that actually I wrote with Jean-Marcel Ribaut from the Integrate Breeding Platform a few years back about new crop breeding strategies. And what I'm trying to illustrate here is the breeding cycle that starts from, you know, non-elite germplasm making parents selections, developing breeding materials, segregating populations, doing simple trait selection, complex trait selection, developing elite material that gets developed into, you know, marketable cultivars, and that elite material also gets essentially recycled as elite germplasm into, you know, generating more breeding material and so on.

And then once that's been started, you know, after a while, you can essentially have a cycle that feeds on its own developments of elite germplasm and also bringing in non-elite germplasm. What I'm trying to illustrate in this slide is the different types of information that really can help, you know, develop and implement, put in place an efficient breeding program for a new crop. And some of those have to do with phenotype, phenotypic information.

Some have to do with understanding pedigree and pedigree relationship. And some have to do with using genotypic information. And you should just look at this, you see, there's a lot of green in there and what that means is that there's a lot that you can do in terms of developing an effective breeding program without accessing, you know, genotypic genomic information. There's a lot you can do with good understanding of traits, good measurement of traits, and good trait-based selection. So you know, when you design breeding material, breeding populations, it's very interesting to look at trait complementary between the parents that go into those breeding populations. And that's going to tell you a lot about if you understand if you know the parents that go into those breeding populations and understand what you cross with what to develop those breeding populations.

You could get a good understanding of what you should expect in the progeny. And this is, you know, how those breeding starts, those breed crosses are being made is really key to success down the road. Trait phenotyping.

I mentioned it earlier. When I talked about trait accuracy as the level of genetic gain. Trait phenotyping is critical to success.

And trait phenotyping, I'll touch upon trait phenotyping later on. But it's important for simple trait selection. And it's important for complex trait selection. It's important for, you know, development of essential elite material into marketable cultivars.

It's important to characterize the germplasm and manage germplasm and can mix elite germplasm with non-elite germplasm to make decisions about breeding starts and creation of new breeding populations. Understanding pedigrees is also something very important, and keeping track of pedigrees, understanding where things come from. And when we talk about pedigrees, I cannot help but talking about germplasm pool management. You may be contemplating a crop where you want to, you know, develop hybrid varieties, and there are already some basics around, you know, how to efficiently breed for hybrid products that have to do with germplasm pool management. And this has a lot to do with understanding that, you know, the pedigree relationships between materials.

And so, that's important for germplasm pool management. That's also important when you set up breeding populations, understanding, you know, the pedigree relationship. And essentially, managing your portfolio of breeding population of breed starts. What percentage of breed start do I want to be, you know, nail in terms of variation, you know, maybe closely related materials that are being crossed to another out of which I don't expect necessarily tremendous gains, but of which I expect some small incremental gains that could be very valuable. What percentage of my breeding starts, my breeding populations do I want to be, you know, very wide breeding starts where, you know, out of which I expect a lot of variation in the progeny and, you know, probably high potential projects, high potential breeding projects, but also high risk as well.

So you know, this is also, you know, understanding pedigree relationships between material is about, you know, handling of diversity, and essentially risk management. And risk can be managed, and it's very important to manage that risk and, you know, define essentially the risk level that you're willing to take. And then, of course, there's everything around genomic information, genotypic information. That's very useful for, you know, handling diversity and pedigree verification. Pedigree verification, again, is something that often is not, doesn't come to mind.

It's just, you know, when you make an F1, to start a breeding population, and you've given very careful thought to, you know, making that specific breeding population, and you want to be sure that the F1 you have is actually a cross between the two materials you intended to cross. And you know, things can happen, contaminations, errors. And before you put a lot of resources on phenotyping, the progeny of that cross and maybe genotyping the progeny of that cross, well, you know, a little bit of quality control there to make sure that that cross is where it's supposed to be, can go a long way.

Genotypic information can be useful for, you know, for germplasm management. Can be used for marker-assisted trait selection, marker-assisted trait introgression for simple traits. And you may notice here that I didn't put genomic selection on that graph.

And really reason I didn't put genomic selection, which is an approach that's using genotypic information, markers for selections. Complex traits is that genomic selection is really not something that is easy to put in place when you're starting breeding very much from scratch for a new crop. It takes some understanding of trait.

It takes some amount of phenotypic data. It takes having specific germplasm to define training set to really be implemented. And it is definitely a very interesting approach in plant breeding.

I just didn't put it there because this is not something that I would recommend to jump into when you're starting the breeding of a new crop or are doing breeding for a crop with, you know, limited amount of resources. Okay. So it's not there, and happy to discuss that with anyone who would want to later on. Talking now about, you know, phenotyping, what things you may want to think about when you're looking to phenotyping and, you know, for a new crop, an orphan crop with limited resources. There are today very effective at what I call resource-conscious experimental designs.

An experimental design is a key element to getting high-quality phenotypic data. That again will allow to act on that selection accuracy level of the genetic gain equation. Designs that allow to control, you know, micro-environmental variation.

And you know, some of those designs include. You know, incomplete block designs, lattice, alpha designs, and also some of those -- some partially replicated designs, augmented design, p-rep design. And those are really interested because [inaudible] partially replicated designs are very interested, because as their name indicates they include partial replications, and they're very resource conscious. And your resources are typically very limited for, you know, new crops, orphan crops, and the like. Quality phenotyping is also a tool that's available for pretty much any crop today.

And I'd like to point, you know, a lot of work that's being done, you know, with image capture and in image analysis. Those are technologies, the technologies themselves, you know, the data capture technologies are very inexpensive. And really, you know, the analysis that needs to be done, the models that need to be developed that involve artificial intelligence also. Are also things that are within reach for some small crops. And I think it's something that's very important to think about as you move into a new crop.

What can I gain from maybe getting involved with, you know, image capture and analysis for some specific traits? Does that really give me such an advantage in terms of phenotypic data quality, that again, it will allow me to action that selection, accuracy level of the genetic gain equation very effectively? And also, you know, in terms of services, there's a number of, you know, CROs out there, that would be more than happy to conduct trials for you. They will do phenotyping for you, you know. You may want to do some phenotyping in some region where you don't have any physical presence. You just can't get there. And essentially, you know, with those organizations, you have access to turn in locations, pretty much anywhere in the world, and probably in areas that, you know, and environments that are very interesting to you. And so this is again, this is something that is very important because it allows you to generate data that probably you could not generate with a small in-house organization.

It allows you to generate the data essentially, you know, without the fixed cost of setting up, you know, breeding stations or whatever. So, I think it's something that's very important too. And again, that is so much more available today than it was 20 years ago. If we look at genotyping for new crops, and again, this is something that, gosh, it's evolved so much and so fast and really faster than any of us would have thought 20 years ago. And so today, really, the genotyping platforms, genotypic have been democratized so much, and they're really accessible, you know.

I was actually just reading something before the call about something I saw on LinkedIn from the CGIAR Excellence in Breeding Platform and a new platform. They're opening with low-density genotyping. They had a high throughput, high-density genotyping service available. Now, they have a low density, which is actually very appropriate for breeding applications and that they're making available to lots of people. And you know, through some agreements, they've worked out with service providers.

And so, you know, again, this is really part of, you know, those tools are being available to more and more people at a lower cost and very easily available. So there are today, you know, high-quality, repeatable, low-cost SNP genotyping platforms available. I'm thinking about, you know, amplicon-based sequencing methods.

You can today generate SNP genotypes without a reference genome. So you don't have to have a genome sequence for your crop to be able to do your markers, breeding for the crop. And again, there's numerous service providers. And some offers, you know, through groups like, you know, the CGIAR are very interesting. And then, again, that are really democratizing the access to genotypic data for plant breeders, wherever they are. And that's particularly interesting for people working on new crops and, you know, low-resourced crops.

If you're thinking about, you know, discovery and sequencing and, you know, there's what I call less expensive than expected genome sequencing. Again 20 years ago, nobody would have thought that genome sequencing would be so cheap as it is today. And cheap is maybe not the right word. But it was just unimaginable 20 years ago, you know.

And you can do anything, you know, from skim sequencing, to long-read sequencing. You can mix things based -- depending on what your project. You can target sequence-specific regions in the genome. So that's really helpful to develop, you know, diagnostic markers to follow simple traits. And again, here, there are numerous service providers.

So all those things can be done without having to go through the expense of establishing, you know, infrastructure. And so, this is very interesting, you know, definitely to get started and potentially even, you know, long term. So the world is open. And you know, I'm not mentioning any technology or any provider, in particular, there's just lots of things, you know. But those tools are available, very much available today. And they'll be a lot more available, you know, two years from now, or five years from now, for sure.

So something that is very important also, you know, when you're talking about plant breeding. There's a lot of data that is generated. And it's really important to -- just showing here, one that I think is really interesting and stands out from -- because of where it came from.

This is something that was actually initiated within the CGIAR, as part of the programs they had that were inner center and very open programs that were called the challenge programs. And so it's called the Integrated Breeding Platform. And they have a tool, that's called the BMS Pro, Breeding Management System Pro. That was developed originally to provide some database tools to bring programs in developing countries that work on very, very limited resources. And it's been extended, and it's now, you know, their tools are being offered also to private breeding companies.

But I think it's again, to me this tool, and I've been helping them a little bit, here and there. But you know, I have no commercial interest in what they do. But I think it's a very interesting example of an effort into democratize the access to tools and platforms for the greater good.

And in a similar mindset, I would say, there are on the genotypic and genomic data side of things, there are repositories, and there are numerous models, there are numerous databases that have been developed. I'm thinking, in particular, about something that started as cassava base, and that has grown into yam base, and to sweet potato base, into a number of databases for different crops. And there's an effort that's called AgBioData, and the website is agbiodata.org. That is essentially a consortium of databases, genotypic and genomic databases, and they are developing essentially best practices and data standards. And it's very interesting resource to look at, you know, to organize genotypic and genomic data for your crop of choice.

Looking now into data analysis and decision-making. Tools available. This is out of a paper from Rajeev Varshney and collaborators of ICRISAT from a few years back. They looked at a number of tools available, publicly available. And as you see here, there's a lot of tools available to do data analysis.

And there are a few tools available for decision-making. But a lot fewer tools for decision making. But again here, this is something where you'll find what you need, for your new crop, and you won't have to develop tools specific for you. So again, you know, this is something you don't have to worry about.

You know, so for data analysis, really numerous tools available. I guess one caveat that they've mentioned that in the paper is that those are generally standalone tools, not interconnected. So there's, you know, it makes moving data from one tool to the next to essentially process analysis longer. A whole chain of data analysis and decision making a little complex. For decision-making support, there are few tools available, few platforms. Something that I think is very relevant to new crops and working on simple traits.

As I mentioned earlier, something that I think where there's enough genetic gain that can be expected for simple trait crops is markers-assisted trait introgression. And just, you know, mentioning here, two tools, Flapjack, which stood up by The James Hutton Institute and CERTAIN-TI, which developed by DELTAGee, a company that I'm involved in. And those are, you know, one of these tools is actually freely available. The other one is not freely available. You know, they provide different approaches to marker-assisted trait introgression.

But again, the message here is that, you know, you really don't have to, you know, develop your own tools to be able to do something, at least there are platforms available out there to help you make this so that you can concentrate on making the decisions and making the decisions knowing what your breeding objectives and your breeding strategy is. And that takes me too -- brings me to this next slide about objective definition. And I think this is something that is absolutely key. It's not technical.

But I think, it's very important when you're, you know, moving into a new crop. You need to have clear quantitative and simple objectives. This is really a prerequisite to a successful start. If you don't know where you're trying to go, it's just going to be hard to get there.

And I think, your objectives need to be simple to be able to see progress and success coming, you know, fairly soon. And I think it's very important when you're, you know, moving into a new crop or trying to revive some breeding on the crop that, you know, hasn't gotten much attention. Because if you just don't have the, you know, clear objectives, if you don't really know where you're going, you may just, you know, find that, you know, breeding really doesn't take you anywhere. And essentially, you know, throw the baby with the water of birth. And you know, you don't want to do that because, you know, breeding will deliver what you need if it's done well and if you're persistent enough.

But, you know, if your objectives are the wrong objectives, then you know, the impact is just not going to be attainable. So I think it's just something that's very important to pay attention to, especially when you're starting with something new, you know, you could go all kinds of directions. And having again, those clear objectives allows to focus on the few specific things and going after the low hanging fruits first, and that's really what's going to help build confidence in the process and help also, you know, bring along people to tackle more complex things down the road. And the next point I want to mention is about essentially organizing the breeding in stages. And that has very much to do with clear objectives because those objectives, you know, translate into essentially, you know, stage promotion criteria.

And this is very important. It's very important to have some level of organization of breeding into stages. Even if, you know, you have a small crop and that you just have one breeding program. And because it allows you to -- those milestones and those stages are essentially -- What should I say? Thresholds, you know, levels, product performance levels that, you know, that you don't fall back once you've reached a certain stage, you don't fall back below that. And it's really very important to know that, you know, the material that's more advanced in this stage has more confirmed performance levels than material that is [inaudible].

And that realize also, you know, people who support you financially in your endeavors, people who are waiting eagerly for you to turn, you know, some products to them or ingredients, whatever to understand what they need to look at. And how they should, you know, again view performance. So I think it's something that's very important to do. It also has some implication on experimental design. You know you don't run a program with the same experimental design in the early stages when you're sorting through lots of genetic diversity as is in the late stages. So it really allows you to understand, you know, what kind of experimental design should be put in place for different stages.

So I think it's, again, something that's very important to have to really see what, you know, the value of the good stuff that comes out of the breeding programs. Okay. And I just wanted to show as I'm concluding a few examples of actually private initiatives that have been launched recently. And I know of just a few examples things that I find remarkable of people essentially putting private funds into, you know, new breeding initiatives.

And this is a company. It's called The Plant Pathways Company. They're working on Stevia. You know, stevia is a natural sweetener, 300 times the sweetening power of sugar, this is absolutely non-caloric because our body cannot metabolize it. And they are, you know, looking at adapting, the plant to new growing conditions, you know, more so in the Northern Hemisphere and well, you know, in the U.S., in North America, in

Europe from current cultivation growing area being mostly in, you know, South America and China. Looking at increasing steviol glycoside yields. And you know, they're working with modern tools, molecular markers, understanding of biochemical pathways, genome sequence. And the one thing that's very interesting about this and that relates to this seminar series is that one of the individual in that endeavor, in that company is actually Professor [inaudible], professor at NC State University. The next project, the next endeavor I just want to mention is a company is called Stony Creek Colors.

They're out of Tennessee, and they've decided to embark into breeding of Indigofera tinctoria to do up a natural dye for textiles. So they're interested in high dye yield and they're interested in agronomic performance. And they are using genome sequence, molecular markers. And actually, if you go on their website, they're looking for Director of Plant Breeding. And so, you know, those are things that I think that again, that I see as very exciting things and, you know, again, private endeavors, you know, jumping into the breeding of indigo, very interesting. And the other example I want to show is an example, it's a company, it's called Semilla Nueva.

That's out of Guatemala, and it's a non-for-profit company, and they're working on corn. And you're going to tell me why corn. That's not an orphan crop.

But I would say they are working on an orphan trait. They're working in highly nutritious corn with especially high zinc content because corn is a staple food for a lot of the population. So you know, they're trying to combine high zinc content, with high yield, with white grain color. And really, you know, the tools that are available -- I mean and the resources that are available to do that are very, very limited because providing corn seed to poor farmers in Guatemala is not a place where a lot of private data go. And so, you know, they've decided to set up a company. They're getting most of their germplasm out of [inaudible].

And again, so they're working with the sequence of the genome, molecular markers, QTLs. But you know, with very limited means and a trait that is complex to measure. And so again, you know, very much, you know, their crop is really what I would consider a new crop, or, you know, really a niche kind of crop because it's an orphan trait within a nature crop.

So you know, those are three examples of people who've really jumped, essentially jumped into the breeding game, you know, for, you know, new crops, niche crops, niche traits and have set up, you know, private endeavors around that. So, you know, new crop breeding, is it a go? Is it a no-go? I'd say it's clearly a go. There are effective and cost-efficient methods to all services that are available to enable, you know, high-efficiency modern breeding to be conducted.

Some may be high-level recommendations. And you know, you could call that as advice. I think you'll keep it as simple as possible. Things tend to get complex just by drift.

And so, trying to keep things simple is important for success. You know, aim at genetically easy gains first and don't use technology just for the sake of technology. And I think about, you know, when you're about to make a decision, think about the genetic gain equation. How does that decision allow you to act on the levers of genetic gain? And if it doesn't, just take data as something that's interesting that's not for you, period.

Make sure your objectives are pertinent that there's a need for breeding and there's value with respect to the product you're targeting. And then be ready for an exciting ride, you know, that's going to be full of obstacles and successes. [inaudible]. >> Thank you, Michel, for that very comprehensive and interesting presentation. Again, please post your questions in the Q and A. We already have a question for you, Michel.

Right at the beginning, where you presented the funding from the different crops, there's a question about why tomatoes figure is so high? >> Well, you know, I think, it's really the market, the seed market for tomato is a very high-value market. And so, all the major vegetable seed companies are reinvesting in tomato. So it's really, yeah, I think, it's the value of the market. >> Okay.

All right. Again, post your questions in the Q and A. What is the role of genomic prediction, you know, for crop breeding? >> So that's genomic selection, genomic prediction, you know. It is a very interesting approach. Again, I think developing those prediction equations is something that takes some effort. It takes some understanding of the, you know, genetic diversity that you're working with.

It takes a significant amount of phenotypic data collected on, you know, on the training panel, it takes some understanding of the genetic -- again, of the germplasm that you're working with to decide which materials should go into a training panel. And so it is something that I think, you know, should eventually be mobilized as a method, you know, for new crops, orphan crops. I think, in my opinion, it is not the most urgent thing to do when you're launching a breeding program in a new crop, just because of the, you know, the complexity of setting it up. >> So next question is, what do you see as number one limiting factor for a new startup company and how you go around it? >> I would say today probably the ability to collect enough phenotypic data of high enough quality. So I'd say field resources are probably the most limiting factor. >> That's interesting.

Okay. Any other question? I do have a question. This is the first time I pose a question myself to panelists.

So Michel, I wanted to ask why is that, and I imagine the answer. But why didn't you mention gene editing [inaudible]? >> Why didn't I mention gene editing? Well, I didn't have time to talk about everything. >> Okay. >> Gene editing is, again, it's a very powerful approach. You know, I'd say there's two limiting factors to gene editing.

You need to have a target to edit. So you need to have to identify some gene that has enough of an impact on the trait you're interested in to, you know, to be able to start doing something. And then, gene editing is also something that has a lot of regulatory strings attached to it, you know, and not necessarily a clear, you know, path to market in all geographies and potentially acceptance. And so, you know, again, this is probably not the first thing I would aim at when setting up a breeding program for new crop.

>> Okay. >> But you know, they're actually some very -- you know, Europe, which is very close to those new technologies, is actually relaunching some evaluations of those new technologies. And so there might be, you know, there might be the end to the dark technology adverse tunnel in Europe. >> Yeah. And I've been following the work that Cornell University has been doing for crops and gene editing.

And it seems that they're basically resulting in the relationship across species to identify genes. I mean, things that are evolving, as you were saying genotyping 20 years ago, was not feasible on the cost or the at level you can do it now. And I think gene editing, probably 20 years from now, will be quite different. >> Yeah.

You know, when you go into gene editing, I mean, you have to understand also you still need to have the ability to essentially regenerate plants. You have to have the ability to transform plants, and, you know, it's a whole different world from breeding. >> Okay. A question here very quickly. Is there a place where they can find contract research organizations like a website or a list of contract referrals? >> A list of research organizations. Well, I think probably on SeedQuest, there's probably a list of contract research organizations.

>> Okay. If you have, we can share with the participants right here, okay? >> Yep. >> There is another question here.

The trait is the first hurdle, but seed production that seems also to be another hurdle. What do you suggest in terms of planning for this need and the resources available, seed systems? >> Yeah. So seed production is definitely very important because, you know, once you have some varieties, you need to be able to produce them and disseminate that seed.

You know, I would say that goes -- you know, seed production traits can be traits that one activity breeds for if that is important. You know, when you think about seed production, you know, not all varieties of all crops have to be F1 hybrids, you know, it doesn't have to be that way. You know, you can have, you know, open pollinations, and you can achieve genetic gain with open pollinations. You can have in-breed lines.

You can have, you know -- When I say open pollinations, I mean, essentially, you know, synthetic varieties that can be made with few parents. So you know, I think the choice of varietal type is, you know, if there's a choice that can be had, I think it's something that -- it's a decision that's important to make at, you know, essentially at the onset of setting up a breeding program. Because that's going to determine to a large extent, you know, what your breed for. >> There's a comment from Craig, which links to the next question. And Craig says that for him, the most limiting factor is the financing of the enterprise. And then the question that follows related to that is, do you see venture capitalists entering to financing new breeding programs, or it's just seed companies or food producers that are seeing interest in these new crops? >> Actually, I don't think seed companies are interested in new crops.

I think because -- I mean, some of those crops, I mean, you know, they really don't have a seed market, you know what I mean? And so, I mean, definitely, I think venture capitalists could be interested. Yeah, and also, I think, you know, there are examples out there of essentially when you're talking about ingredients, for example, all of the, you know, companies that, you know, those ingredient companies, you know, interested in investing in breeding. I mean, you know, there are examples.

I mean, there are, you know, Nestle has had some breeding programs in coffee and cocoa. PepsiCo, I mean, a long time ago. I think, you know, Lay's before actually Lay's was acquired by PepsiCo, I think in the '70s. They decided that they weren't getting the potato varieties, they needed to make good quality chips, and they launched their own breeding endeavors, and that program is still going on in Wisconsin. So yeah, I think, you know, I think those are not -- most of those, you know, small crops are not large seed markets. And so I think the finance to get those started probably will not come from seed companies unless, you know, they have venture capital branches.

>> Yeah. Another question here is the connection between the field and lab work. And the question is if a breeding company is most experienced in lab, do you suggest that they get consultation on designing and implementing field trials? >> Yeah.

I think, you know, there are a lot of people out there who are very skilled, you know, in the lab side of things, in the field side of things and getting advice from skilled people is definitely a good idea, you know. I'm not a big proponent of reinventing the wheel multiple times, and sometimes, you know, through your own experience and, you know, you need to get your own failures to make progress. But I think, again, you know, there are plenty of people out there available and to really help fill whatever weakness, you know, any organization, you know, recognize they have. It's hard to be good at everything, but it's not hard to get help.

>> Okay. Michel, thank you so much for your time. I'm sorry.

There's a few questions that have not been answered. We'll try to send them to Michel and have him respond. >> I will. >> Yes.

The recordings are going to be available, and we'll share that. Again, recognition for the music early on today is High Life by a group from Burkina Faso, Mini Vandals. And please share photos so we can enlarge our photo library. And thanks to Brandon, Janine, and Anthony for their help. And next week will be the last seminar of this first series by Sarah McNeil, from Ventria Bioscience, talking about, Quality by design and breeding for high-value products.

Which I think it connects kind of good with today's seminar. Thank you so much, Michel. And again, let's stay in touch and look forward to talking to you again. >> Thank you for allowing me to talk about this. >> Thank you.

Thanks to everybody. I look forward to having you again next week. Okay. Thank you. >> Bye now. >> Bye.


2022-06-18 12:11

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