The ISC Blog

Improving the Soybean, One Gene at a Time


Disclaimer:

The views and opinions expressed in this article are those of the authors and do not necessarily reflect the official policy or position of any agency of the U.S. government.


Illinois is the United States’ top soybean-producing state. In 2014, Illinois farmers produced about 550,000 bushels of soybeans over almost 10 million acres – a swath of land almost the size of Switzerland!  But, with a global health crisis, a growing population, and a changing climate threatening our land, our state’s soybean crops are under threat.  Fortunately, the Agricultural Research Service (ARS) at the US Department of Agriculture (USDA), in partnership with several universities, is trying to find ways to increase the strength, nutritional value, and viability of our most valuable crops, including soybeans, so that they continue to prosper well into the future.

This week, we interviewed Dr. Carol Fox, a plant geneticist and postdoctoral fellow at North Carolina State University in Raleigh, North Carolina. As a postdoc at NC State, she works with the USDA ARS to find ways to improve soybean yields using genetic techniques.  We interviewed Carol to learn more about the important and exciting work she does both in the lab and in the soybean fields.

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Dried soybeans.  Click on this picture to learn more about soybeans!

What influenced you to become a soybean scientist? How did your fascination with soybeans develop?

I actually grew up just outside Milwaukee, WI and had no experience with plants, except with a family that loved gardening. I studied biology at the University of Wisconsin in Madison for my undergraduate degree, and while there, I happened to take a plant genetics course. I was immediately struck by how interesting crop improvement was and switched my focus during my junior year to plant sciences. After graduating, I came to the University of Illinois at Urbana-Champaign (UIUC) in 2005 and completed my Masters degree, studying wheat. I found that I loved being in the field and contributing to our understanding of crops. With growing confidence, I then switched into soybean research and pursued my PhD.

What degrees and/or certifications do you need to do what you do? What sort of training prepared you for this job?

There are lots of cool jobs available in agriculture and these jobs require anything from an Associate’s degree to an advanced education. For me, I was interested in coming up with ideas and projects to benefit people, so I knew I wanted a leadership role as a senior scientist. For this career path, I received my PhD at UIUC in 2012 and then continued at Illinois working on a two-year postdoctoral project on soybeans before coming to North Carolina. In all, my training consisted of 7 years of graduate school after I completed my Bachelor’s degree, using a combination of coursework and hands-on graduate research to prepare me.

What does your typical work day look like?

A soybean combine harvester
A soybean combine harvester.  Click on the picture to learn more about combines!

My work day varies greatly, depending on the time of year. We are a very field-based program, and I spend a lot of time in the field with the plants. The program here grows 150 acres of soybeans each year across five locations in North Carolina – that’s about equivalent to 60 city blocks, to give you some perspective. Winter is my most ‘normal’ scientist job, where I work 8-5 and spend my time at a computer analyzing data. In the spring, we take all the findings from the past year and get the soybean seeds organized to be planted into new experiments. During the summer, I might be at a field location by 7am to take notes on how the plants are growing or to hand-pollinate flowers to make new genetic combinations of soybeans to study for the next year. In the fall, you can find me riding on a combine harvesting machine or leading a hand-harvesting crew. In between these busy times, I try to jam in as much regular research as I can and also some greenhouse work!

 

Can you tell us a little bit about the soybeans you work with?

Soybeans are pretty neat! They originated in Asia and were mainly found in China, Korea, and Japan thousands of years ago. They were first grown in Georgia in 1765 as forage for animals, but didn’t become an important agricultural crop in the United States until the 1900s. Now, soybeans are grown in 31 US states (Iowa and Illinois are the top producers!), South America, and Southeast Asia. The cultivated common soybean, Glycine max, is a bushy green plant that produces around 40-45 bushels per acre of dry soybeans (a bushel is eight gallons). The common soybean has two wild, weedy relatives, Glycine soja and Glycine tomentella, that are viney and low-yielding but have the potential to contain many beneficial genes. At the USDA soybean unit here in Raleigh, we are working on long-term and difficult projects to mine genes from the wild relative G. soja and move these genes into cultivated soybeans. Important traits we are looking to improve include protein content, yield, and drought resistance.

This is a “checkerboard” soybean field with cultivated Glycine max soybean plants alternating with wild Glycine soja plants. The cultivated crop plants are taller and bushier and the wild relative lies low to the ground and has a weedy appearance.
This is a “checkerboard” soybean field with cultivated Glycine max soybean plants alternating with wild Glycine soja plants. The cultivated crop plants are taller and bushier and the wild relative lies low to the ground and has a weedy appearance.

 

What is a yield gene? What is a drought-resistance gene? Why are these genes so elusive?

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DNA.  Click on the picture to learn more about DNA!

Genes are building blocks that dictate what an organism will be like, and every organism gets half of its genes from mom and half from dad. A yield gene is a gene that causes a soybean plant to have higher yields during the harvest. The exact causes for high yield can vary greatly and aren’t always known – the gene may actually improve water use in the plant, or cause bigger seeds to grow, or modify an enzyme that helps the plant gather light energy more efficiently. Drought resistance genes are similar, except that they act to help the plant produce a reasonable yield even when water is limiting.

As plant breeders, our main goal is to identify plants that have high yields or drought resistance (meaning they must contain good genes for these traits) and stack many of these genes together to create a better plant by using plants with these desirable traits as parents. This is difficult for many reasons. Oftentimes, the effects of a gene are very small or are caused by a number of genes acting together. Sometimes the outside growing environment makes it difficult to accurately assess the “true” performance of a plant. If it rains, you can’t measure drought resistance, and if a disease hits your field, you can’t measure yield very well. Even with as much as we know about soybean genetics, we are still struggling to learn more and continue to fill in the gaps of our knowledge.

Can you describe what “crossing soybeans” means?

 

Comparison of soybean seeds. On the far left is wild Glycine soja, which has small black seeds. The far right is cultivated Glycine max, which has large yellow seeds. In the middle is a plant that is a hybrid between the two; it is still black-seeded, but the seed is bigger. The plant stem is from Glycine soja; it is very viney, similar in shape to a morning glory.
Comparison of soybean seeds. On the far left            is wild Glycine soja, which has small                              black seeds. The far right is cultivated                       Glycine max, which has large yellow  seeds.  In the middle is a plant that is a hybrid between the two; it is  still black-seeded, but the seed is bigger. The plant stem is from Glycine soja; it is very viney, similar in shape to a morning glory.

Soybeans are naturally a self-pollinating plant. For other plant species, when a flower blooms, pollen containing the plant’s genetic material is carried from that flower to flowers on other plants with the aid of wind, bees, birds, or other animals. When pollen from one plant comes in contact with the pollen of a different plant, the genetic material within them mixes together and ultimately yields seeds that contain a unique combination of DNA from the two parent plants. The soybean plant, however, pollinates itself before its flowers open and therefore, the plant only passes on its own genetic material to its seeds – as a result, all seeds are identical to the parent plant.

As plant breeders, we want to create new and better varieties of soybeans, so we hand-pollinate, or “cross”, two different soybeans together. We are using the bumblebee’s method of genetically modifying plants! Before the flower pollinates, I take a tweezers and carefully open the mother flower and then dab on some pollen from the father plant. This allows us to do things like combine a plant with high yield and a plant with disease resistance to create a new plant with both of these traits.

What is a GMO, and are they related to what you do?

A GMO is a Genetically Modified Organism. In the broadest sense, it is an organism (any living thing) that has new combination of genes that would not have occurred in nature by itself. Humans have been genetically modifying crops for thousands of years, as we tamed wild plants and made them the plants we see today. This is the type of genetic modification that our program does – we carefully take pollen from one soybean or species of soybean and hand-pollinate it to another soybean. This allows us to mix up the DNA in a way that is unlikely to have occurred in nature.

In the biotechnology sense, a GMO is made by taking a specific section of DNA from one organism and inserting it into the DNA of a different organism. This insertion could be done in a number of ways. One of the most common ways is using bacteria (called Agrobacterium tumefaciens) that naturally insert whatever DNA they have into plants. Other options include using a gene gun to “shoot” the DNA into the plant cell randomly (the DNA is coated on the gun’s tiny bullets).  Alternatively, thanks to recent developments, there are now techniques that allow scientists more precision in inserting the DNA, which makes the process more efficient. Interestingly, scientists recently discovered that the sweet potato may be the first naturally occurring GMO, originating thousands of years ago! The cultivated sweet potato genome was found to have DNA from Agrobacterium tumefaciens, meaning that these bacteria infected the ancestor of sweet potato and helped it to develop into the delicious crop it is today.

Can you comment about your personal views on GMO regulation and GMO foods? Can GMOs be good for us? Is there anything to be afraid of?

On the farm, all breeding is a form of creating GMOs, but only recently have we been able to efficiently and more precisely incorporate new genes into a plant in a controlled manner. I personally see GMOs playing a part in a larger solution to feed our growing world population. In addition, GMOs have the potential to improve human nutrition in so many ways. What if we could take a gene from a desert plant and put it into a food crop plant so that the crop now has the ability to conserve water in a drought? What if we could create a soybean with a healthier set of oils to combat heart disease, or a peanut with reduced amounts of the peanut allergen in it? There are many ways that people could benefit from GMO crops because they open doors that aren’t accessible via traditional breeding.

Unfortunately, scientists have done a bad job at explaining what GMOs are, and many people are not getting the real facts. Right now, most GMOs on the market are aimed at making it easier for farmers to grow the crops, but I’m hoping that scientists will soon be able to release GMOs that directly and beneficially impact consumers. Genetic modification is a tool that could be used to greatly help improve the quality of food many people eat.

Why did NC State and the USDA decide to study and create GMOs together? Why isn’t this research simply funded and managed by one of these two institutions?

Many universities with agricultural programs, like NC State and UIUC, have USDA scientists co-located at the university. It’s a really great deal for both groups because they share a common research goal of improving agriculture to benefit people. The university side is often more focused on educating the next batch of scientists to tackle future problems, and the USDA side is more focused on research to develop products and new technologies. But they go hand-in-hand because both sides train graduate students, work together, and share ideas to enhance each other’s research. Public research programs can also tackle important projects that don’t always have guaranteed success or a huge financial payoff, while private companies are more cautious around these types of projects.

Do you feel that it is important for the federal government to invest in projects like this?

I think that most people would agree that companies are looking for projects that will make money and are less willing to invest in very risky, low gain projects. The federal government through the USDA is able to tackle these risks and make the results available to other programs, with the end result getting to the public. Often, public programs can work on long-term and difficult projects, like increasing genetic diversity and discovering new genes, because direct revenue is not the main goal.

Do you have any comments on the fate of farms and food availability, from a genetic perspective? What are the biggest scientific problems facing farms?

One problem that may soon be facing modern agriculture is a loss of genetic diversity. Most breeding programs have a small set of favorite lines and continually cross these lines back and forth with each other, only rarely adding in new lines. For now, companies have been successful and are continuing to pull yield gains out, but it is taking increasing amounts of work to get each bushel to increase in yield. Our program at the USDA is working to incorporate new genetic diversity into southern soybean lines, and we have a sister USDA program located at UIUC that is doing the same thing with northern soybean lines. Programs like ours sift through exotic and otherwise undesirable looking soybeans and search for gems among the pebbles. Diversity breeding programs have found valuable disease/stress resistance genes, seed protein and oil genes, and yield genes from these crummy looking soybeans and moved them into elite soybeans that could be crossed with other elite lines. This “pre-breeding” effort is critical to maintain genetic diversity in soybeans and make sure that we don’t breed ourselves into a corner and get stuck without any new genetic options to turn to.

Want to learn more?

Click here to learn more about what we use soybeans for.

Click here to learn more about the latest advancements in soybean genetics from the ARS.

Click here to learn about the ARS’ other projects.

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