seeds

How one bad seed could take on climate change

August 1, 2017 By Samantha Kummerer in Research Tags: seeds

By Samantha Kummerer | Bond LSC

It’s no secret that the 21st century continues to set records with the warmest years in earth’s history and rising carbon dioxide and sea levels. These significant changes threaten the planet’s future and already challenge farmers.

Mannie Liscum, a Bond LSC investigator, said research in his lab may help address these problems.

They accidentally came across a variation of a plant that reveals multiple adaptive traits, including early flowering

“A variant that flowers early and has other advantageous traits could be very useful because that variant could be grown in more northern latitudes where the day length is shorter than in Missouri, but temperatures are rising to allow its optimal growth,” Liscum explained of the possible implications of the mutant discovery.

Katelynn Koskie, a Ph.D. candidate, waters young Arabidopsis plants. Koskie studies what causes changes to a plant mutation called HPH. | Photo by Samantha Kummerer, Bond LSC

Liscum is referencing a shift in temperatures across the world due to climate change.

“We’re seeing broader swaths of the earth undergoing long periods of drought, so we’re getting less arable land, less agriculturally productive land, as we see temperatures rise,” explained Liscum.

These shifts are turning longstanding agriculture norms on their head. Northern U.S. areas are becoming more suitable for growing, while southern regions become less.

Plants designed and adapted to grow in a certain region over decades are suddenly becoming less suited for their region. If you suddenly have to grow corn at higher latitudes with less daylight, the timing of harvest is thrown off. This is because light and temperature affect when plants flower. A shift away from optimal growth regions will increase the time it takes to grow a crop.

The mutant Liscum’s lab discovered is also more tolerant to drought, produces more seeds, and has a larger biomass. These attributes could lead to increasing crop and biofuel production.

“Any one of those traits, if it actually translates into a crop could be a really big deal,” Liscum said.

Ph.D. student Johanna Morrow holds up a dish of three-day-old genetically modified Arabidopsis seedlings. Morrow studies how Arabidopsis responds to light. | Photo by Samantha Kummerer, Bond LSC

How is a plant like this possible?

Researchers are still trying to determine the precise mechanism.

They found this mutation in a model plant, Arabidopsis . Arabidopsis is a simple weed that scientists use to test hypotheses due to its fast growth cycle and their extensive knowledge about its DNA.

Now, to determine if crop plants like corn or soybeans will behave similarly to Arabidopsis, researchers need to understand the mechanism behind these improved characteristics.

The science behind it

This mutation is called hph, hyper phototrophic hypocotyl. The mutation is connected with how plants perceive and interpret light cues.

“Just like we have photoreceptors in our eyes to interpret light cues, plants have different photoreceptors that can sense different qualities and intensities of light, so they can tell high energy or low energy light and that can direct their growth and development patterns,” explained Johanna Morrow, a member of Liscum’s lab.

In the model plant, these photoreceptors fall into several classes, one of which are the phototropins that are utilized to sense direction and intensity of blue light to optimize photosynthesis.

These phototropins play a big role in how a plant interprets light and how it develops. If they were altered or removed, it has a significant impact.

Johanna Morrow uses a tool to collect samples of leaf tissue. Morrow will use the DNA from the samples to genotype the plant. | Photo by Samantha Kummerer, Bond LSC.

If you remove the phototropins from the genone the plant loses fitness. When grown in the field, one of the fitness consequences of a plant lacking phototropins is increased drought sensitivity. This results in mutants lacking phototropins making less biomass and seed,” Liscum elaborated.

Liscum explained the phototropin sees the light and initiates developmental functions, similar to how an eyeball sees something and then connects it to the brain that then tells your body to move.

Some phototropin can still take in light or “see” but can’t pass the signal properly to the “brain.” Liscum says this is how the hph mutation affects phototropin – he calls it a ‘bad’ copy of the phototropin. Past experiments revealed plants with two bad copies developed worse while plants with two good copies developed better.

However, the best development came from a plant that had one copy of the bad and one copy of the good, as present in the hph mutant.

“When we found this mutation we expected this plant would be blind, functionally blind because it couldn’t interpret the perceived light signal,” Liscum said.

It turned out a plant with one copy of a broken phototropin and one normally functioning phototropin actually developed better than a plant with two functioning phototropin.

“You would expect if you have a bad copy and a good copy you would get worse, not better,” Liscum said.

The lab is still working to determine why the hph mutant does better rather than worse, than a normal plant, but that doesn’t stop Liscum from envisioning the ways this mutant could help the industry.

Liscum's lab — A member of Liscum’s lab, Katelynn Koskie, pours a jello-like substance into a dish to plant new plants. The substance allows the plants to stands in place by giving the roots something to grow in. | Photo by Samantha Kummerer, Bond LSC

Considering the potential effect on the genetically modified plant industry, Liscum explained this method would not have any negative side effects to humans because the modification is already naturally found in the plant.

“This would be literally putting a gene that’s normally present in a plant back into the plant but putting a copy in that, on its own, isn’t functional, so it’s not like you’re creating a monster. You’re putting a piece of DNA in that’s normally there but, only you’re using a dysfunctional version in of what’s normally there,” Liscum said.

The hopes are high for the agronomic impacts, but the transfer of the mutant to crop plants won’t be simple.

Katelynn Koskie, a PhD candidate, who is working on applying hph to soybeans, explained soybeans are more complex than the model plant because they have more phototropins.

While more complex, it is not impossible and the team is hopeful.

Experiments begin soon on soybeans and corn and Liscum said he hopes the lab will have answers in the next year.

Mannie Liscum is a professor in Biological Sciences at the University of Missouri. He is also a member of MU’s Interdisciplinary Plant Group that explores new ideas in plant biology. His lab in the Bond LSC studies plants’ response to light on multiple levels and the potential agronomic impact.

The Necessity of Fungi

July 5, 2017 By Roger Meissen in Research Tags: germination, mutualism, orchids, plant fungus, seeds

Graduate Researcher Sarah Unruh explores the essential role of fungi in orchid germination

By Emily Kummerfeld | Bond LSC

The blooms of orchids are unmistakably beautiful, and how they reproduce has fascinated biologists for centuries.

But, orchids might not even exist if not for the help of fungus. Up to 30,000 species of orchids require the intervention of fungi since their seeds do not contain the necessary nutrients to sprout.

Sarah Unruh, a fifth-year biological sciences PhD student in the lab of Bond LSC’s Chris Pires, seeks to discover and record the specific types of fungi utilized by many orchid species. By studying their specific genetic expressions, she hopes to uncover what allows these fungi to interact with orchids in this way, how these fungi are related to each other and what genes each organism is expressing with and without each other.

Blooming orchid — A blooming orchid in the Tucker greenhouse. Although this orchid grows in a pot, like most species of orchid it is an epiphyte and naturally grows on tree branches. | photo by Emily Kummerfeld, Bond LSC

“The main question for me is, what is the nature of this relationship? Is it more mutualistic or parasitic? You don’t often get something for nothing, so why is the fungus participating in this relationship? Most fungi that live in plant roots receive carbon from the plant. Orchid fungi are doing the opposite and that is weird. I want to know how this relationship works,” Unruh says.

Unruh first studied orchid evolution and how each orchid species related to each other genetically. “My assumptions of what a plant was were so violated by orchids and it still fascinates me! So many orchid species grow on trees, many don’t have leaves, some species never even turn green or photosynthesize.”

This focus soon evolved into her interest in the relationship between orchid plants and fungi. Fungi are neither plants nor animals, and have their own branch on the eukaryotic family tree. They are nonetheless essential to plant biology, “eighty percent of plant species have beneficial fungi in their roots,” says Unruh.

Many orchids are technically classified as epiphytes, which means they grow on the surface of another plant and get all their food and water needs from the air, rain and what accumulates nearby. That doesn’t leave a lot of extra nutrients to put into seeds, which typically need the store of food to sprout and grow its first leaves.

Germinating orchids seeds. A small mass of fungus is placed in the Petri dish to assist in germination. | photo by Emily Kummerfeld, Bond LSC

That’s where fungi come into play. Some types of fungi can even germinate several species of orchids, and studying the DNA sequences of these fungi could be vital in the future for endemic endangered orchids and their associated fungi. “I’ve always been interested in relationships between organisms or symbioses,” says Unruh, “the fact that orchid seeds need fungi to survive was too weird not to research.”

"Super Fungus" — Tulasnella calospora, nicknamed the “Super Fungus”. This type of fungus can germinate several species of orchids. | photo by Roger Meissen, Bond LSC

But the process of studying fungi DNA is not a simple one.

“In order to look at their genomes, I need to grow a lot of fungi and then grind it up and add certain substances to isolate only the DNA. I send this DNA to a facility called the Joint Genome Institute where they send it through a machine that spits out a file with a list of lots of small pieces of the genome – like puzzle pieces. I then use computer programs to put the pieces together and try to assign a function to each gene.”

So, the established relationship between fungus and seed helps the orchid, but it’s not known what the fungus is getting out of this arrangement. One idea, based on recent published research, is the fungi receives a certain form of nitrogen from the orchid seeds. Another experiment Unruh is working on is growing the orchid seeds by themselves through special media, growing the fungus by itself, or growing them together. She then measures the gene expression to see if there are big differences when the plant or fungus is alone or together. “This will help answer my question of how mutually beneficial this association is,” says Unruh.

The data collected from this research will form the bulk of her PhD thesis. However, there remains many questions regarding the relationship between orchids and fungus that Unruh would like to explore in the future, such as which fungi are best for reintroducing endangered orchid species or what other roles fungi play in their environment. “I foresee fungi, especially plant and fungal relationships, becoming the focus of more and more research in the future.”

In 2014, Unruh received a three-year National Science Foundation (NSF) Graduate Research Fellowship. More recently, she has received a grant from the Joint Genome Institute to sequence 15 full genomes of orchid fungi.

The seeds of progress

October 11, 2016 By Roger Meissen in Research Tags: amino acids, seeds

Efforts to understand the genome of one plant through its many genetic varieties could lead to nutritional improvements in the staple crops billions of people depend on

By Phillip Sitter | Bond LSC

Ruthie Angelovici stands next to some Arabidopsis thaliana samples in the basement of Bond LSC. She is leading projects to study the relationships between genotypic and phenotypic variation in Arabidopsis and how this affects the amino acid content of the plants, and the resistance of their seeds to drought conditions. | Phillip Sitter, Bond LSC

It’s hard to avoid corn, rice or soybeans in your diet, and you’ve probably eaten or drank something today with at least one ingredient from them.

Unfortunately for the billions of people worldwide who depend on these crops as a staple, they aren’t actually all that nutritious. Specifically, they lack sufficient quantities of amino acids.

Twenty amino acids are required to build any protein, and within that about ten are considered essential, Bond Life Sciences researcher Ruthie Angelovici said. “Without amino acids, you can’t live.”

Amino acids might seem minor, but important parts and processes in our bodies from our muscles to enzymes are built from or work through them. That’s why Angelovici wants to enhance their availability in key foodcrops.

In the case of amino acids, “What we’re trying to understand is the basic question of how those accumulate in seeds, and then from that basic concept we’re going to try to improve that in grain,” Angelovici said.

The evolution of poor nutrition

No one really knows why so many of our most important crops that essentially sustain humanity lack sufficient essential amino acids.

Maybe plants don’t synthesize amino acids because the cost in energy for the plant is too high, or because higher levels of amino acids might make them more vulnerable to attacks from hungry insects. Maybe if plants produced higher levels of amino acids, the taste would be too strong for human palates, and so our ancestors long ago selectively bred those traits out of crop populations. Or, maybe in ancient farmers’ pursuits of other traits in their crops, like higher quantities of starch, humanity accidentally boosted one nutritional trait at another’s expense. There are a lot of unknowns when it comes to these theories, Angelovici said.

What is clear — and something Angelovici said she cannot stress enough — is how powerful a genetic tool she and her fellow researchers at Bond LSC have in the form of a collection of a vast amount of genetic variation of Arabidopsis thaliana.

“Arabidopsis thaliana is a model [plant] system that a lot of plant scientists use, although it is not a crop, or anything like that, but it’s a great model plant to start with, and then everything we learn from it, we can try and figure out if it’s the same in maize, rice, soybean, and translate it,” Angelovici explained.

Part of the mustard family, Arabidopsis grows quickly so researchers can study four or five generations in one year. As an added bonus, this huge genetic variety but can be grown in just one room instead of large fields. For Angelovici, that room is in Bond LSC’s basement and the basement of greenhouses nearby.

“We are growing right now 1,200 ecotypes of this Arabidopsis thaliana. So, what is an ecotype? It’s basically from the same species, but they have a slightly different genotypes. So, we’re looking at a vast genetic variation that represents genetic variation of this species across the world. Each ecotype comes from a different place,” she said.

For those of you wondering, a genotype is the specific sequence of information in an organism’s genetic code — its genetic identity. A phenotype is an observable physical trait controlled by the genetic sequence. For phenotype, think in terms of color, size, shape — just like in different breeds of dogs and cats, for example.

Even the smallest differences in genetics can produce the range of traits we observe, like the size difference between a Chihuahua and a St. Bernard — even though all the breeds are the same species. The same thing applies to plant species, too.

Angelovici said researchers can use all the genetic variation in their extensive Arapidopsis collection understand questions of how observable traits relate to genes, and vice versa.

Once that connection is established, “we basically have an address on the genome, and then we can go after the gene itself, understanding the function of the gene, and how that is affecting our variation of the phenotype, basically to help us understand the mechanism,” Angelovici explained.

“And if you understand the mechanism, we might be able to improve it, change it, either through genetic engineering or breeding. Basically, mining what Mother Nature has already done throughout many generations, and trying to figure out if we can utilize that in crops,” she added.

“We can measure the level of amino acid, but does the plant really care about the absolute level of amino acid, or relative level, and how they correlate with one another? It appears that these relationships are really important.”

All this algorithmic analysis can eventually improve results.

“When we get a candidate gene that we think affects one of the traits that we are interested in, we either knock it out or over-express it, and go back to the phenotype and figure out if it changes, and how,” Angelovici said.

“Along the way, we also try to understand if the phenotype is correlating with something that is larger, for example the plant’s growth, its development or the development of seeds.”

A plant under stress

An understanding of seed development might be especially important in understanding how drought affects the nutritional quality of future generations of water-stressed plants.

“Surprisingly, those are processes that are not well-understood — how the seed itself is adapting to water stress. A lot of people are working on water stress and drought at the plant level, in the yield [of a crop], but we’re trying to really understand what is happening on the level of the seeds, on the bio-chemical level, and then how that affects the next generation,” Angelovici explained.

If she and her fellow researchers find a super-resilient seed, they could learn to transfer its resiliency to drought to future generations of seeds.

Something they’ve seen already is that if you really water-stress a plant, while it may produce less seeds, seeds that it does produce are bigger.

“Right now the question is, are they bigger because they are trying to adapt for their harsher environment, or are they just trying to survive?” she said. Is the parent developing its offspring in a certain way to ensure the best possibility of success of that offspring, or just so it can survive to reproduce another day?

“We can only provide the data,” Angelovici said of her work in trying to answer questions like these, in order to improve the quality of human life by understanding and improving the quality of our food.

“This is the mechanism, and that is a tool we can provide,” Angelovici said of what the research can offer to people like farmers and other plant breeders. “Knowledge is power. What we do with this power is up to a lot of people.”

Ruthie Angelovici is an assistant professor in the Division of Biological Sciences, and is a researcher at Bond Life Sciences Center. She received her degrees in plant science from institutions in Israel — her B.S. and M.S. from Tel Aviv University, and her Ph.D. from the Weizmann Institute of Science in Rehovot. She was a postdoctoral fellow at the Weizmann Institute and at Michigan State University, and has been at MU since fall of 2015.

This file photo shows at least one other ecotype of *Arabidopsis thaliana* in a greenhouse in Bond LSC. Even small variations in the species’s genome can create the large number of observable varieties, sometimes with distinct sizes and shapes, other times with genetic differences that can only be observed on the microscopic level. | Roger Meissen, Bond LSC

Searching for the gene: MU scientist works to find link to nutrient content of seeds

November 8, 2013 By Roger Meissen in Research Tags: seeds

David Mendoza-Cozatl uses Arabidopsis plants like these as a model to understand how plants transport nutrients from soil to seeds and leaves.
Courtesy Randy Mertens/CAFNR

Forget fruits and vegetables, seeds provide a critical part of the average person’s diet. From beans to cereal grains, understanding how genes and soil types impact nutrition could one day help produce more nutritious food.

One University of Missouri researcher wants to know which genes control the elements in these nutrient-rich packages.

“Iron and zinc deficiencies are considered two major nutritional disorders in the world, so there’s a lot of interest in developing plants with enhanced amounts of these micronutrients,” said David Mendoza-Cozatl, a Bond Life Sciences Center plant scientist. “The question for labs like mine is how can you convince a plant to accumulate more of these metals even though high concentrations can be toxic to plants?”

In a five-year collaboration with researchers at the University of Nevada and UC San Diego, the group measured the amounts of 14 elements in both plant seeds and leaves of mutant Arabidopsis thaliana plants planted in different soil types (salty, alkali, heavy metal and normal).

These mutants were special. Each plant had a different gene disabled, allowing researchers to tell if the disabled gene affected uptake of minerals into the seeds or leaves.

The teams found that 11 percent of genes influence proteins relevant to the nutritional content in seeds. Soil types also played a role in the significance each gene’s impact.

The approach could be likened to understanding how a car works.

“What we are doing here is we have a car with different parts missing, and the question we are asking is what happens to the car without each of these parts,” Mendoza-Cozatl said. “In plants we ask how more or less elements or nutrients can accumulate without each of these parts, these genes. That’s how we are trying to assign the function of a gene to nutrient homeostasis.”

Mendoza-Cozatl’s work with the group focused on soil laced with non-essential heavy metals (e.g. cadmium and arsenic). They grew mutant plants from seeds and compared nutrient content of those plants’ leaves and seeds to a baseline. To do this, researchers “digested” leaves and seeds, separately, then quantified the amounts of elements.

“We turn everything into basic elements by putting the seeds or leaves in a tube, adding nitric acid and boiling them,” Mendoza Cozatl said. “We found that the mineral makeup of the seed and leaves can be different.”

This surprised him since nutrients in seeds come through the leaves via the phloem. The phloem is living tissue that transports nutrients throughout a plant.

Nutrition isn’t the only area that could benefit from knowing what controls the transport of minerals in plants.

A newly engineered plant could be made to use less fertilizer or move particular types of minerals, like toxic heavy metals.

“Many former industrial areas contain fields contaminated with heavy metals like cadmium and arsenic,” Mendoza-Cozatl said. “Understanding genes important to nutrient transport could help both with bioremediation in soil and bio fortification in food.”

Genes identified through this study will lead to new research in the Mendoza lab as well as other labs involved in this large project.

“The mechanism underlying these changes in nutrient seed composition are not known, so we still need to find how these genes are affecting the seed composition,” Mendoza said. “That’s where the advance will be more significant, and we’re not there quite yet.”

A grant from the National Science Foundation funded this research. Mendoza-Cozatl is an assistant professor of plant sciences in MU’s College of Agriculture, Food and Natural Resources and a member of MU’s Interdisciplinary Plant Group.

Read details about the research in the science journal PLOS ONE.