The soybean is a crop that could boost biofuels and fertilize fields. So in 2010, the JGI helped publish the original genome sequence for the soybean, Glycine max. With a full genome sequence, researchers have been able to look into soybean’s strengths – along with a fungus that threatens this important crop. Hear more about that work from researchers Gary Stacey (University of Missouri), Peter van Esse (The Sainsbury Laboratory) and Sebastien Duplessis (INRAE).
Allison: And now, a JGIota – a snippet about JGI-related research, tools, people, discoveries and more. I’m Allison Joy, your host for this Iota.
Allison: For 25 years, the JGI has been supporting genomics research. In honor of this year’s 25th anniversary celebration, we’re taking a look back at all kinds of species JGI researchers have studied. And today, we’re focusing on soybeans.The soybean plant is a flagship genome of the JGI’s Plant Program, and there’s a major reason researchers study it.
Gary Stacey: There’s a huge market for soybean oil.
Allison: Gary Stacey is a professor of plant science and technology at the University of Missouri. And he knows about the soybean oil market, because he’s been studying soybeans for decades. Specifically, soybean crops. The kinds of plants that leave fields and become biodiesel.
Gary Stacey: Since it’s renewable, then it’s a green fuel. And, and of course in transportation now we’re moving to electric cars, and so on and so forth. There’s still a lot of thinking that truck fuel and airplane fuel and things like that are not going to be replaced by electricity anytime soon. And so there’s going to be a need for these biofuels. And that’s a good niche market for soybean oil.
Allison: Right now, about a third of the soybeans grown in the US become biodiesel. But with federal mandates pushing growers toward more biofuel production, that share is set to grow. And there are other environmental and energy reasons for growers to fill fields with soybeans.
Gary Stacey: Soybean has another impact on the environment from the standpoint of reducing the need for nitrogen fertilizer. About 1% of the global energy use actually goes to produce nitrogen fertilizer.
Allison: Nitrogen is an essential nutrient for all kinds of crops.But nitrogen fertilizers can be hard on the environment — they often make their way out of the field and into our waterways and beyond. We also burn natural gas to create it, using multiple finite resources. Soybean plants, on the other hand, function like a fertilizer in plant form. They pull nitrogen from the air into fields – it’s a process called nitrogen fixation. Basically, the soybean plants leave behind nutrients that other crops can use.
Gary Stacey: And so soybean then contributes to the sustainability of cropping systems.
Allison: So Gary and other researchers have been working to understand the soybean plant, to pave the way for stronger soybeans and bigger crop yields. He and collaborators published the original sequence for the soybean genome in the journal Nature in 2010, and Stacey’s work on the legume continues.
Gary Stacey: We’ve been studying the questions of interest to us, like symbiotic nitrogen fixation, but we’ve been applying the knowledge of the genome sequence to that.
Allison: With the soybean genome sequenced, researchers have also looked at another key part of getting the most out of soybean crops: keeping the plants themselves healthy. Which has brought them not just to soybeans, but to the kinds of diseases they’re prone to. To that end, the JGI has helped researchers study the most devastating soybean pathogen out there: a fungus called Phakopsora pachyrhizi that causes brown rust pustules to form on the leaves of a plant.
Peter van Esse is a group leader with The Sainsbury Laboratory in the UK. He’s part of a consortium working on this fungus.
Peter van Esse: The disease that I study can cause up to 80-90% yield loss if it’s not properly managed.
Allison: But it’s not the easiest pathogen to study, for a number of reasons. First, the sheer size of its genome. The genome is 1.25 gigabasepairs, that’s billions of basepairs, in size, compared to other fungi which are usually around 50 megabasepairs, that’s millions of basepairs— which is a significant size difference. It also contains a lot of repetition, meaning, a lot of stuff just looks the same. And so what scientists are looking for, and really interested in, gets hidden.
Also – it can’t really be grown in a lab. Here’s Sebastien Duplessis. He’s a researcher at the French National Institute for Agricultural Research or INRAE, working in the same consortium as Peter.
Sebastien Duplessis: Compared to other fungi that we can cultivate on synthetic media, in laboratory conditions, this one has to be cultivated on the host
Allison: So they collected these fungi from soybean plants – the hosts themselves. JGI annotated not one but three separate genomes for the fungus.
Peter van Esse: Now we have three isolates, annotated in exactly the same way, so there cannot be confusion about which gene is which. This is a very powerful data set and it’s gonna yield results for years to come. And we’re really, truly grateful for the JGI for enabling that to happen, because it’s really a treasure trove for the community.
Allison: And Peter says that work is already afoot with industry partners to develop resistance traits to soybean rust.
Peter van Esse: One thing I find very powerful about the JGI actually is that they do this for a lot of diseases. People should not underestimate what a key resource that has been created and, and, what a national treasure it is actually.
Allison: Shucks, man – if it were possible to make an institution blush, that would do it. Well, that’s a wrap on this JGIota, but you can learn more about the JGI’s work related to soybean on our website and Youtube channel. We’ve also got a number of highlights on our website about other discoveries the JGI has made in its 25-year tenure. There’s a link in the show notes!
This episode was written and hosted by me, Allison Joy! I had production help from Menaka Wilhelm, Massie Ballon and Ashleigh Papp.
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Genome Insider is a production of the Joint Genome Institute, a user facility of the US Department of Energy Office of Science located at Lawrence Berkeley National Lab in Berkeley, California.
Thanks for tuning in – until next time!
- JGI@25 Stories
- The original soybean sequence: Nature
- Gary Stacey presents at the 2010 JGI Annual Meeting
- Soybean on Phytozome
- Phakopsora pachyrhizi on MycoCosm
- Our contact info:
- Twitter: @JGI
- Email: jgi-comms at lbl dot gov
Genome Insider is a production of the Joint Genome Institute.