Archives For plant research

It’s like having a time machine—supercomputers and gene sequencing allow scientists to study early events in plant evolution. 

One of our conservation scientists, Norman Wickett, Ph.D., is co-leader of a global initiative involving some 40 researchers on four continents. The team has spent the past five years analyzing 852 genes from 103 types of land plants to tease out early events in plant evolution. The results, published recently in the Proceedings of the National Academy of Sciences, expand our knowledge of relationships among the earliest plants on land.

An Infographic About Plant Evolution

Want to print out this infographic? Download a print version here.


Illustration by Maria Ciaccio
©2014 Chicago Botanic Garden and my.chicagobotanic.org

There’s less mystery in the natural history of aquatic green algae and its relationship to land plants, thanks to research co-led by Chicago Botanic Garden scientist Norm Wickett, Ph.D., published this week in the Proceedings of the National Academy of Sciences and GigaScience.

The study examined how major forms of land plants are related to each other and to aquatic green algae, casting some uncertainty on prior theories while developing tools to make use of advanced DNA sequencing technologies in biodiversity research.

“We have known for quite some time that all plants on land share a common ancestor with green algae, but there has been some debate as to what form of algae is the closest relative, and how some of the major groups of land plants are related to each other,” explained Dr. Wickett, conservation scientist in genomics and bioinformatics.

Over the past four years, he has collaborated with an international team of researchers on the study that gathered an enormous amount of genetic data on 103 plants and developed the computer-based tools needed to process all of that information.

The study is the first piece of the One Thousand Plants (1KP) research partnership initiated by researchers at the University of Alberta and BGI-Shenzhen, with funding provided by many organizations including the iPlant Collaborative at the University of Arizona (through the National Science Foundation), the Texas Advanced Computing Center, Compute-Calcul Canada, and the China National GeneBank. The results released this week were based on an examination of a strategically selected group of the more than 1,000 plants in the initiative.

Researchers dove into the genetic data at a fine level of detail, looking deeply at each plant’s transcriptome (the type of data generated for this study), which represents those pieces of DNA that are responsible for essential biological functions at the cellular level. In all, they selected 852 genes to identify patterns that reflect how species are related.

The study is consistent with ideas and motivations that parallel research Wickett is pursuing in work funded by the National Science Foundation program called “Assembling the Tree of Life.” Both studies seek to better understand how the earliest land plants that first appeared more than 460 million years ago evolved from green algae to yield the diversity of plants we know today.

DIAGRAM: Land plant tree of life.

The “land plant tree of life”

Understanding those lineages, Wickett explained, allows scientists to make better-informed decisions in their research pursuits, and illuminates historical environmental conditions that may have impacted evolution. “Knowing that set of relationships offers a foundation for all evolutionary studies about land plants,” he said.

Using Bioinformatics to Better Understand Our World

Wickett’s expertise in a field of science called bioinformatics allowed him to serve as one of the leaders in the data analysis process, which relied on a set of tools developed by the research team. Using those tools, Wickett helped develop the workflow for a large part of the 1KP study. “The tools we have developed through this project are able to scale up to bigger data sets,” he said. This is significant because “the more data you have, the more power you have to correctly identify those close relatives or relationships.”

By working with a large amount of data, explained Wickett, the team was able to resolve patterns that were previously unsupported. Until recently, the scientific community has largely believed that land plants are more closely related one of two different lineages of algae—the order Charales or the order Coleochaetales, which share complex structures and life cycle characteristics with land plants. However, the study reinforced, with strong statistical support, recent work that has shown that land plants are actually more closely related to a much less complex group of freshwater algae classified as Zygnematophyceae.

A Simpler Ancestor

It may mean that the ancestor of all land plants was an alga with a relatively simple growth form, like the Zygnematophycean algae, according to Wickett. More than 500 million years ago, that ancestral species split into two new species; one became a more complex version that colonized the land, and the other continued on to become the Zygnematophyceae we know today. The unique direction of both species was likely influenced by environmental conditions at the time, and this study may suggest that evolution could have reduced complexity in the ancient group that formed what we now recognize as Zygnematophyceae.

“Our new paper suggests that the order of events of early land plant evolution may have been different than what we thought previously,” said Wickett. “That order of events informs how scientists interpret when and how certain characteristics or processes, like desiccation tolerance, came to be; our results may lead to subtle differences in how scientists group mosses, liverworts, and hornworts, the lineage of plants (bryophytes) that descended from the earliest land plants.”

Wickett can’t help but feel encouraged by the wave of enthusiasm around the release of the publication. “When you get involved in these kinds of projects, it never seems as big as it is—you just get used to the scale. It’s been really great to get the public reaction and to see that people are really excited about it,” he said.

PHOTO: Norman Wickett, Ph.D.

Norman Wickett, Ph.D.

Where We Go from Here

Wickett will convene with the research team in January in San Diego to discuss next steps for 1KP, which will lead to the analysis of some 1,300 species. The team will likely break into subgroups to focus on sets of plants that share characteristics such as whether they produce flowers or cones, or have a high level of drought tolerance.

With the publication of this research, a door to the past has been cast wide open, offering untold access to natural events spanning some 500 million years. After such significant discovery it’s hard to imagine that there could be more in the wings. But with the volume of data generated by the 1KP project, there are certainly exciting results yet to come.


©2014 Chicago Botanic Garden and my.chicagobotanic.org

Interested in new perennials for your garden? How about ones that have proven to be exceptional—fragrant, colorful, drought tolerant, resistant to disease and pests, and hardy in the Midwest and similar climates? Just turn to our scientists, who have done the legwork for you through the Chicago Botanic Garden’s plant breeding and evaluation programs.

Breeding and selecting new perennials is a long, intense process that begins with cross-pollinating two plants, or moving pollen by hand from the flowers of one plant to the flowers of another plant with different traits. The two related plants—which ideally will produce exceptional offspring—are selected for breeding based on desirable attributes.

PHOTO: Jim Ault poses in a bed of bright pink- and purple-blooming asters he developed at the Garden.

Jim Ault, Ph.D., with Symphyotricum (aster) hybrids developed at the Garden

PHOTO: A closeup of the rich purple buds of Twilite false indigo.

Twilite false indigo (Baptisia × variicolor ‘Twilite’)

PHOTO: Using tweezers, Jim Ault hand-pollinates a Baptisia.

Pollinating Baptisia

“In the best-case scenario, from the first cross to the final plant worthy of introduction, it takes about seven years, maybe eight to ten. I have to think long-term in generation time, from seed to first bloom to maturity,” said Jim Ault, Ph.D., plant introduction manager and Gaylord and Dorothy Donnelley Director of Ornamental Plant Research.

The most promising new plants are propagated by cuttings or tissue culture and then scrutinized by the Garden’s Plant Evaluation Program, managed by Richard Hawke. He compares the plants to cultivars and species already in the trade to ensure that the plants from the breeding program are unique and worthy of introduction. Hawke also recommends plants for use as parents in the breeding program.

PHOTO: Richard Hawke crouches down, examining the progress of a cultivar planted at the Garden.

Richard Hawke at work

“The public can see about 80 percent of the breeding program plants as we are growing them in the ground in the evaluation gardens,” Dr. Ault said. Plants with the highest marks move to licensed commercial nurseries that also conduct field and container trials and then propagate the new plants for sale to home gardeners and the horticultural trade.

In recent years, popular offerings from the breeding program have included the first orange coneflower ever released, Art’s Pride coneflower (Echinacea ‘Art’s Pride’), and Forever Pink phlox (Phlox ‘Forever Pink’). “The interest in ‘Forever Pink’ has exploded,” Ault said. “It has three weeks of peak bloom in late May to early June and then it repeat-blooms on about 10 percent of the plant all summer and fall. It’s compact and, unlike other summer-blooming phlox, has had no powdery mildew whatsoever.”

You can expect to see more noteworthy perennials in coming years. Ault is hybridizing several types, including ground-cover phlox, asters, and other genera. “Something really wonderful should bloom this spring out of the hundreds of new seedlings that we’re growing,” said Ault.

Visit chicagobotanic.org/research/environmental/breeding for a full list of the perennials released commercially through the Garden’s Plant Breeding Program.

PHOTO: A closeup of the unusual bright orange color of Art's Pride coneflower.

Art’s Pride coneflower (Echinacea ‘Art’s Pride’)

PHOTO: A bed of a dozen plantings of Forever Pink phlox in full bloom.

Forever Pink phlox (Phlox ‘Forever Pink’)

PHOTO: Tidal Pool prostrate speedwell.

Tidal Pool prostrate speedwell (Veronica ‘Tidal Pool’)

Support for the plant evaluation program is provided by the Bernice E. Lavin Evaluation Garden Endowment, the Woman’s Board Endowment for Plant Evaluation Research and Publication, and the Sally Meads Hand Foundation.

This post was adapted from an article by Nina Koziol that appeared in the spring 2014 edition of Keep Growing, the member magazine of the Chicago Botanic Garden.

©2014 Chicago Botanic Garden and my.chicagobotanic.org

Treasure in the Tropics

Undercover Science

Julianne Beck —  October 9, 2013 — Leave a comment

Hungry for progress, Nyree Zerega, Ph.D., set off in early June to the forests of Sabah, Malaysia, on the island of Borneo.  She was searching for plants in the genus Artocarpus, whose nearly 70 species include jackfruit—the world’s largest tree-borne fruit structure.

Her mission? To gather detailed information about species within the genus, including those that could provide food in tropical areas where it is needed most.

PHOTO: Dr. Zerega and Dr. Joan Pereira climbing hill in tropical forest.

Dr. Zerega in Sabah with Dr. Joan Pereira, her Malaysian collaborator.

On their research trip this summer, Dr. Zerega, a plant evolutionary biologist at the Chicago Botanic Garden, and her research team crossed a small stream on their way into a tropical forest on the edge of a large oil palm plantation. They searched there for an uncommon species until sunlight faded and the light rain turned to a downpour. On the way back, they found that the stream had grown into a raging river several feet wide and deep. Covered in leeches, they held hands tightly and waded across to safety. On other days, they searched for species with leaves as tall as any one of them, and collected fruit weighing more than 20 pounds apiece.

The dish

It’s all in a day’s work for Zerega. She has long traveled to places like this, where she works closely with local scientists to study underutilized food-bearing plants.

PHOTO: Jeisn Jumian with a huge jackfruit over one shoulder, and a cut jackfruit in his other arm.

Jeisn Jumian, field assistant, carries jackfruit back from the field for dinner.

Currently, she explained, the world relies on roughly 30 species to provide the majority of our food. The top three crops—rice, corn, and wheat—account for approximately 40 percent of all food consumed worldwide. We are merely scratching the surface of the thousands of edible plant species in existence, including at least a dozen in the genus Artocarpus.

It’s possible, even likely, that some underutilized crops have as much potential as the current favorites, but simply have not been as developed. “Underutilized crops have the potential to diversify the world’s food supply and improve food security,” said Zerega. She believes the development of these crops, produced close to where they would be consumed, could also reduce the amount of energy used in growing and exporting large quantities of crops around the world. The more options we have, the better off we are, she maintains.

Stocking the pantry

Now back in the Harris Family Foundation Plant Genetics Laboratory of the Daniel F. and Ada L. Rice Plant Conservation Science Center, Zerega and her lab members are busy extracting plant DNA from leaves collected in Malaysia. Also the director of the Northwestern University and Chicago Botanic Garden Graduate Program in Plant Biology and Conservation, she has plenty of helping hands from her master’s and doctoral students.

“We’ll be studying DNA to understand the evolution of Artocarpus, and patterns of the diversity of cultivated members of the genus, such as jackfruit, breadfruit, and the lesser known cempedak, a species believed to have originated in Malaysia. Understanding and conserving genetic diversity is as critical in crop species as it is in wild species,” she said.

PHOTO: The market in Sabah, Malaysia.

Breadfruit is sold at a market in Sabah, Malaysia.

The work is part of a National Science Foundation grant for which Zerega is assembling a taxonomic revision, which is like a genealogical history. It will include descriptions of all the Artocarpus species, how to identify them, where they originated, where they are found today, how they are used, and how they are related to one another.  

Dried, pressed specimens of all the plant samples used for DNA will be stored in herbaria in Malaysia and the Garden’s Nancy Poole Rich Herbarium. Zerega serves as director of the herbarium. These specimens, along with photographs, serve as documentation of each plant.

Cooking up solutions

PHOTO: A plate of fried breadfruit with dipping sauce.

Fried breadfruit from a market near Kuala Lumpur, Malaysia.

Next, Zerega hopes “to focus on ways to conserve the diversity and increase the use of underutilized species such as jackfruit and breadfruit, because they hold great potential for increasing food security in food-insecure parts of the world, many of them in tropical areas where Artocarpus species grow.”

As she considers her research, Zerega occasionally finds time to stroll her favorite areas of the Garden—the Dixon Prairie and the McDonald Woods.

From working with students and collaborating with scientists around the world, she hopes her work will contribute to the conservation of underutilized crop diversity and food security around the world. Although she has already accomplished a great deal, it seems that Zerega’s work so far is just a taste of what is to come.

Read more about Zerega’s research in Papua New Guinea, the Northern Mariana Islands, Hawaii, and Bangladesh in the Spring 2013 issue of Keep Growing.


©2013 Chicago Botanic Garden and my.chicagobotanic.org

The Evolution of a Research Idea

Krissa Skogen finds inspiration in the relationship between moths and evening primroses

Krissa Skogen —  October 7, 2013 — 1 Comment

Five years ago this past May, I found myself starting a new job and a new research project. My job, of course, was as a conservation scientist here at the Chicago Botanic Garden, and the research project had me sitting on the side of a road at dusk in Pueblo West, Colorado. I sat there in front of a group of plants that produce lovely-smelling flowers, waiting for their impressive pollinators to show up. And when they did, I snapped some of my very first photos of these beauties: hawkmoths, better known as the five-spotted hawkmoth, or to the scientific community as Manduca quinquemaculata.

PHOTO: Night photo of hawkmoth sipping nectar from evening primrose.

A five-spotted hawkmoth (Manduca quinquemaculata) drinks nectar from the Colorado Springs evening primrose (Oenothera harringtonii) as the flower begins to open. Pueblo West, Colorado, May 2008. Photo: Krissa Skogen

Just this past Friday, I visited the National Science Foundation’s Dimensions of Biodiversity Program, to find this very same photo—and the research that my colleagues and I will conduct over the next five years—highlighted.

So how did this one photo go from being taken in the spring of 2008 to being highlighted on the NSF’s website? How does a research project evolve and grow over time? Ask any scientist what they are currently working on and their answer will almost always start with, “I was first fascinated by x back in y….” Something caught their attention, sparked a thought, pulled them in—and they continued asking question after question, developing hypotheses and gathering data to test them, with their answers pushing them forward, sometimes down unanticipated paths, and sometimes into much bigger or smaller arenas. The more one knows, seemingly, the less one knows; old questions are answered and new ones are developed. This is what pushes scientists, and science, forward.

The evolution of a research idea

PHOTO: Krissa Skogen poses with primrose in New Mexico.

Krissa Skogen poses with an evening primrose in New Mexico. Photo: Chris Martine

In 2008, I started my current research program. After many conversations with Rob Raguso (Cornell University) and Tass Kelso (Colorado College), I drove out to Colorado with a plan to collect as much information on as many different populations of the Colorado Springs evening primrose (Oenothera harringtonii) as possible in a short period of time. That year, my timing was off—I arrived in Colorado on June 10. Oenothera harringtonii flowers primarily in May. Most of the plants had stopped flowering and so instead of collecting data on floral features, nectar, scent, and pollinators, my field assistant, Evan Hilpman, and I collected data on plant size, health, reproductive success (how many fruits did they produce?) and population size (much like a census). And one striking thing we noticed was this: small white “galls” on some of the green, developing fruits. We took notes on how often we saw this, never anticipating the importance that these little white dots would play in just a few years’ time.

PHOTO: Closeup image of a tiny, white foamy-looking dot (one of many) on a host plant.

We noticed small white “galls” on some of the green, developing fruits. These are parts of the cocoons of tiny little moths, called microlepidopterans, of the genus Mompha. Photo: Krissa Skogen

In subsequent years this project grew, and in the last four years—with the help of conservation scientist Jeremie Fant and other colleagues, and many research assistants and students—we’ve collected data on flower size, nectar volume and sugar content, floral scent, who pollinates and when (hawkmoths come at dusk and visit overnight; bees generally visit in the morning), how populations grow and shrink over time, which other plant species are flowering at the same time, and more. We know a lot of things about this species now, and one thing has been a constant: those little white balls have been observed year-in and year-out in some populations, but not in others.

We know now that some of our populations have an important compound—linalool—and some do not. We know that genetically speaking, our 25 populations function more like three, likely due to the fact that hawkmoths can fly so darn far (some estimates are up to 20 miles in just one night). And more recently, we started gathering more data on those little white balls. It turns out that they are parts of the cocoons that surround the larvae of tiny little moths called microlepidopterans, which belong to the genus Mompha. These moths lay their eggs on flower buds, fruit, and stems. If the larvae eat flower buds and/or seeds, they reduce the number of offspring that the plant produces. This is bad for any plants upon which these moths decide to lay their eggs, but everything must eat, right?

PHOTO: Trio of photos of each life stage of the moth: adult, larva, and cocoon.

Mompha stellella microlepidopteran adult; larva inside fruit (seed predator); cocoon inside O. harringtonii fruit. Photos: Terry Harrison and Krissa Skogen

In speaking with colleagues across the country and in Canada (plant and moth experts, alike), we developed an intriguing story and series of hypotheses we felt were compelling. Do pollinators and floral antagonists both respond to the same attractive scent? Could floral scent be telling hawkmoths and Mompha moths where the flowers are? Pollination is good for plant reproduction, but anything that eats flowers or seeds is not—so how would this trade-off play out in evolutionary time?

These questions have led us to the project that we will pursue on a much larger scale, thanks to recently awarded funding from the National Science Foundation’s Dimensions of Biodiversity Program for our proposal, titled “Landscapes of linalool: scent-mediated diversification of flowers and moths across western North America.”

PHOTO: Bee coated in pollen, inside primrose bloom.

A Lasioglossum species bee robbing pollen from O. harringtonii at dawn. Photo: Sadie Todd

Relationships among flowering plants and insects represent one of the great engines of terrestrial diversity. Floral scent and other plant volatiles are important drivers of these relationships (e.g., pollination, herbivory, plant defense), but remain poorly integrated into floral evolution and pollination ecology. Few studies have tested the spectrum of plant fitness outcomes when scent attracts both pollinators and floral/seed enemies. Thus, the hidden diversity of floral/seed predators and their potential as selective agents constitutes a considerable gap in pollinator-centric understanding of floral evolution. These “forgotten predators” have co-diversified with flowering plants and are likely influential in the evolution of most plant-pollinator interactions.

PHOTO: Five-spotted hawkmoth extending its proboscis (longer than its body) into a primrose bloom as it hovers.

A five-spotted hawkmoth (Manduca quinquemaculata) probes an opening evening primrose flower for nectar with its proboscis. Photo: Krissa Skogen

This project is ambitious and large and pulls upon a wide variety of expertise. In total, there are 11 Ph.D. scientists collaborating on it, including myself, Jeremie Fant, and Norm Wickett here at the Garden. The others include Robert Raguso (Cornell University), Rachel Levin (Amherst College), Terry Harrison (University of Illinois at Urbana-Champaign), Jean-Francois Landry (Agriculture & Agri-Food Canada, Eastern Cereal and Oilseed Research Centre), Sylvia (Tass) Kelso (Colorado College), Kathleen Kay (University of California, Santa Cruz), Mike Moore (Oberlin College), and Warren Wagner (Smithsonian Institution).

We are excited about what we’ll uncover in the next five years and will update you with progress as our discoveries unfold!


©2013 Chicago Botanic Garden and my.chicagobotanic.org