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Episode transcription:
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Drew Lyon: Hello, welcome to the WSU Wheat Beat podcast. I’m your host, Drew Lyon, and I want to thank you for joining me as we explore the world of small grains production and research at Washington State University. In each episode, I speak with researchers from WSU and the USDA-ARS to provide you with insights into the latest research on wheat and barley production.
If you enjoy the WSU Wheat Beat podcast, do us a favor and subscribe on iTunes or your favorite podcast app and leave us a review so others can find the show too.
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My guests today are Dr. Camille Steber and Dr. Scott Carle. Camille is a research geneticist with the USDA-ARS Wheat Health, Genetics, and Quality Unit. She has an adjunct faculty appointment in the WSU Department of Crop and Soil Sciences in Pullman. Camille obtained her Ph.D. from the University of Chicago in molecular genetics. She did her post-doctoral work on how hormones control seed germination at the University of Toronto. She has been with the USDA-ARS for 26 years, working on seed germination and the falling numbers problem in wheat. Hello, Camille.
Dr. Camille Steber: Hello.
Drew Lyon: And Scott is a postdoctoral research associate at Washington State University in the Department of Crop and Soil Sciences. He received his Ph.D. in the Molecular Plant Sciences program, researching freezing tolerance in wheat and wheat genetics. He’s currently working with Dr. Steber to map and develop molecular markers for genes preventing low falling numbers in wheat. Hello, Scott.
Dr. Scott Carle: Hello. Great to be here.
Drew Lyon: Nice to have you. So, let’s start off with what is a falling number and why are low falling numbers a problem?
Dr. Camille Steber: The falling numbers method is the way that the wheat industry detects elevated alpha amylase enzyme levels in wheat grain. Alpha amylase is an enzyme that digests starch, and when the starch gets digested, it can lead to quality problems like cakes that sink in the middle or sticky bread that’s difficult to slice. The farmers receive a discount when the falling number is too low indicating that there is too much alpha amylase and too high a risk to end-use quality. A falling number below 300 seconds results in a discount.
Drew Lyon: Okay, so why does the plant produce alpha amylase to begin with?
Dr. Camille Steber: It’s an essential part of seed germination. So, the whole reason that wheat is good food is because it has a starchy endosperm. And we turn that into flour that makes wonderful baked goods. The seed mobilizes that into sugars that fuel seedling growth so we can plant our seeds quite deeply. When the seedling first germinates, it can’t reach the sun. It can’t do photosynthesis and provide its own fuel, so it has to mobilize that endosperm to get the energy it needs in order to clear the surface of the soil.
So, yeah, we can’t solve this problem just by knocking out all of wheat alpha amylase; we would make sick seedlings.
Drew Lyon: We wouldn’t get our wheat up in the fall, would we?
Dr. Camille Steber: No.
Drew Lyon: Okay. So, you’ve kind of explained what causes low falling numbers, but Scott, can you tell us a little bit more about why it occurs and why it’s such a problem for the wheat industry?
Dr. Scott Carle: Sure. So, there are two main causes that are affecting the wheat in the field. You’ve got LMA, late-maturity alpha amylase, and pre-harvest sprouting. In either case, it is that enzyme alpha amylase that is going to be causing the degradation in wheat quality. But susceptible varieties, when you get cool temperatures during the soft dough stage of grain filling, in that particular stage, that will induce LMA within the seed, which will cause those lower falling numbers.
Likewise, for susceptible varieties to pre-harvest sprouting, if you get rain in the field after they reach a certain point of maturation, but before harvest, that’s going to cause pre-harvest sprouting where they start germinating and that also causes degradation by alpha amylase.
Drew Lyon: Okay. And those two processes are unique? Are they basically the same?
Dr. Scott Carle: It gets a little complicated. We think they are somewhat linked, but also substantially independent.
Dr. Camille Steber: Yeah. Until recently, we really thought that they were genetically apples and oranges because none of the QTLs that had been mapped for those two things overlapped. But that’s starting to change. We’ll get back to that.
Drew Lyon: Okay. It seems like this science is–we’re learning a lot over the years. I remember interviewing, I think maybe it was Amber [Hauvermale], and I had a certain notion and I was blown out of the water because that’s a notion that was, like, two years old and totally wrong now. [laughter]
Okay. How does your work reduce farmers risk for low falling numbers? It sounds like you can’t control rain. You can’t control low temperatures at soft dough stage. So, how does this work help them?
Dr. Scott Carle: Yeah. We’ve been focusing on mapping some of the genes for tolerance to LMA and pre-harvest sprouting. So, yeah, as you said, inducing these problems in the field, it’s weather dependent and your field experiments sometimes you don’t get the weather you need. But, doing it manually in either the field or the greenhouse is a really labor-intensive process. We have ways to do it, but it’s a lot of work. And it’s just too costly to perform every year or on all the breeding lines that we really need to screen to be optimally selecting for this trait–or for the tolerance to these problems.
So, the idea is to replace most of the labor-intensive screening with molecular markers so that we’re not trying to manually screen all this material every year, which we can’t do anyway.
By making these molecular tools available to breeders, they’ll be able to screen a lot more material cheaply early on in the process, and hopefully that’ll help us get some better selection for these.
Dr. Camille Steber: So, yeah, I mean, we’ve been focusing on identifying these genes and just saying the words, “We’re going to develop molecular markers,” sounds easy, right? But, my lab has been at this for 10 years. We’ve reached the point where we have mapped these traits in multiple winter and spring wheat mapping populations. We’ve identified hundreds of genes. And that left Camille sitting there in the position of hundreds of genes [thinking], “Which ones do I focus on? What’s actually going to fix this problem?”
Drew Lyon: So, if you can identify these genes and which genes are important, you mentioned earlier, you can’t just knock them out or you won’t have a plant that can germinate and grow. So then, I guess I’m struggling with– what do you do with this knowledge about these genes that actually reduces the risk of having low falling numbers in your wheat after harvest?
Dr. Camille Steber: I think the point is that alpha amylase is the end point, the thing that’s causing the problem. But there are large networks of genes upstream of alpha amylase that control the timing of its expression and the response of the seed to the environment. It’s those genes upstream that we’re going to want to modify so that instead of having off or on, we’re instead having a rheostat and having degree of response or how long is the lag time before you respond?
But, bringing us back to the idea—so, I was in the position where we had identified hundreds of genes and I needed to figure out which genes to focus on. And that’s where Scott comes into this. Scott, what approach did you apply to the problem?
Dr. Scott Carle: So, I found that data visualization can be really helpful in sorting out confusing situations. Back when I was a graduate student, I built some tools that helped bring together data from different studies to look at them collectively, different mapping studies, so they could be put onto a single graph and directly compared.
I’ve continued to refine some of those software tools. And I brought together all the past studies that our lab has done, including one that we have just submitted for publication, along with some studies from previously published research from around the world, and brought it into one place. And it wasn’t a situation where the same markers were being found by different groups and different studies. But once you brought it all into the same framework, there were some really obvious hotspots that emerged where repeatedly different groups and repeatedly our group was landing on pretty much the same spot, which indicates that there is some variant there that is causing tolerance and susceptibility to these traits.
So, I’m in the process of tracking down what the most likely plants are to have these tolerant and susceptible variants. And we’re going to pursue the genetic causes for these.
Dr. Camille Steber: Was there any particular candidate that sprang out?
Dr. Scott Carle: We are also taking a look at the only gene mapped as an LMA-resistance gene by some Australian researchers and some pre-harvest sprouting—well, one particular pre-harvest sprouting gene that’s previously been mapped by wheat from Japan and Kansas.
Dr. Camille Steber: So, there was another really interesting example that came out of Scott’s work where we mapped an interesting gene on chromosome 1A that first we mapped it as a gene involved in LMA tolerance, and then we mapped exactly the same single nucleotide polymorphism as a gene providing pre-harvest sprouting tolerance.
So, this is exciting for me because it means that if breeders selected for that gene they could get two for one. They could select for two things at the same time. It also suggests that there may be some overlap in the regulation of the two traits. I don’t think we’re going to be able to give up screening for LMA and pre-harvest sprouting as two separate things, but I think it means that it may help us to better choose our QTLs that we’re going to chase down.
Drew Lyon: Okay. So, it sounds like you are making some progress on whittling down those hundreds of genes to the ones you really want to focus on. What’s the next step then? Do you give this information to breeders or do you still have more refining to do before you are able to do that?
Dr. Camille Steber: Well, initially, we were going to start with the low hanging fruit, but there are three genes, one for LMA and two for pre-harvest sprouting that have been cloned by other groups. The LMA gene was cloned in Australian germplasm. The two genes for pre-harvest sprouting tolerance in Japanese and European germplasm. We have found that some of our mapping in Pacific Northwest germplasm has landed on some of the same locations as hotspots. So, the first thing to do is to see if we can find specific differences in the DNA that are associated with tolerance in PNW wheat and to turn that into molecular markers that our breeders can use to reduce the risk for our farmers.
Drew Lyon: All right. Well, it sounds like progress is being made. New things are being learned almost continuously. If our listeners want to go learn more about what you’re doing, Camille, I believe you do have a lab website they can go to and see some of your work?
Dr. Camille Steber: They can go to Steberlab.org. That’s where we keep our falling numbers of the cereal variety trials.
Drew Lyon: All right. And, Scott, you’re going to continue on with this visualization work. And what else are you going to be working on.
Dr. Scott Carle: Looking at some sequence tracking down which variants are the causes so that we can get the right markers to the breeders that will help them make these selection decisions.
Drew Lyon: Excellent. Thank you both for being my guests today. It’s really exciting to see this progress. It seems like I need to have you two on every six months or so, because the advancements seem to be coming fast and furious, at least faster than I can keep track of them. So, thanks again for being my guests today.
Dr. Camille Steber: Thank you so much for inviting us.
Dr. Scott Carle: Thank you for having us. And we’ll try not to disappoint.
Drew Lyon: Excellent.
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Thanks for joining us and listening to the WSU Wheat Beat podcast. If you like what you hear don’t forget to subscribe and leave a review on iTunes or your favorite podcast app. If you have questions or topics you’d like to hear on future episodes, please email me at drew.lyon — that’s lyon@wsu.edu — (drew.lyon@wsu.edu). You can find us online at smallgrains.wsu.edu and on Facebook and Twitter [X] @WSUSmallGrains. The WSU Wheat Beat podcast is a production of CAHNRS Communications and the College of Agricultural, Human, and Natural Resource Sciences at Washington State University.
I’m Drew Lyon, we’ll see you next time.
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The views, thoughts, and opinions expressed by guests of this podcast are their own and does not imply Washington State University’s endorsement.