Sustainable Solutions: Animal Breeding Genetics with Dr. Michael Lohuis

In this episode, UF Agricultural Education and Communication doctoral student Jenn Morgenthal interviewed Dr. Michael Lohuis about his experience as the Vice President of Research and Innovation with Semex Alliance and his research in animal breeding genetics. Listen to learn more about sustainable genetics practices in the animal agriculture industry. 

Transcript

Jenn Morgenthal: Hello everyone and welcome to Sustainable Solutions from Guelph to Gainesville, a podcast brought to you by the Streaming Science Project. Streaming Science is a student driven program committed to connecting you with leading experts, exploring how science shapes our world, and how we can build a more sustainable future together.

Throughout this podcast series, we're not only delving into topics of sustainable agriculture, natural resources, and science communication and literacy, but we're also taking an international perspective as we connect with alumni and experts from the University of Guelph, Ontario Agricultural College in Ontario, Canada.

I'm Jen Morgenthal, a graduate student in the Agricultural Education and Communication Department at the University of Florida, and I'll be your host for this episode. Today, we'll be speaking with Dr. Michael Lohuis about his experience as the Vice President of Research and Innovation with CMEX Alliance and his research in animal breeding.

During our conversation, we'll explore Dr. Lohuis journey, his exciting work in advancing sustainable practices, and his insights into how we can all continue to pursue a more sustainable future in agriculture. natural resources, and broader science. So without further ado, let's dive into our conversation with Dr.

Lohuis and explore the sustainable solutions he's promoting, bridging the gap from Guelph to Gainesville. Hi, Dr. Lohuis. I'm so happy to have you here with us today, and I appreciate you giving of your time and expertise for this podcast. I'm going to go ahead and let you introduce yourself. 

Dr. Michael Lohuis: Nice to be with you, Jenn.

It's a real pleasure to talk about Science and agriculture, it's, it's really close to my heart. I am presently the Vice President of Research and Innovation at CMEX Alliance in Canada. We are a partnership of farmer co ops and we are destined to be the last farmer owned and directed animal breeding, or I should say dairy breeding organization in Canada or in North America, actually.

Jenn Morgenthal: That's a very unique thing. I definitely did not know that those existed. Obviously, co ops exist within agriculture all over the place, but this is very unique to me and learning about that. We're going to dive into some starter questions. So what picture forms in your mind when I ask what a scientist is? 

Dr. Michael Lohuis: I think most people think of someone in a lab coat.

You know, in my case, I'm a quantitative geneticist, so we do a lot of work on computers. So we rarely wear lab coats. We are curious, so maybe from the outside, you can see every kind of creature. A scientist, whether they're in a lab or behind a computer, or they're working in a barn or a field, you know, collecting data.

There's a lot of different ways scientists can look, but I think one thing is similar. It's really on the inside, it's curiosity. It's wanting to understand the world better and to answer some of those really interesting questions about science and in our case, agriculture. 

Jenn Morgenthal: I like when you say anybody, really anybody can look like a scientist because I think the generations that are coming in schools now don't necessarily make that connection within all the fields that exist.

I was raised by a scientist. He doesn't think he was a scientist, but my dad was an educator and very much so a science teacher. And that is one reason why I love science. His response was always, I don't know, let's see what will happen. Let's try it out. Always have that mindset with things. I think it's a cool way to look at the world like that.

So where are you from originally? Where do you live? 

Dr. Michael Lohuis: Well, I'm a dairy farm kid. I grew up on a family dairy farm about an hour west of here, near Woodstock, Ontario. And I now live in Guelph, which is It's the home of University of Guelph, which is one of the premier ag schools in North America. It's certainly probably the biggest ag university in Canada.

Our farm was large enough to raise a family, but I'm talking 40 milking cows, a hundred head, 200 acres, you know, not, not a big enterprise, but a fun place to grow up. 

Jenn Morgenthal: So when you started the university. What was your degree field that you picked to begin with? 

Dr. Michael Lohuis: Well, just because I was from a dairy farm, I picked animal science.

So that was where I started. I think in the second year, we had to choose a major. And so that was an obvious one for me And that's actually where I finished is in animal science. 

Jenn Morgenthal: Why did you decide to concentrate on genetics in that area versus going into production and taking over the family operation?

Dr. Michael Lohuis: Well, I guess it started on the farm. I really enjoyed understanding the breeding side of things. My dad was more interested in the crops. And so the breeding side naturally fell to me, but really when I got into university, some of the courses that really got me hooked on genetics, uh, were some of the basic genetic courses that, you know, it was more basic genetics across all species and animals.

But in the final year, there was an animal breeding course taught by Larry Schaefer, who was one of the premier geneticists. And I got hooked, it was just so interesting what you could do to improve the genetics of the population and the tools that he describes to remove all the noise and you're left with a genetic signal.

That was just so cool and actually drove me to apply for my first job, which was in the video industry. 

Jenn Morgenthal: Oh, very cool. I love when it's, it's also semi attached to an educator that brought you into that as well, because I think that that is when we're picking. It's, it's always interesting to see the educators, how they teach and open your eyes or minds to something that makes you really interested and engaged.

So it's very cool to hear about that. The professor that you had for sure. And I think a lot of times when Get into college. They feel like they have to have it figured out then. That's why I love asking that question because a lot of times the path between the beginning and the end isn't traditional.

Sometimes people change their minds and they take a course that makes them interested in a different area than they thought. So how has your passion for science in the field you're in developed over the 

Dr. Michael Lohuis: years? I never saw myself as a scientist that would be writing papers and, you know, diving into the literature and the publications.

I was always more interested in the application, and maybe it was because of my farm background or perhaps the first job I had working for For a farmer co op, I wanted to see science be applied and be useful to farmers. My research and my career has really been more focused towards applied science. And I guess there's been some basic science that is going to drive that, but how can we Take what we know and how, or this latest tool or this newest discovery, how is this, how could this be used in the field or on the farm?

You know, that was my driving passion. 

Jenn Morgenthal: I love, it's like the solution based science is what, that's what I really love. And I think one thing when I got in, back into my grad program, I realized just how many, I don't want to say problems because that kind of sounds negative, but how many challenges there are, how many barriers that exist in certain fields.

I definitely want to provide solutions. There's so many. Areas that you can focus on. And I want to give solutions in a lot of different areas. So I have to pin my focus down to one spot, but definitely I like the solution based science as well. Being able to apply that and help in the field that we're in.

Give me a quick summary of animal breeding. I know my ag teacher Taught us the Punnett square, big B, big B, big B, little B. And we talked about this on the other day, you always say hybrid vigor. But just describe animal breeding and the role it plays in agriculture and maybe just some examples of how we utilize it.

Dr. Michael Lohuis: You know, a lot of people start with an idea of genetics and breeding as the large A, small A, large B, small B, and component square. That's a really interesting start on how you approach breeding. Mendel's P experiments, for example, were really interesting to understand how genetics works. For some traits that are controlled by one gene.

However, what you quickly learn in animal breeding is that most traits are controlled by several genes, maybe hundreds, maybe even thousands of genes controlling a trait that's like milk production, meat production, you know, those are traits that are affected by so many metabolic pathways and so many genes that control those metabolic pathways.

So, animal breeding has become more of a quantitative field where it's really applied statistics. And that means that you take measurements of various traits that have an economic value or, you know, a welfare value for the animal, and you measure those traits with the purpose of improving them. But to do that, you need to remove all the noise around those traits.

So a lot of management, environment, just random error comes in. And you need to have good statistical tools. And one that we use in animal breeding is called Best Linear Unbiased Prediction. Well, what that does is it simultaneously removes all of the environmental effects, management effects, herd effects, regional, um, year, season effects.

All of those have a systematic effect on the phenotype, on the trait that you're trying to measure. So if you can remove those, what you're left with is It's the genetic signal and that's what breeders want to have so that they can make selection that's actually going to move the population in the direction you want to go.

Jenn Morgenthal: So I know genotype and phenotype, what is the difference 

Dr. Michael Lohuis: between those? Phenotype would be the trait that you actually measure, you know, if that is, let's say stature or if it's body weight or milk production, that would be the phenotype that you're actually measuring. The genotype would be. When you remove all of the management effects, environmental effects, random effects, I should say random error, what you're left with is the genetic signal, and that we would refer to as a quantitative geneticist.

We refer to that as the genotype, the underlying genetics. That is driving the animal's breeding value. However, you know, genotype, you know, if you're going to come up with a definition, it can also be referred to as specifically gene. So, if you have a capital A, small a, that would be a heterozygous gene.

Genotype or a specific gene. So that's another way to look at genotype. So 

Jenn Morgenthal: what are some ways that we have used animal breeding to our benefit or effectively in the industry? 

Dr. Michael Lohuis: Let's take dairy breeding, for example. Um, it's been a huge success story in terms of driving milk production. fat, protein yield, reducing somatic cell count, improving longevity.

There's a lot of functional traits, the shape of the udder, the shape of the feet and the legs, things that have helped animals be more productive, last longer. Now we're starting to get into more of the health and welfare traits, reducing incidence of disease. Improving reproductive performance. Now, sometimes there's unfavorable correlations.

You know, if you produce more and more milk, that what they're becoming is like metabolic athletes. So you're really pushing them to be as efficient as possible. So you consume large amounts of. And convert that into milk, fat, protein, and that requires a really good metabolism. But sometimes those things can have unfavorable consequences, for example, in reproduction.

So the more, you know, an animal produces milk, a lot of the energy reserves are diverted towards producing milk. And so they naturally are going to be less reproductive. It's going to take longer to get them bred and back in calf because they're diverting so many resources. to milk. That's something that we've been able to improve lately where reproductive performance was decreasing over time, but actually with the advent of genomic selection, we've been able to turn that around.

And that's one thing we should mention is that the field of animal breeding has really changed significantly since the mid to late 2000s because of genomic selection. Genomic selection, just for the benefit of your audience, is rather than just measuring the trait and assuming that the genetics is kind of like this black box, what we've been able to do is to break open that black box and break down the animal's genome into little parts.

So, if you have the ability to genotype an animal, we typically use 50, 000 markers. These are SNP markers called single nucleotide polymorphisms, and those are spaced broadly across the genome. And then you can break down the genes into little segments, 50, 000 segments, and you can, you know, look How much each segment contributes to each trait and that has made a huge difference to animal breeding.

Jenn Morgenthal: Oh, I think that just you mentioning the animal welfare, that side of things, I would think that would make people more comfortable that Increasing milk production at the cost of the animal. We're also paying attention to how it can affect other things. That's extremely important, which is also, again, responsible use or effective use.

And I think there's a lot of misconceptions about utilizing this tool within agriculture. What are some of the most important traits? that have been targeted through animal breeding. 

Dr. Michael Lohuis: I would say milk production and all of the component traits of milk, longevity, reproduction, confirmation of the animal, you know, reduced mastitis, things like that are important in dairy cow breeding with beef and swine, poultry.

You know, these can be Mostly meat and meat production traits, growth rate, efficiency. Chickens in particular, they've done a great job in selecting for feed efficiency, which means that you get more eggs or more, more meat per kilogram of feed that goes in. Same thing with slime, they've done a great job.

Beef, uh, also focuses quite a bit on feed efficiency or feed conversion, as they call it. So you can make tremendous, Uh, improvements on whatever you choose to focus on, as long as the trade is heritable and you have 

Jenn Morgenthal: good data. So how can genetics impact the future of agriculture, large scale and small scale day to day production for the industry?

Dr. Michael Lohuis: I think the biggest impacts that we don't really talk about with the public that much Is how efficient animals have become and for example, in dairy production, we used to have 3 to 4 million dairy cattle in Canada. Now we have less than a million, but we're producing more milk from 900, 000 cows than we were before when we had 3 million.

So we've actually made milk production much more efficient. More milk per animal means less feed per kilogram of milk, and less water, less land, less methane emissions, for example. These are all things that have been a byproduct of just greater efficiency. And on the meat animal species, it's It's the same idea, you can produce the same amount of meat with less resources.

So that animal gets to market rate much more quickly and therefore uses much fewer resources and emits a lot less methane. 

Jenn Morgenthal: I mean, that So you work within animal breeding and then plant breeding as well, and there's similarities and differences. Can you tell us some of those similarities and differences that you've seen within those two areas?

Dr. Michael Lohuis: From a genetic standpoint, it's all DNA, and DNA is very similar. Plants, animals, whatever. But the application of breeding is very different. In the plant breeding world, it's much bigger scale, first of all, and as you might imagine, when you put a plant in the field, it's at the mercy of the environment.

That plant has to survive and has to do well in a variety of weather and in a variety of soil conditions, and you need to look for plants that are going to do very well in different geographical locations, different environments. Different types of weather that you could expect in that particular year.

So they have to be drought tolerant, or they have to be able to stand up if there's too much rain, right? So there's more attention in plant breeding paid to how robust they are for a variety of conditions. Whereas in animal breeding, we tend to have Animals housed and protected more and so you can select for production in a specific environment and that's what's happened in pigs and chickens in particular is that you have a very efficient environment and the feed is perfected to have the best growth rates.

So you can really focus on that environment. And I guess the other big difference between plants and animals is the plant breeding industry was able to take advantage of genetic modification more easily and earlier than animal breeding. 

Jenn Morgenthal: It seems like it would be easier to do research and collect large quantities of data, maybe within plant breeding.

Dr. Michael Lohuis: I should have mentioned that. So when I first moved from animal breeding to plant breeding, I was just so impressed with how. They could plan out their experiments and they could, they could plan how, how many replicates they would have in different environments and in different years. And so you could, you could test a particular hybrid or inbred in multiple environments in multiple years, and you can see how that inbred or hybrid is going to do across those environments.

And it was very, um, structured and you knew exactly how many, how many inbreds you were going to test and in which years in. Animal breeding, you kind of take what you can get, and you try to sort it out later, and you use very sophisticated statistical models to separate the noise, uh, from the signal. And, um, so as a, you know, animal breeders tend to have more sophisticated statistical model because of that.

Whereas plant breeders, they have a structured environment, planned experiments, they can use simpler statistical models and still get a very good signal. 

Jenn Morgenthal: So that's what I was thinking, especially when you're talking about data collection in that realm. I just thought it definitely would look different from that too.

So let's move into your research area, very solution space, right? 

Dr. Michael Lohuis: One that we're working on lately is methane emission or methane efficiency is what we call it. It came about from a large study done at the University of Guelph. They were looking at feed efficiency and measuring how much feed was eaten by cows and to look at what the conversion into milk fat and protein were from that feed.

But in that experiment, they also said, well, okay, let's also look at methane emissions. Because that's something that we know is, has an impact on the environment. So, feed efficiency is great. If you have animals that eat less feed, there's going to be less impact on the environment. You don't have as much land required and you don't need as much fertilizer, right?

All of those things help the environment. But methane has a direct impact on climate change and warming of the atmosphere. The University of Guelph scientists also installed these machines called green feed machines where a cow would be eating at a trough and this would be done three times a day and there would be air from the trough would be sucked out and analyzed to understand what was the methane flux and CO2 flux of that animal while its head was in the trough and that helped us get some detailed phenotypes on methane emissions.

That was a great start, but the breakthrough came when some of the scientists said, well, this is a very expensive and time consuming phenotype to measure. That thing is very difficult. These machines are like 150, 000, and it requires a lot of, you know, labor to make sure that these cows get fed three times a day in this trough, and you can only do a certain number.

So, you couldn't really get the amount of data that was required to do anything with it. However, there is a fantastic, uh, group of researchers at the university that asked the question, Hey, I wonder if we can predict methane emissions from some other traits. And one that they focused on was using milk spectral data.

What that means is to shoot a beam of light through a milk sample and you look at the mid infrared spectral data that you can see. And so it shows. What are the components of that milk? 

Jenn Morgenthal: And why would they have used that tool to 

Jenn Morgenthal: begin with? 

Dr. Michael Lohuis: That was already being collected for the milk recording organizations to understand the components of milk already.

So this was something that had already been in use. It was a different phenotype. That we have lots of samples, right? So they thought, okay, we have the methane emissions from these experimental cows. Can we predict the methane from the milk sample? And lo and behold, they figured out that there was about a 70 percent phenotypic correlation between the milk sample, mid infrared data, and the actual method.

And that was a urethra moment, because now you have a very cheap Abundant phenotype that can be used to predict highly correlated one that's. Expensive and difficult and time consuming to measure. So now you've got a great proxy trait that you can use to predict the other thing.

Jenn Morgenthal: That's very cool. Having all that data there already, which I love when people that work in statistics, when they're working in very large data sets, get very excited.

Dr. Michael Lohuis: The reason they get so excited is because if you're a PhD student or a master's student, you spend 80 percent of your time trying to get your data together. And it's time consuming and it's a slog. Thank you. But if you have access to, uh, you know, a nicely curated data set. Oh, it's like winning the lottery.

You can go right to doing your analysis and drawing conclusions. It's just great. And that's where we found ourselves is that we had this great data set available. And where we got involved was realizing that, oh, okay, you've got this. Let's see if we can produce a genomic evaluation, and it just so happened that, you know, from those 60 million records, there was about 2 million animals that had those, those infrared spectral phenotypes.

And then of that, there was about 150 to 200, 000 animals that had genotypes already. So, in other words, they were genotyped. We had SNP data on, you know, a really good subset. And what this made, made available was a very large, very accurate reference population from which we could create. And so that's where we got involved together with LactaNet and the University of Guelph scientists to create a genetic or genomic evaluation for methane.

Right. 

Jenn Morgenthal: And that obviously in the world we live in right now, that's super important. So how can animal breeding further address challenges within methane, climate change? You know, when we're looking at those issues, 

Dr. Michael Lohuis: well, first thing we have to have the traits in a way that farmers are going to want to use it.

So nothing, when we first calibrated this traits, we found that it was unfavorably correlated with fat production, a fat yield in the milk. So this is where butter comes from our ice cream, and that was not good because that's, that's what farmers are paid for, for fat. And protein in milk. So we needed to recalibrate the trait so that it was independent of fat and protein.

And then it became a new trait called methane efficiency, which was neutral for the economic traits that farmers were interested in. And this allowed farmers to additionally put selection pressure on methane without negatively impacting the traits that they're paid for. So that was, that was an important next step.

Now, what we're working on is to Validate it to show that animals actually do use methane when you select for it. That just takes time and effort to create that validation data set. But that's really important if we want our milk processors and retailers to reward farmers for selecting for it. Because farmers, they get paid for milk.

They don't get paid for reducing methane. Unless somebody's willing to pay them, you know, farmers are logical human beings, right? And they're going to do what makes sense for them economically. So we provide that carrot or that incentive for farmers to select for reduced method. 

Jenn Morgenthal: So looking ahead, What technologies or future innovations are within animal breeding that can help shape the future of ag?

Because I know AI is a huge conversation right now, but are there other technologies and innovations that are coming? Well, 

Dr. Michael Lohuis: for sure, um, you know, gene editing is something that animal breeders are looking at. GMOs, which is a lot less exact. Then gene editing, gene editing, you can make specific alterations to specific parts of the genome, which wasn't possible in the original GMO technology.

That was a little bit more trial and error, which was possible in plants, but not so possible in animals. 

Dr. Michael Lohuis: So gene editing is providing opportunities for us to make specific alterations for specific traits. For example, could you make an animal more heat tolerant, or could you make an animal uh, hornless, or could you make an animal Less mastitis susceptible, what about disease tolerance?

Like, if you have animals that are in Africa or India, can you make them resistant to certain insects or certain diseases that are a real problem in those areas? So those are things that We don't do such a good job with from a quantitative standpoint, but if there are specific sort of qualitative traits that are controlled by a few genes, you can use gene editing to make some of those alterations more quickly and efficiently.

Jenn Morgenthal: So, I'm going to kind of wrap up in the science communication realm. How do you envision The outcomes from your research having broader implications for ag and natural resources. And how do you make sure that's communicated to those producers and growers and people that are using that? 

Dr. Michael Lohuis: Yeah, that's a great question.

We, first of all, you need to have a vision, right? Um, what it is we're trying to achieve. Uh, one of the big goals that we're seeing in agriculture is a concept called net zero. So if we can produce the products that society needs and have a zero carbon footprint. So, in other words, yes, we are going to emit some methane.

Yes, we are going to emit some CO2. But can we also capture carbon in the soil? Can we do things that are going to make the equation balance out? It's not easy to do, but a lot of different supply chains are saying, we are going to try to get to net zero by 2050. The refineries of Canada have made that commitment.

I believe the U. S. Dairy Farm Associations are also working in a similar direction. And this is really important to have a goal that the industry can focus on. And then use whatever technologies, whether it's breeding, whether it's methane inhibitors in the diet, if it's just, you know, making animals more productive and more efficient.

And the management systems that We house them, you know, can those be made more efficient? One of the things that, um, I think is going to be a big challenge is not so much in the developed world, but it's in the developing world where, you know, in Africa and India, there's so many more animals. There's more people and amount of feed, the quality of feed being used to feed those animals is quite poor.

Relative to the developed world. And so the efficiency of those systems is low. The amount of methane produced is high. So the per unit of milk produced, it's a lot more, you know, greenhouse gas intensive. Because we're, it's just much less efficient. And you know, sustainability at its core is really efficiency.

It's producing more using fewer resources. And that's the big challenge we face as a global agricultural endeavor, is to do, produce more with less. We have to feed people on the planet. It's just how can we do it with having the lowest possible footprint on the planet. 

Jenn Morgenthal: And I think in a communication standpoint, net zero, that's an easy thing to remember.

So what are your next steps in your research journey? Where, where are you headed next?

Dr. Michael Lohuis: I guess with the methane story, you know, our next goal is to validate so that we can demonstrate that methane is actually lowered, you know, when, when we breed for it. And that's something that's just going to take a little bit of time to get the data together to do that.

We also need to make sure that farmers get credit for it. So we need to develop the incentive systems to do that. That may not be You know, hard science, but it is important to make sure that the science gets used. We need to follow through with developing incentive schemes, making sure everybody is comfortable, you know, in the supply chain from start to finish.

You're comfortable with what we're doing. We're pulling in the same direction. Finders are being rewarded for doing the right thing. And that's going to translate through the whole supply chain all the way through the consumer. 

Jenn Morgenthal: So any last Key messages or takeaways that you'd like to leave the audience with?

Dr. Michael Lohuis: One of the key messages that we're trying to get across is that, um, animal breeding is a vital tool to have in the toolbox. It's by no means the only tool, right? There's a lot of other tools. I mentioned in the area of methane, you know, you have methane inhibitors in the diets, you have more efficient production systems, but uh, breeding is a very low cost, easy to apply.

Tool for farmers. One nice thing about genetic improvement is it's permanent. And it's cumulative across generations. So that each generation that you. You put selection pressure on a trait like this. It continues to build and accumulate over those generations. So by the time you get to 2050, you get a huge change at very little cost.

Jenn Morgenthal: I appreciate you giving the time and your area of knowledge to this. I think communicating this in a way that's understandable is very important. 

Dr. Michael Lohuis: Yeah, and you know, maybe one final thought is for people that are worried about climate change and all the impacts that agriculture is having on the planet.

I just say, don't lose hope. Because we already have a lot of the tools that we need to, to make substantial change, you know, to achieve net zero, we know how we can get there for the most part. And some things still need to be invented. But if you think about agriculture from a surface area, it's the largest endeavor on the planet, right?

And we can have a huge impact on animals, the soil. We just need to have the will and the money to do it. 

Jenn Morgenthal: That's all. And people like you that are creating these pathways for sure, that'll make huge changes hopefully before 2050. Again, I thank you for being here and thank you for taking the time to do the podcast and spread a little knowledge in this area.

Dr. Michael Lohuis: You bet.

Thank you so much for listening to the Sustainable Solutions from Wealth to Gainesville series on the Streaming Science Podcast. Make sure to check out our website and social media for more of our work. If you enjoyed this episode, we encourage you to tune in to other episodes in our series and to visit the University of Guelph OAC webpages and social media for more info.

Once again, I'm your host, Jenn Morgenthal. Thank you so much for listening today. For more information about this episode, visit the links in our show notes.