American Scientist

As the codirector of the Ecological Genomics Institute at Kansas State University, plant ecologist Loretta Johnson seeks to understand the genetic mechanisms that underlie how organisms adapt to their environments. She applies functional genomics techniques to characterize genes with both ecological and evolutionary relevance. Her research focuses on a prairie grass species that varies greatly in appearance depending on whether it’s in an area of low or high rainfall. When she received a Grants in Aid of Research (GIAR) award, she recalls that it was her first grant, and it kicked off her career with successful funding: “As a beginning graduate student, I had never applied for any grant. I didn’t know how to do it. Then I got a GIAR and I realized I could really do this. As a graduate student, it has a huge impact on confidence. It might be a small grant, but it gives you a track record so that then you can go on and get larger grants, and more of them. It can have an impact, throughout someone’s lifetime, that is way more than just the grant amount, both monetarily and professionally.” Johnson spoke about her career path from traditional ecology to ecological genomics with American Scientist editor in chief Fenella Saunders. This interview has been edited for length and clarity.

How did you get into the field of research that you’re in now?

I had a very different trajectory. I started out in a traditional ecology field—in particular, a narrow part of ecology called ecosystem ecology. I continued that work until about 2005. Then with all of the genetic and genome sequences and the tools that were becoming available, I thought, “Wouldn’t it be great to combine ecology and genomics?” That’s what I’ve been doing for the past 15 years. I use genomic tools to help understand how plants respond to the environment, and how they might respond to changes in the environment.

Why did you focus on the prairie grass species known as big bluestem, Andropogon gerardii?

Ecologically, big bluestem is very important. It’s the dominant grass of the prairies and can make up 70 percent of the biomass. It really controls the whole structure and function of the prairie, and it has effects throughout the ecosystem and communities. Then it’s also a dominant grass for forage for cattle, and grazing cattle is a big deal here in the Great Plains. It’s huge in terms of the economic impact; something like $8 billion a year is generated from cattle sales. Many of these cattle are grazed on tallgrass prairie before they go to feedlots. Also, bluestem is widely used in restoration. We have a program called the Conservation Reserve Program, which is a nationwide program to take marginal lands out of agricultural production and to restore it back to grassland. We have about 2 million acres [8,100 square kilometers] in the program here in Kansas. What we want to know is, What are the plants and ecotypes of big bluestem that are best suited for restoration? If we want to anticipate a warmer and a drier climate in the future, what would the best ecotype be?

Does this plant species already show that type of adaptive behavior?

It does show very strong ecotypic variation. If you look at a wet ecotype and a dry ecotype side by side, they’re distinct genetically and phenotypically. What we’re studying, then, is whether we should take this dry ecotype and plant it farther to the east as the prairie becomes warmer and drier.

What does the term ecotype mean?

It’s a genetically differentiated form of the same species. They can still interbreed, but they’re genetically distinct. Like different types of dogs or cats or tomatoes, right? They all look a little different, but they can still interbreed. This is the plant version of that.

An ecotype is more genetically determined than a phenotype, but there are different phenotypes of big bluestem too. There is some element of plasticity. But in the case of our wet and dry ecotypes that we’ve been studying for 10 years now, they’re really quite distinct in terms of the phenotype and genotype. That has been shaped by the very strong rainfall gradient that we have here. That’s why it’s so interesting to study it in these grasslands. We have 500 millimeters of precipitation in western Kansas, and then 1,200 in Illinois. There’s a huge range of precipitation. That rainfall regime has been in place since the last glaciation, about 10,000 years ago. There has been plenty of time for these different populations to adapt. That’s what we’re seeing as ecotypes. We have a wet ecotype and a dry ecotype.

What genomic tools are you using?

We use what’s called genotyping by sequencing. It’s kind of like genetic fingerprinting. We have thousands of what we call single nucleotide polymorphisms. These are places where there’s just one single change in the DNA sequence. We have, in our studies, maybe 10,000 differences between the wet and the dry ecotypes of big bluestem. That’s based at the DNA level. And then we also look at expression of genes using RNA. We look at how the wet ecotypes and the dry ecotypes respond differently at the level of gene expression.

Recently the whole, full genome of big bluestem has been sequenced. That really provides a wealth of information for us. Interestingly, big bluestem has a genome about the size of the human genome. It’s just a grass that doesn’t look very complicated, but there’s a lot going on in it. It has multiple sets of chromosomes. For us, we have 23 pairs, except that big bluestem has 10 chromosomes as the base number, but it has six copies, or maybe nine copies of all of them. So it’s not 10 chromosomes, it’s 90. That makes it more difficult to work with genetically.

“The wet ecotype is this ginormous plant, and the dry ecotype is this little itsy-bitsy one, and a single genetic difference in a key pathway can explain why these tall ecotypes are so tall and can capture more light.”

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Are you looking at what causes different gene expressions, or are you looking at an adaptation and seeing whether you can find the gene that causes it?

We really would like to get at the candidate genes that are involved in ecotypes. What makes them different? They could still interbreed, right? But there are clear phenotypic and genotypic differences and gene expression differences. We’re trying to find out what’s the genetic basis for the ecology that we see. That’s what has been driving me for the past 15 years. And it’s exciting.

What have you been able to put together about ecotypes by looking at genes?

One of our biggest and most important results is, we’ve found why the wet ecotype and the dry ecotype differ in height. The wet ecotype is this ginormous plant, and the dry ecotype is this little itsy-bitsy one. Even if they’re growing together side by side, they look different. What we found is a single nucleotide polymorphism difference in a gene that’s called GA1. This gene codes for a part of the gibberellic acid pathway, and gibberellic acid is a plant hormone that controls things such as internode elongation and height. Essentially we found a genetic difference in a key pathway that can explain why these tall ecotypes are so tall, and then we related that to height with genome association techniques. As the plant gets taller and taller, you get more of the alternate GA1 variant expressed. Height is important because that basically determines biomass and competitiveness. If something is taller, it can capture more light.

How are these discoveries helping you to better use the different variants?

We’re working with different government organizations that are developing new plant materials for reclamation. For these conservation reserve lands that are millions and millions of acres, do we want to plant them, say, with one cultivar? Or do we want to be thinking about mixing it up? Maybe you want to consider planting the dry ecotype farther to the east, where there is less rain.

So the purpose of the reclamation is to restore the ecosystem?

During the Dust Bowl in the 1930s, all of these lands in the drier part of the Great Plains had been turned over for agriculture. And it was way too dry there. There was a lot of wind and soil erosion in general. It’s in these areas where it’s too dry to really support productive crops. Or it might be that it’s too sloping, where there’s too much runoff. So it’s much better to have it go back into natural prairie. These prairie grasses are long-lived perennials. Once you get them established, they can store carbon in the roots and take carbon from the atmosphere, as opposed to cropland; where the crop is removed every year, the soil gets disturbed and can blow away. In those areas where there’s marginal lands for crop growth, then these kinds of land restoration are encouraged. This is a government program; people get paid to take their land out of agricultural production and put it into grassland for about 10 years.

Does your work essentially select for a particular cultivar that is better adapted?

We have found these dry ecotypes that are better adapted. We could see in our experimental plots, which are now ongoing for 12 years; over time, the weather is quite variable from year to year. We had a big drought in 2012, the worst since the 1930s. The wet ecotype, when it was planted out in western Kansas, totally tanked and never really recovered, whereas the dry ecotype is going gangbusters. So we have identified these, both phenotypically and genetically, through greenhouse experiments and also these long-term field studies.

What research questions are you hoping to look at next?

We spent probably the past 10 years looking at how these ecotypes are adapted to climate; we have the wet ecotypes and the dry ecotypes. But now, instead of climate factors being important in adaptation, we’re looking at biotic factors, in particular microbes. Clearly the climate is important for these wet and dry ecotypes, but how much of this phenotype is due to the microbes that are growing there? What are these microbes doing? There are microbes on the leaves, on the roots, inside the stems. What we’re looking at now is, if you have a dry ecotype, does it grow best with the dry microbes? Does the dry ecotype tank when it has the wrong microbes? We see that the dry ecotype, when it is with the dry microbes, we have a 30 percent increase in growth. Now, this research is done in the greenhouse, but clearly the potential is there for a big impact from the microbes. We have sequenced the microbes, and we’re also going to be looking at gene expression differences, both in the microbes and also in these ecotypes. As you might expect, it’s not just climate that is the controlling factor in how plants grow. The living environment around it—its neighbors, competitors, microbes—how much do they contribute?

Is there increasing awareness of the extent to which plants are symbiotic with their environment?

It’s like what scientists are finding with the microbes in your gut, how much that controls your metabolism. It’s the same thing with plants. What is the microbiome that’s infiltrating the plant doing? We’re finding it does a lot. We’re pretty excited about that.

Do you feel that people don’t appreciate the complexity of plant ecosystems as much as they do that of animal ecosystems?

Well, you know, plants are viewed as kind of primitive. In fact it’s just the opposite. They’re not mobile. They can’t walk away when a predator comes. Not being mobile, they have a whole set of problems they have to deal with in place. I think that’s pretty interesting.

Does your work establish protocols that could be used in other research?

Genome sequencing is widely used now, mainly because it’s so available. If you have a plant with a relatively small genome, you can sequence that genome. It’s easy to do now. Fifteen years ago it would have seemed impossible, but it’s all possible now. This can be done—it’s not just with tallgrass prairie on the Great Plains. This sequencing can be done anywhere, and people are catching on and doing it.

A podcast interview with Loretta Johnson.