Stem Rust Research with Arjun Upadhaya

Photo credit: USDA-ARS.

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For questions or comments, contact Arjun via email at

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Episode Transcription:

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.

[ Music ]

Drew Lyon: My guest today is Arjun Upadhaya. Arjun is a Ph.D. student in the Department of Crop and Soil Sciences at WSU. He is originally from Nepal and is born into a small farming family. He came to the United States to fulfill his dream of higher education. He received his master’s degree in plant pathology from North Dakota State University. Arjun’s Ph.D. advisor is Dr. Robert Brueggeman, the barley breeder at WSU. Arjun is a geneticist, breeder, pathologist and bioinformatician by training. His Ph.D. work focuses on the stem rust disease of wheat and barley, which is a devastating disease of wheat and barley. Hello, Arjun.

Arjun Upadhaya: Thank you, Dr. Lyon.

Drew Lyon: So how did you get started working on wheat stem rust disease?

Arjun Upadhaya: So I came to WSU in August of 2019 following my advisor, Dr. Robert Brueggeman. When he took a new position of barley breeder over here at Department of Crop and Soil sciences. I think on the first week or second week of August, Bob made some field trips to Spokane region and in Davenport, which is ten miles south east of Spokane, there was a barley field which was planted with malting barley varieties Palmer and Lyon and he spotted some minor epidemics of stem rust on those fields. Later we observed a severe infection of stem rust over here at Spillman Farm, Pullman in barley nurseries as well as some class of club with nursery too. I was kind of excited. And one of the interesting things Bob mentioned is like he worked over here for ten years from 1999 to 2009 and he never saw a stem rust in the field. So I jumped into the project and at the beginning I was just working with stem rust on barley first and we got a very exciting preliminary results, meaning many of the individual stem rust isolates that we got from this region, hey were highly virulent. So I was interested to expand my results and it started to work on the wheat side, also. So that’s how I started to work on all this stem rust on both cereal crops.

Drew Lyon: Okay. So describe for us what wheat stem rust disease is and why it’s important.

Arjun Upadhaya: Wheat stem rust is a fungal disease of both barley and wheat. And barley and wheat they are to measure a cereal host in agriculture ecosystem. Generally, the infection of stem rust occurs late in the earnings season and within a week of infection, reddish-brown colored pustules, they appear at the site of infection. And the stem rust disease appear on can appear on any of the above ground parts whether you have a green soft tissues like the stem, lips, head anywhere and eventually at the end of the growing season, those rediscovered pustules, they turn into black color. And at the time of the harvest, you can see black color stems, which are broken, and you will have the grains which are stripped out. So these are the general signs and symptoms of stem rust.

Drew Lyon: Okay. So it really can affect the entire aboveground plant.

Arjun Upadhaya: Absolutely.

Drew Lyon: Okay. So not just the stem?

Arjun Upadhaya: No.

Drew Lyon: All right. Can you please tell us about your work on this disease? What what have you been doing?

Arjun Upadhaya: So I collected around 200 stem rust isolates from barley, wheat, mahonia, and berberis also. And the first thing I did was I said on barley lines, I mean, there are fiber stems in barley, which are the major one. And I did the good notes experiment to see what is the virulence level of these pathogens on barley lines, right. And we found that some of the isolates, they were virulent on almost all known pathogens. After that, I started to screen a 500 barley lines from all white collection, which includes which are the representative lamps throughout the world. And after that, we found some of the lines which carry a new source of resistance over there. On the wheat side, there are 20 rust resistant’s which are the standard one. So I screened all of my isolates, around 100 isolates, on those 20 roster assistance genes on wheat, and we found that there are many lines which are virulent and many of those are rust resistant. In the field what we did last year was we knew what isolates are more virulent on barley and what isolates are more virulent on wheat. So we made a cocktail of both isolates, which are brilliant on barley and wheat and did adult plant resistant is skinning on the field condition Unfortunately for the wheat, whatever breeding lines we have from WSU, none of them were effective.

Drew Lyon: Uh oh, that’s not good.

Arjun Upadhaya: Yeah. Against the against this population. But the good news is there are some barley lines from the Oregon Breeding Program that were effective. On the wheat side, Dr. Kim Campbell she provided her breeding lines, Club wheat breeding lines. And we did the same thing for Club wheat also.

Drew Lyon: Okay. And what did you find there?

Arjun Upadhaya: On Club Wheat. I mean, there were like a very good number of lines with scattered resistance, so compared to barley, I mean, it was good and Club wheat, I mean there were susceptible to, but it was not too bad.

Drew Lyon: Okay. You mentioned berberis earlier. Can you describe kind of how how stem rust is dependent on berberis, I guess?

Arjun Upadhaya: So the stem rust lifecycle is a very complicated life cycle. If you think our life is complicated, you have to look at stem rust. It’s very complicated. So it has a ascospores poristus, right. There is ascospores like what we see on the field on barley and wheat that is asexual ascospores which is rooted in the spore. But in order to complete its sexual life, it has to jump into another host, like a barbary or mahonia plant. And the mahonia plant that we have widely distributed over here, I believe that the ascospores I mean, it’s known that ascospores is a sexual host. And I believe that they play a major role over here compared to barberry. And when pathogen and begins to complete its sexual life cycle, it can generate many billions of stem rust like we know about COVID variants, Delta/Unicorn. So there are so many variants, more than 100 variants, a thousand variants can be created. That is a big trouble.

Drew Lyon: Yes. I think, I forget when it was in the fifties or sixties, they they did a barberry eradication program to try and stop that sexual reproduction.

Arjun Upadhaya: Absolutely.

Drew Lyon: I think that’s gone by the wayside now. So is that why we’re seeing more stem rust perhaps in this area than we have?

Arjun Upadhaya: So we did have that Barberry Eradication Program in our region, too. But one thing I would say is like there are some isolated barberry bushes in our region, but I’m not sure if the by those isolated barberry bushes are playing a major role or the mahonia, which has been recently identified possibly as a sex soloist. And mahonia is very much abundant over here, although although all classes of mahonia are they do not sub as a host. But I have found, like many mahonia plants over here where I have seen this stem rust disease.

Drew Lyon: Okay. So what are the important findings of your research?

Arjun Upadhaya: There are three important things I would like to say over here. The first thing is, like I mentioned earlier, we have many variants. We have a lot of diversity of this pathogen in in our region. So that’s the first thing. The second thing is, considering the barley host, we have very few different isolates and we do not have any good source of resistance on barley. And we have to find a new source of resistance and deal with this population. The third thing on wheat, like I said, I screened a quantity standard of rust resistance in wheat, among them fourteen are ineffective against this population. But there are six including the ASR-6, ASR-30, ASR-24 and others which are effective against our population. So what we should do is probably use those ARS’s which are effective and try to integrate in our wheat lines if they do not carry those sources of resistance.

Drew Lyon: And can you move the source of resistance from wheat into barley, or is that not easily done?

Arjun Upadhaya: It’s doable, but it takes up more time. I mean, generally they don’t do that. But having said that, in the 1950s, when they tried to incorporate resistance and wheat, they got those from rye.

Drew Lyon: Okay.

Arjun Upadhaya: So it’s a doable.

Drew Lyon: So better to search the Barley World Collection and find something there.

Arjun Upadhaya: Absolutely. That would be more easier.

Drew Lyon: Okay. So,  stem rust is a reemerging disease of wheat and barley in Washington. In fact, around the world, it has caused major epidemics in the past in the U.S. How do you think we should move forward or fight back to avoid potential epidemics?

Arjun Upadhaya: So what I would say is we should try to do the things which are very easier to do and which can be done very quickly. So going to that, the first thing would be I would recommend, if it is possible, farmers would avoid growing susceptible cultivars, because if you grow a susceptible cultivar, then you are making a hotspot over there and then that will build up and it will affect the nearby fields also. And we know that if stem rust can travel thousands of miles and exports will still be alive. So that would be a first thing to do, avoid susceptible cultivars. The second thing would be we should do early planting, but not late planting. If you do early planting, then you are very much likely to prevent the infection at the early heading, or around heading days if you do early planting, but if you do late planting, you can catch infection at maybe around tillering or early heading days. So if you have infection at earliest days, you will have more yield loss compared to infections at latest days when there is already grain feeling. If there is this person that’s not a big problem. So we should try to prevent letting solid planting. And the third thing is as a researcher, we saw the regularly monitor the virulence of the population in this region because like I said, we have barberry, mahonia, and different types of barley’s regulated So we should know what is the virulence level in wheat and barley over here. And we sort of pass that information to a breeder and breeders to try to integrate multiple source of resistance in on the wheat, our barley and release the cultivar. How about having said that? This path evolves regularly, so you cannot sleep thinking that, okay, we have resistance in our alliance. Once the late Dr. Norman Borlaug, who is the recipient of a Nobel Peace Prize and pioneer of Green Revolution, he said that, “rust never sleeps”. So if we want to keep rust in bay, then we have to work hard, you know, to prevent epidemics in the future.

Drew Lyon: All right. Well, of a disease that’s been with us a long time and sounds like it will be for a long time in the future, requiring much vigilance on our part. Arjun, thank you very much for sharing your research with us and for being my guest today.

Arjun Upadhaya: Thank you, Dr. Lyon.

[ Music ]

Drew Lyon: 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 — ( You can find us online at and on Facebook and Twitter @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.

The views, thoughts, and opinions expressed by guests of this podcast are their own and does not imply Washington State University’s endorsement.