- Welcome, everyone, to Wednesday Nite @ the Lab.
I'm Tom Zinnen.
I work here at the UW-Madison Biotechnology Center.
I also work for the Division of Extension Wisconsin 4-H.
And on behalf of those folks and our other co-organizers,
PBS Wisconsin, the Wisconsin Alumni Association,
and the UW-Madison Science Alliance,
thanks again for coming to Wednesday Nite @ the Lab.
We do this every Wednesday night, 50 times a year.
Tonight it's my pleasure to introduce to you Scott Brainard.
He's a tree crop breeder with the Savanna Institute,
and he also works here
in the new Department of Plant and Agroecosystem Sciences,
which is a conglomeration of horticulture and agronomy.
- Scott: Agronomy, yep. - Great.
Scott was born in Schenectady, New York
and went to Niskayuna High School there.
Then he went to Swarthmore College in Pennsylvania
to study biology.
He got his master's in plant science
in Wageningen in the Netherlands.
And then he came here...

Way to go; she's a horticulture person.
[Brian chuckling]

Then he came here to get his PhD in plant breeding and genetics.
As I mentioned, he continues as a research associate here,
and he's also a tree crop breeder
with the Savanna Institute.
Tonight, he's gonna be speaking with us
about "Breeding Tree Crops to Fight Climate Change."
Would you please join me in welcoming Scott Brainard
to Wednesday Nite @ the Lab?
[audience applauding]

- All right, thanks.

All right, thanks so much.
Happy to be here.
Glad everything's working.
And yeah, so tonight,
I want to talk about some of the research
that we're doing at Savanna Institute,
specifically focused on the breeding of tree crops.
And as the title suggests, the motivation for myself
and a lot of us at the organization
is the potential for these tree crops
to mitigate climate change.
So I wanna start with a discussion
of how that whole kind of motivation
and possibility exists,
and then move on in the second half of the talk
to discuss specifically the breeding.
So just a bit about the organization
where all of this is happening.
The Savanna Institute's a nonprofit based here in Madison,
but we have work and projects
that kind of goes across the Upper Midwest.
Our sort of unofficial region of focus
is the prior extent of the oak savanna biome.
And yeah, I will discuss a little bit more
about the different forms of work that we're engaged in.
But to start off right from the outset,
the main mission of the organization
is to promote agroforestry.
So what is this thing, agroforestry?
It's a somewhat hard to pin down kind of concept
or set of practices, but in short,
I would say a good working definition
is trees, on farms, on purpose.

And the "on purpose" part is where the sort of technique
of agroforestry comes in.
You don't just let trees grow in your fields.
You integrate them in rather deliberate ways.
So to set the stage a little bit more specifically,
I think this is a maybe unrealistic slide
in the very stark boundaries that it draws,
but I think this is a reasonable kind of conceptual way
of thinking about
how agriculture is typically practiced
in relation to nature sort of in the corners,
you know, preserved areas and conservation areas
that may be deliberately managed in a specific way
but are nonetheless very much separate from agriculture.
You know, row crop agriculture as it is practiced
across most of the Upper Midwest.
Agroforestry attempts to blur those stark boundaries
and try to incorporate conservation practices
as well as just natural ecosystems onto farms.
So this makes it different
from just a, you know, traditional orchard setting.
Agroforestry kind of has baked into it a little,
a sort of notion of specifically cultivating a diversity
of species with trees and shrubs being very critical components.
So here's some cartoons, and I'll pair them with photos
of some examples
of what might constitute agroforestry systems.

I think a very classic, simple to understand possibility
in planting trees on farms is alley cropping.
So you have row crop agriculture happening
between widely-spaced rows of trees.
And those trees may be providing fodder,
they may be providing fruit or nuts,
they may be providing timber,
or they may just be providing habitat.
You're still kind of practicing traditional agriculture,
traditional annual agriculture in between these rows
in a more or less undisturbed way.
And here's an example of this just getting started
down in Urbana, Illinois.
One of the nice things about this particular system
is these trees take a long time to establish and grow.
And while that's happening,
you still are cash flowing your operation
by growing a row crop.
Silvopasture is another kind of classic example
of agroforestry.
This is the integration of trees onto pastured systems
where you may be grazing livestock.
And I think this particular practice has a ton of potential
because the planting of trees on these pastures,
the right kind of trees
can allow a very high-quality pasture to grow,
but also provide additional fodder for livestock,
whether that's leaves, whether that's fruit or nuts,
or just whether that's shade,
which is increasingly becoming a very sought-after commodity
by livestock suffering in the heat.
So this is just a real win-win when it's practiced well.
And here's an example of cattle grazing
in a silvopasture system here in Wisconsin.

A few other practices that are really kind of like additions
that don't have as much
of a agricultural sort of bent to them
are conservation practices like windbreaks.
Windbreaks can be really essential in breaking wind
and thereby reducing, you know, windborne soil erosion.
But they can also have very valuable roles
in providing habitat
for different types of animals on farms
and can definitely improve crop health as well,
depending on the field where they're planted.
So here's some hybrid poplar planted in Illinois.

Riparian buffers are in a similar vein to windbreaks.
These are strips of trees and shrubs planted
along waterways, specifically planted to prevent the flow
of excess nitrate and phosphorous fertilizers
into those streams and rivers
as well as to slow down soil erosion.
So really a kind of strict ecological motivator there
for that kind of practice.
And here is a photo of such a practice.
And yeah, so hopefully,
that gives you just a little bit of a flavor
of what agroforestry might look like.
It's not one set of practices.
It's not, you know, a entirely well-defined principle,
but it can take a lot of different forms,
and the ultimate result is trees on farms on purpose.
So now to return to Savanna Institute a little bit.
Our work, and here, this is a very rough schematic,
not of the oak savanna biome,
but really where we have either projects of our own
or partners that we're working with on projects.
We work in several different areas.
I'll be talking a lot about the research side
of the organization.
But I just wanna mention
that promoting these kinds of systems
is not simply accomplished by studying them
or commercializing them.
There's a lot of education outreach,
sort of extension-type activities
that really needs to go hand in hand in terms
of giving farmers the knowledge
and the tools to implement these practices.
And then since a lot of this has not been practiced
on a wide scale before,
we also try to, as much as possible,
actually develop farm scale demonstration and pilot farms
where folks can come, see these practices actually
in the real world.
And I will talk about some of the land
where we're doing that in Spring Green.

So now to move from, okay, so we're getting trees on farms,
we're getting shrubs being planted.
How is that related to climate change?
And this may be a very rudimentary slide
to those of you who are following the sort of science
behind climate change.
But in general, responses to climate change
can be lumped into two camps.
There's mitigation strategies
and there's adaptation strategies.
Mitigation is trying to draw down greenhouse gas emissions
or greenhouse gas equivalents.
You know, reduce the warming and forcing effects
of greenhouse gases that are in the atmosphere
to try to slow climate change.
Adaptation is an equally critical
and important set of practices
that accept that the climate is warming,
it already has warmed,
and we're dealing with those consequences now.
We need to adapt to them.
I'm not really going to be
talking about adaptation tonight,
although I think that, you know, the ways
in which tree crops fit into that latter set
of activities is a very interesting
and fruitful conversation.
I'll be talking about the, to some extent,
much more straightforward mitigation set of activities.
And this is, you know, a somewhat just obligatory slide.
I don't think we really need to cover what's happening
with climate change.
But just to motivate, why should you care
about mitigating the effects of climate change?
Here is one way of visualizing the, you know,
potential outcomes of unmitigated climate change.
These are projections of the state of Illinois
and what region of the country now,
its climate might look like at mid-century
and at the end of the century
in these different emission models.
So, you know, even under a sort of low emissions scenario,
we're still looking at Illinois having the climate
of a sort of southern Gulf State by the end of the century.
And this is already predicted to have pretty massive impacts
just on extreme precipitation events.
But, of course, that's not, you know, the beginning
or end of the kind of consequences
that specifically, you know, agriculture is going to face
from this kind of changing climate.

So to return to agroforestry,
it's very difficult to put these kinds of,
you know, meta-analysis slides together.
And this is a somewhat busy figure.
What this is showing is that if you do try
to stack all the different kinds
of sort of mitigation practices that could have the capacity
to draw down levels of greenhouse gas
in the atmosphere,
agroforestry is very repeatably found
to have a massive potential to sequester carbon
relative to other agricultural practices.
And to dig into that a little bit deeper,
the reason for that potential, the reason that in general,
changing the way we practice agriculture
can have such a positive impact
on the rates of greenhouse gas emissions
is that today, agriculture is a very significant source
of greenhouse gas emissions in the U.S.
So this is total greenhouse gas emissions shown
on the left here for the U.S. in 2020.
And this is that 11.2% sort of piece of the pie broken out
in the smaller pie chart on the right.
So 11.2% of U.S. emissions
are coming from the agriculture sector.
The reasons for that are, it might not be what you think.
There are some direct CO2 emissions.
This would be from just, you know,
driving tractors, burning fossil fuels,
but a lot of what's emitted on farms
is direct CH4, methane emissions, from livestock
and direct N2O or nitrous oxide emissions.
And that's coming from excessive rates of fertilization.
The way in which N2O is released in the atmosphere
is a little bit complicated,
but farmers spread nitrogen on their fields as a fertilizer,
very essential to pretty much all crop production.
And when that fertilizer is not directly taken up by plants,
it sits in the soil.
If it doesn't run off into a stream,
bacteria will break it down
through processes referred to as denitrification.
And the byproduct of these denitrification reactions
is the release of nitrous gases into the atmosphere.
And nitrous oxide is a far more potent greenhouse gas
relative to CO2 and has an outsized impact
on the warming of the climate.

So why agroforestry?
How does that change this equation
and get that 11.2% piece of the pie to shrink?
Well here, I think a useful model for thinking about
agriculture and its sort of net impact on the climate
is to think about sources and sinks.
So agriculture produces greenhouse gases;
it also has the potential to sequester them.
So here I'm just showing the N2O emissions associated
with annual crops.
And this is a byproduct of fertilization.
In addition, below this, you know, this zero line
where the y-axis is a little bit complicated,
tons of carbon equivalents per acre per year.
So if you got a negative number here,
that means that you're drawing down levels of carbon.
There are two main ways that annual agriculture
can have a positive impact in this regard
and have a negative carbon equivalent.
And that's this no-till SOC.
That stands for soil organic carbon.

Carbon is stored in the soil.
There's inorganic forms of carbon stored in the soil
and there are living things in the soil
that have, they're made up of carbon.
When you till the soil less,
less of that carbon is broken down through respiration
and more of it stays in the soil.

Cover crops can also have a positive impact
on the size of this,
what is called the soil organic carbon pool
by increasing the amount of organic matter
stored in the soil.
What this sort of bar chart tries to represent
is those are, you know, this is again integrating results
from a number of different recent studies.
But in general, the finding is that in annual agriculture,
you can tinker around the edges and you can implement
what are sometimes called
precision agricultural practices.
No-till, you know, direct drilling of corn, for example,
planting more cover crops.
You can improve annual agriculture,
but you cannot make it a net sink for carbon.
It is always going to emit more than you are able to capture.
And that is the kind of fundamental shift
that we're able to, according to these, you know,
the current research is that agroforestry
has the potential to flip that relationship.
You not only can reduce the amount of N2O emissions;
you are able to make more efficient use
of nitrogen fertilizer in agroforestry systems.
That's largely a function of the greater diversity
of root systems.
And you are also able
to massively increase the soil organic carbon pool.
Trees stay on the land year after year after year.
You sort of, by definition, never are tilling
in those strips where trees are planted.
And that permanent root system leads
to a relatively large expansion
in the soil organic carbon pool in the soil.
And then this might be, you know,
the most sort of obvious thing
that trees have going for them in this respect.
There's the wood.
Trees and shrubs have woody biomass.
That's kind of what makes them unique.
And that wood is made significantly of carbon.
Plants take up carbon dioxide during photosynthesis,
and they store it in this woody biomass,
which as long as that tree is alive and not burned,
is going to stay in that woody biomass.
And that is, relatively speaking,
a huge sink for carbon,
and it is the main reason that you're able
to flip this relationship in perennial agroforestry systems.
So that in a nutshell
is sort of the very long-winded motivation
for the actual work that I'm gonna be talking about tonight.
Agroforestry systems have this potential
to draw down levels of carbon in the atmosphere
and turn agriculture from a net source
of a pretty significant piece
of our total CO2 equivalent emissions
into a sink for carbon.

What we are working on in the tree crop improvement program
at Savanna Institute
is trying to overcome some of the barriers
that are limiting the adoption of agroforestry systems.
So right now,
most of the systems that I showed you earlier,
alley cropping, silvopasture systems,
these are relying on crops
and to the extent that varieties for these crops even exist,
they are relatively unimproved.
And when I say relatively,
I mean relative to major agronomic crops.
Corn and soy, for example, you know,
as the dominant sort of species
on the landscape receive massive amounts of investment.
And massive amounts of energy
is put into continuously breeding
and improving these crops.
Improving their yield, improving their water use efficiency,
their disease resistance.
It's pretty incredible when you look out
on the landscape and see how productive these plants are.
And that's not some sort of unique thing
about their biology.
That's a consequence of a huge amount
of human effort and money that's been put into that.
And trees and shrubs have not received that investment.
And so that is the need
and that phenomenon, that lack of investment

has really slowed the rates of adoption
because it has not allowed for farmers
to have access to really great sort of versions
of these crops that I will, I promise you,
talk about in a moment.

What's the reason for this?
What's the barrier to breeding these crops?
Well, relative to these annual crops,
there are very large acreage requirements associated
with breeding them.
They're huge.
These trees are quite large,
and they have extremely long generation times.
And not just long generation times
to making crosses with these crops,
but they have even longer times to maturity,
to seeing the performance of these crops,
you know, seeing their yield.
They may start flowering or fruiting
in five years, let's say,
but they may not reach a sort of physiological maturity
for a decade.
So the solution or what we're trying to bring to the table
that hasn't really been tried before
are a set of high throughput.
And by that, I mean very efficient phenotyping.
And by that, I mean measuring trait performance
and genomic selection methods.
I'll explain what I mean by that as well in a moment.
That's really just using new ways
of sequencing the tree's genome
to more efficiently screen very large breeding populations.
And we're doing this in Spring Green,
just west of Madison here.
So before going any further,
I just want to acknowledge some of the members
of the team of people who are doing this with me.
Like I said, the organization does a lot more
than just breed trees,
and there's a lot of additional folks
who aren't pictured here who don't fit on this slide
who are doing very important work
relative to extension, and outreach, and education.
But here are some of the technicians working for us.
We have a great farm crew out there.
We're managing hundreds of acres of land,
and I certainly could not do that
[chuckles] without a excellent crew of farmers.
We have a research staff.
Here pictured are three folks who are not doing breeding work
but are really studying other pieces of the puzzle,
specifically studying those, measuring carbon
basically stored in these systems.
That's a whole science in and of itself
that is quite complicated,
and the gloss that I gave earlier really
was probably insufficient if you ask our climate scientists.
And we have breeders like myself
who are doing the selection and the crossing
that I will describe in the next few slides.

I also wanna introduce the crops we're working with.
I've sort of been talking about these practices
in a very abstract way,
but these are the actual six species that we're working on.
And these might not be species that are familiar to you
or may not be the first species that you think of
when you think of tree crops.
You know, you might think of apples, or pears,
or you know, things that you actually see
in the grocery store.
These crops have, well, I'll talk about
their sort of uniquely well-positioned role to play
in agroforestry systems.
But the other thing is many of these crops
are native to the U.S.,
and many of them are native to the Upper Midwest,
and they really thrive here.
So they do very, very well
with very limited management and inputs.
So these are, yeah, these are the six crops
that we're working on,
and I will have a lot more to say
about each of them in a moment.
But first, I want to just give a sense
of how this actually looks on the ground.
We're adopting a very similar breeding approach
for all of these crops,
and so I just wanna show some photos and videos
and also discuss kind of what our general scheme looks like.
So when I say we're doing breeding, what does that mean?
Well, in general, we are growing breeding populations
for these crops.
So what is that?
Those are diverse plantings of around here...
This n standing for sample size, around 1,500 to 2,000 genotypes.
That means unique seedlings
that are different genetically from every other seedling.
They are descended from controlled crosses
that we've made between existing varieties.
And we also have about 10% to 20%
in all of our fields devoted to any given crop.
About 10% to 20% replication of the parental varieties
that we use to make these populations,
we have those clones sort of scattered throughout
as essentially checks to make sure
that we're making progress.
So that's generally speaking what we're planting,
and that's our basis for doing selection
is that you need this genetic
and phenotypic diversity to select from,
and this is how we're going about building it.
Taking existing varieties, crossing them together,
and planting out thousands of their progeny.

So, but here's some drone footage of one of our fields
from this year.
And you can see it was a drought year.
It's a very dry field, but this just gives you...
You can't see any plants,
but I hope this gives you a sense of the scale.
This is one of those breeding populations.
This is just across from the Spring Green Preserve,
if any of you are familiar, literally across the street.
And this whole field is planted to hazelnuts,
primarily American hazelnuts
and some hybrids with European hazelnut.

And here is, if you can make out those little dots
in the lower right-hand corner,
that's the farm team mulching away to control weeds.
So that's one of our main research fields.
I also have some drone footage of another one of our fields
from the gloriously non-droughty year from 2022
of another field, just another farm just up the road.
Here is one of those pilot farms that I mentioned.
These are actually all clonal hazelnuts.
So these are not seedlings,
and they're being grown more to represent
what a sort of realistic production system
in the Driftless Region might look like.
And I'm just gonna let this play a little bit longer
so you can see the Wisconsin River there flowing
in the background.
The camera will turn, and that's a really beautiful wetland
that we're really lucky to be located next to.

Now just a bit about the genetic tools
that we're developing.
I sort of mentioned that we're trying to bring something new
to the table here.
And some of that is on the phenotyping side,
how we're measuring these plants' performance,
but a lot of it is on the genetics side.
And there have been a lot of advances
in the last decade and a half, I would say,
in terms of our ability as a small organization
with not a lot of resources to actually kind of engage
in the cutting edge of genetic research.
And this really has taken three forms.
One is we're able to build genome assemblies
for these crops.
The human genome, you know, back in the year 2000,
took a million dollars,
took an immense number of people working for years.
Now, we can build a chromosome scale reference genome
for any one of these species for about $10,000.
So that's a huge advancement.
And that is extremely valuable in allowing us
to quickly identify molecular markers.
And molecular markers are regions of the genome
where there is variation in a population.
And this is really the basis
for using genetic sequence data in a breeding program
is finding these, what are called polymorphisms
or markers for short,
that are indicators of genetic variants.
We use what's called whole genome sequencing.
One of the services provided right here
by the Biotech Center.
And it's a very low-cost way
of identifying these polymorphisms
in large populations.
The final thing that we do is we use these sets
of genetic markers
to build what are called genomic prediction models.
And this allows for us to predict the performance
of plants when they are still just little seedling babies.

So in words, genomic prediction is what I just said.
It's a way in which you take genetic markers,
and you use it to make a prediction about a plant
that you don't know, it's just a seedling,
you haven't seen it grow up yet, but you can use its genotype
to make a prediction of what it will look like
when it's an adult.
How do you do this?
So you genotype and phenotype, so measure the performance
of a very large training population.
And those basically are the breeding populations
I was showing you videos of earlier.
You grow out a whole bunch of plants,
and you genotype them and you measure their performance,
and you build a linear model that relates the genotype
to the phenotype.
Then you can do two things with this model.
You can predict the phenotype of plants
that you only have a genotype for
'cause you have this regression model.
For example, seedlings.
Maybe you have 10,000 seedlings in the greenhouse
and you want to plant specifically the ones
that are going to be the best.
You only have a small field, let's say,
or even let's say you have a large field.
You still have more seedlings than you can plant;
you wanna pick the best ones.
That's one way of using this model.
The other thing you can do is you can improve your ability
to predict who's going to be a good parent
for the next generation of crosses.
And this is really kind of the bread and butter of breeding
is making selection from breeding populations
and identifying specifically,
not just the plants that you think would do well on farms
that you wanna sell to farmers,
but the plants that you're gonna cross together
to make the next generation.
And those are not always the best plants
in and of themselves.
The capacity of a plant to give rise to good offspring
is what's typically called the breeding value of that plant,
nomenclature taken from animal breeding.
And these genomic prediction models allow you
to very precisely identify which plants
have high breeding values.
So I'll briefly show you
what this linear model actually looks like,
but I really kept this slide in here
just because I already had it.
And don't necessarily wanna discuss this other than to say
that this is a mixed linear model
for any of those of you who may be familiar
with mixed linear models.

This is specifically, just for the record, what we're doing.
And the only thing I'll say
is that letter y here represents the phenotypes
that we're measuring,
and the letter g represents the genotypic values
that we're predicting.

And everything else is, well, I'll also note
that the big W is a big matrix of genetic markers.
So yeah, dwelling on this math
for longer than I really wanted to.
But just to make the point that we are using markers
to fit a model that relates phenotypes to genotypes.
And that's really the fact that doing so
has become cost-effective is what allows us to do this.
It all sounds great on paper.
And, in fact, it has been known that this is a viable way
to sort of do breeding more efficiently for decades.
But it's only really in the last 10 years
that the costs have come down
to allow real breeding programs to utilize these methods.

And yeah, final note about genomic prediction
is that a very key thing that you wanna do
is to validate that they work.

If you're actually using this in a breeding program,
you're not gonna be able to check your work
'cause you're just making the predictions
and going with them.
This is typically done with a cross-validation approach,
where you look at the correlation.
Here, I've snuck in a little abbreviation
for genomic estimated breeding value.
So you look at the correlation
between the genomic estimate of a breeding value
and the true values, and you do this many, many times
using a cross-validation data set.
And you look at that average correlation coefficient.
And the risk of just showing you a bunch of numbers
that you can't even read.
I'll just show you a few of these correlation coefficients
for actual data that we've collected
from our actual hazelnut breeding population,
which if you haven't guessed,
is the one that is far enough along
that we were actually able to do this.
And I'll say that these numbers are encouraging.

So typically, in corn and soybean breeding programs
where we take our inspiration
because they are the ones who have been able to do this
and afford to do this for longer,
an R-squared value, a correlation between prediction
and reality of anything greater than 0.3
is something that people utilize.
They actually say, "Okay, that's enough of a correlation there
to use that in a breeding program."
And these rows
are all different hazelnut quality characteristics.

Maybe you can guess what some of these mean.
Average weight of the kernel,
the percent of the nut that is kernel.
These are all nut and kernel phenotypes.
And for many of these,
we have extremely high prediction accuracies.
So we have a lot of hope
that this method is going to work,
but of course, we have to check our work as we go.

Okay, so just to recap.
The motivation for this method, I hope,
is at this point pretty clear.
We're able to make more efficient gains
in our breeding program
by utilizing this very cheap sequence data
that's now available to us.
This allows us to pick better parents for future crosses,
and it allows us to more efficiently plant out seedlings
on very limited acreage.
So this is all sort of geared towards that major barrier
that is traditionally slowed down tree crop breeding,
which is the long generation times
and the large acreage requirements.
By making more efficient selection,
we're able to, in some ways,
get around those biological problems
with breeding trees and shrubs.

So now I want to shift gears a little bit
and talk about these plants.
And this is, in my opinion, the most exciting part
of this whole work.
And in the lower right-hand corner,
I'll just be showing the logos of some of our collaborators
because with all of these crops, we do not do this by ourselves.
We work with land grants, we work with other nonprofits,
we work with research organizations.
And yeah, we could not do this by ourselves.
So I'll probably forget to mention some people,
but I've tried to put their logos up on the screen.
So hazelnut is a very interesting crop.
American hazelnut is native to all of the eastern U.S.
and much of Canada.
And we are growing hybrids.
American hazelnut crossed with Corylus avellana,
which is European hazelnut.
European hazelnut is what you buy, basically.

It is the hazelnut in the stores.
It's primarily grown in Turkey.
It's grown a little bit in the U.S.
in the Willamette Valley of Oregon.
And basically, it's sold to specialty markets.
It's sold to the confectionary industry right now.
But it has a lot of possible uses
when you start thinking about growing it on large acreage.
And a few of these are listed here,
such as it's extremely high in oil content,
and it's also got, if you do press it for oil,
it has a side product, the meal or press cake,
which has excellent nutritional value as a livestock feed.
So here on the right, I'm just showing a picture
of what this cross has generally generated for us.
American hazelnut is a very spreading, multistem shrub.
And European hazelnut is typically grown as a tree.
It will have multiple stems if you don't control them,
but far less so than American hazelnut.
European hazelnut has a much larger kernel
and American hazelnut has a smaller kernel
with a thicker shell.
So we're trying to combine these traits into one plant
that is well-adapted to the Upper Midwest,
resistant to some of the diseases that are endemic here
that would kill any European hazelnut
from Turkey that you tried to grow,
but has really great kernel quality.
And here is some of the success that we've had thus far.
So a few selections here on the, you probably,
well, these don't have very informative names,
so it doesn't matter if you can't read them,
but here are several of, in the columns,
several of the promising selections
that have resulted from really decades
of this work that's been going on in the Midwest
since the early '90s.
And these are the parents that we have crossed together
to form our breeding populations for hazelnut.

The breeding targets, I sort of already mentioned this.
The really critical pathogen that is endemic
to the eastern U.S. is called Eastern filbert blight.

Yeah, it is deadly on most cultivated Corylus avellana,
and most americana, most native American hazelnut
is fully resistant,
or at least fully tolerant of this pathogen.
We're breeding for high kernel yield density.
And I use that word density
because we're growing this crop as a hedgerow.
So it's not a traditional closed canopy orchard.
We're growing it as a hedgerow
because that's how American hazelnut wants to grow
and that's how farmers want to integrate it
in specifically, agroforestry systems.
It's got extremely high oil content,
but we want to specifically target oleic acids,
which have a much higher nutritional profile,
and we wanna make it machine harvestable.
And you'll see that that's a theme for a lot of these crops
that have not been bred so extensively.
It's actually quite challenging to mechanize their cultivation.
Whether that's, you know, the pruning of these crops
or in particular, often the harvesting of these crops,
that is a really big limiting factor
that is holding back their adoption.
So we want a short, compact bush form.
We want the nuts to ripen uniformly
so we only have to make a few passes with a harvester,
and we wanna be able to have a minimum shearing force,
which means it's really easy
to shake these clusters off of the bush
and get them into the harvester.
The next crop I'll talk about is American persimmon,
second crop that we're working on.
So American persimmon is in the Diospyros family,
which is an incredibly diverse genus.
It's an incredibly diverse genus
with thousands of species on single islands
of the South Pacific.
It's really quite a wonder.
And this is part of the ebony family.
And so typically, species of this genus
are grown for their wood,
but it also has at least 500 fruit-producing species.
And the most common one that you've probably seen
in the supermarket is Diospyros kaki,
which is one of three Asian persimmon species
that are widely cultivated for their fruits.

American persimmon is the most nutrient-dense native fruit
in the U.S.
Lots of superlatives to make this stand out,
but really there's two native fruits in the U.S.:
pawpaw and American persimmon.
And so it's not much of a competition,
but it is extremely nutrient-dense.
It is almost a complete protein.
It's extraordinarily high in sugar.
And because of that, it's been used by Native peoples
as well as early Western settlers
as a not only human feed, but as a livestock feed.
It was called the hog tree in the southern U.S.
It has extraordinarily high yields
that often stay on the tree very late into the season.
And when they do drop,
provide that sort of off-season fodder
that was really critical really up until the development
of corn-based feeds.
So another great thing about American persimmon
is that it has a very diffuse canopy structure,
which allows for excellent light infiltration.
This makes it a perfect species, in our opinion,
for the integration
onto pastured livestock grazing operations.
So into silvopasture systems.
You can grow a very high-quality pasture beneath it,
and in return, you not only get shade,
but you get this incredibly nutrient-dense fruit dropping
into your pastures, which can offset your feed costs.
So our breeding targets, this is not a crop
that you see a lot in Wisconsin.
If you've been in the Arboretum, you might have seen a couple.
It does grow here, you can transplant it here,
but its northern range kinda peaks out
around Central Northern Illinois.
So we are trying to improve that cold hardiness
so that it can be grown here.
We've got about 50,000 seedlings in nursery beds right now,
and we'll be screening them over the next couple of winters
for the most cold hardy.
Once we find cold-hardy varieties
that really thrive in the frigid Spring Green area,
we will plant those out into more of an orchard setting
and look for several fruit quality characteristics,
most importantly, non-astringency.
If you've ever had American persimmon,
you will know that you have to let it ripen off the tree.
It needs to get soft,
otherwise it will make your mouth pucker
like you wouldn't believe.
But that's genetically controlled.
It's actually been identified, the single gene trait
in Diospyros kaki.
And so we'd like to breed for non-astringency
to make it more palatable.
We also sort of in this vein of cold hardiness,
we really need late bud-breaking trees
that also fruit early.
We have a short growing season here
relative to where American persimmon is really common.
And so we want to shorten up its ability
to set fruit in this climate.

Precocity, which is a word that means early fruiting.
That is something that we'd like in all of our tree crops,
but especially in persimmon.
And improved yield partitioning.
And by that, I mean it's putting more of its fruit earlier,
more of its energy earlier on into fruit production.
These trees can sometimes get just absolutely massive,
and that is unnecessary in a silvopasture system.

I wanted to mention here,
use these crops as sort of segues
to discuss some of the innovations
that we're trying to bring to these understudied crops.
I'd mentioned earlier that genomes
are now things that you can basically buy off the shelf.
Well, it's not that simple,
but genome assemblies are a lot easier to build
than they were 23 years ago
when we assembled the human genome.
And we just built the first genome assembly
for Diospyros virginiana or American persimmon
with this variety called Early Golden.
It is a hexaploid, so it has six copies of every chromosome.
Humans have two.
That makes it a lot harder to assemble a genome for.
But we did this with the nonprofit HudsonAlpha.

And this is something that we're very excited about
because it will allow us to take that first step
towards the incorporation of genetic markers
into our persimmon breeding program.
This is a slide
that probably does not make a whole lot of sense,
but I wanted to include it
because I really like the aesthetics
of this black background and all the colors.
On the top here is the, what we call hexaploid,
Early Golden American persimmon, six copies of every chromosome.
But this is just the maternal copies of those chromosomes.
So there's only three of every color here.
Three red, three orange, three yellow,
all colors of the rainbow, three of them.
And they map directly, three to one,
to the diploid Diospyros lotus,
which is one of the Asian persimmon varieties.
And I think this is really neat
because it shows the very close evolutionary relationship
between the hexaploid six-copy American persimmon
and its diploid relative over in Asia.
And this is one of the kind of just interesting figures
that we're able to make.
Aside from breeding better persimmons,
we're also able to learn something
about the evolution of this species.

So what are we gonna do with this genome assembly?
Aside from identifying polymorphisms or genetic markers
that we can use in a genomic prediction model,
we can trace its phylogenetic history,
and we can also develop markers
to allow us to identify the sex of a persimmon plant
when it is just basically a week old.
Persimmon are dioecious,
which means there are male and females.
This is relatively common in the plant,
I mean, it's not at all the norm,
but there's many examples of this in plants,
and it makes breeding somewhat challenging
because we obviously are talking here
about using female American persimmon trees
in silvopasture systems
since they're the ones that produce fruit,
but we also need males there to provide pollen
and definitely need males in our breeding program.
And we want to design our breeding program intentionally,
and we wanna design our farms intentionally.
Markers that allow us to determine which sex this tree is
when it is, you know, many, many years before it flowers
would definitely improve our ability
to incorporate this onto farms.
And so that's something we're excited about.

The next crop I'll talk about is black locust,
Robinia pseudoacacia.
This is a very interesting crop that is native to the Ozarks.
It's nitrogen fixing, has an incredibly high value timber.
It's very, very rot-resistant.
Again, it's one of these crops
that has very, you've probably seen it.
It's got a very diffuse leaf structure
so it allows for very good light transmission.
Very fast growing; it's basically a biofuel crop.
Our breeding targets for this,
well, I'll start with the second bullet point here.
We are in the process of inducing triploidy.
Black locust is a diploid by nature.
It has, just like us, two copies of every chromosome.
It is also considered highly invasive,
especially in Wisconsin,
in areas north of where it is native to.
It can really outcompete lots of other species

in forests of Illinois and Wisconsin.
And so what we're doing
is we are doubling its genome to create tetraploids,
and crossing those tetraploids back to the diploids
to create triploids, three copies of every chromosome.
Triploids, an odd ploidy number comes sterility.
They do not produce viable seed.
And this is a pretty common practice in,

or at least it's not common,
but it's a practice that's been done in a lot
of ornamental crops.
And we think it'll have a lot of benefit
in terms of increasing the capacity of farmers to grow this
in areas where they might be concerned
about growing a very aggressive tree
close to say, you know, a forest or other natural system.
This triploidy has also been shown
to increase the thickness of the bark, which will, we hope,
again, this is studies that are going back
to the last time black locust was bred,
which was almost 100 years ago.
But thicker bark confers resistance
to the black locust borer,
which is a pretty important pest in this country.
And also in general,
artificially inducing polyploidy has been shown
to increase vigor.
So basically faster time to maturity
in terms of harvesting this as a timber crop.
We also want to investigate the potential of this crop
as a leaf fodder for livestock.
There's a lot of evidence from other countries
where black locust is grown quite widely
that the leaves have a very high fodder value.

Now I'll talk about the small fruit shrub crops
that we're working on,
the native American elderberry and black currant.
We are working with two land grants on both of these crops,
and they're pretty similar
in terms of how we're approaching them.
They're very different crops,
but I've grouped them together here
because they are, again, bush-type crops
that are grown in hedgerow systems.
And our goal is to be able to coppice these crops annually.
So cut them down to the ground.
They resprout and they fruit on first-year wood.
That's something that they already do.
And so that's what makes them so sort of attractive
in agroforestry systems.
It's very easy and very fast to get a harvest off of them.
They are very cold hardy.
They're extremely shade-tolerant.
They basically love the difficult places on your farm
where you might not be able to grow a more demanding tree.

Elderberry, American elderberry
has very low cyanogenic glycosides,
which are a toxin that means that European elderberry,
which is, again, what you typically find in the store,
has to be heat-treated.
You can cold press American elderberry.
And there really is existing demand for both of these crops.
The problem is, the selections for American elderberry
are basically all wild selections.
And the only black currant breeding that's really happened
has happened in British Columbia.
So not really relevant to our climate.
So our breeding target for both of these crops
is very similar.
We want a very large fruit set.
These are what, I mean, the clusters,
you can see are very distinct.
These strigs here for black currant in the lower right,
whereas you have these rather large racimes
for American elderberry.
But we want a, whatever the actual fruiting structure is,
we want it large, we want it to not shatter,
we want it to ripen uniformly,
and we want it to, while not shatter,
while not fall off the plant,
we want it to be able to be machine harvestable.
So separate well from the stem upon shaking.
Another critical characteristic for currant
is resistance to this disease, cane dieback,
which is something that we're able to hopefully implement
in greenhouse screening programs.

And finally, I wanna talk about Chinese chestnut.
This is a really interesting crop.
As many of you may know,
there was and still is a native chestnut species
in North America, the American chestnut.
There is, in fact, an entire nonprofit foundation devoted
to trying to restore this species,
the American Chestnut Foundation,
which is doing really great work,
especially in the Southeast.
The American chestnut
was a very important timber tree species
until it was wiped out by an introduced pathogen.
Chinese chestnut is from the part of the world
where that pathogen came from.
So it is very resistant to that pathogen
and really does not need any work to exist in this country.
It also is a very, as opposed to being a timber species,
it's really a nut crop.
It has been bred for thousands of years in China
to be an extremely productive nut tree crop.
And it's very high in carbohydrates.
It has a similar profile, honestly, to corn.
And currently, and there is tremendous demand
for these crops.
You might not believe it,
but especially looking at this spiny burr
that the nuts come in,
but the most common business model
for chestnut orchards is U-Pick,
and they sell out basically as soon as they open orders.
Another great thing about chestnuts
is that seedlings in the Upper Midwest
outperform grafted trees.
This makes farm establishment way easier.
You don't have to go through that laborious process
of grafting a variety.
You can plant out a seed lot from an improved maternal tree,
and those seedlings will perform well enough
for a farmer to actually make a profit.
It's also relatively late-blooming,
which makes it well-adapted to our changing climate,
but also the Upper Midwest in general.

Our breeding targets are "get more;"
it's a late bloomer already.
We need faster ripening
if we really want it to be well-adapted
to the Upper Midwest.
Most of the production of Chinese chestnut
is confined to Illinois and Ohio right now
and parts of Michigan.
There are plants that survive in Wisconsin and Minnesota,
but more breeding is needed to increase that cold hardiness.
We definitely need to select for high yields.
There's a lot of variability,
especially in these seedling populations,
which are very genetically diverse.
And we would love for the nuts to fall free from that burr,
which is one of the sharpest things I have found
in the plant kingdom.
Male sterility is a very interesting trait
that has been identified in chestnut
and would, again, lead towards a greater fruit set
on male sterile trees.
And we also are interested in the kernel ratio.
There's a lot of variability in what percentage
of the nut is actually made up of that kernel.
And I'll close with Chinese chestnut,
I think is a good example of one of the points
that I made earlier about the way
in which we're trying to not just use advancements
in genotyping technologies,
but also phenotyping technologies.
Chinese chestnut is a very interesting tree
because it's what's called a terminal bearer.
It sets all of its fruit on terminal buds, new growth.
So if you take a picture of the tree using a drone,
for example, from above,
you actually can see all of the burrs,
all of the nuts in that tree.
Chestnuts drop over about a three-week period.
That's when you harvest chestnuts
is over that pretty long period.
So it is almost impossible to pick up all the nuts
from a chestnut tree.
It's an enormous task.
So figuring out what the yield of a tree is,
which is obviously a very important thing to know,
is, to date, basically not known.
It's almost impossible.
It's definitely impossible to scale that kind of measure
over large acreage.
So we have started flying drones over chestnut orchards,
and are using advancements in the field
of automated object detection
to pick out all of those burrs and count them
and convert that to a measure of burr density in the canopy.
So we can then, from the size of the tree
and the shape of the crown,
extrapolate how many nuts are up there,
and finally figure out
how much Chinese chestnut trees actually bear.
So that's one of the high throughput phenotyping methods
that we're trying to build into our program.

So just some brief conclusions here
to try to tie a lot of disparate threads together.
Thinking back to the beginning,
agriculture is a major source of greenhouse gas emissions,
not just in the U.S.
It's the data that I showed,
but that's a phenomenon that you see across the world.
And agroforestry has the potential
to change that phenomenon.
And instead of being a net emitter,
agroforestry systems can be net carbon sinks.
Right now, agroforestry's potential in the Midwest,
especially in the Upper Midwest, is not being realized.
And a lot of that has to do
with the lack of very well-adapted
and productive tree crop varieties
for some of these understudied trees and shrubs
that I've been talking about.
And we believe and are trying our best
to implement modern breeding methods
to accelerate that process, make it more efficient,
and as a result, contribute to the increased planting
of trees and shrubs on the landscape.
So I'll close there.
[audience applauding]