The PNW’s Most Widespread and Chronic Soilborne Pathogen with Dr. Timothy Paulitz

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USDA-ARS Wheat Health, Genetics, and Quality Research
International Maize and Wheat Improvement Center (CIMMYT) in Turkey

Contact information: Dr. Timothy Paulitz,

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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.


My guest today is Dr. Timothy Paulitz. Tim is a research plant pathologist with the Wheat Health, Genetics, and Quality Research Unit since 2000. In the last decade, he has explored the soil microbiome of wheat and soil health. More specifically, he has explored how cultural, chemical, and crop rotation affect the microbiome of wheat. This includes glyphosate, tillage practices, and liming.

He has focused on the fungal pathogens Rhizoctonia, Pythium, and Fusarium, and cereal cyst and root lesion nematode. He has collaborated with Dr. Kimberly Garland-Campbell for over two decades, looking for genetic resistance to these pathogens. Hello, Tim.

Dr. Timothy Paulitz: Hi, Drew.

Drew Lyon: So, Tim, your program received $48,200 from the [Washington Grain] Commission in the current fiscal year. Can you tell us what these funds allow you to do that would not be possible without the additional support?

Dr. Timothy Paulitz: Well, this allows us to really do all this research I’m going to talk about on Fusarium crown rot. And it supports a lot of greenhouse efforts. So, it supports half of a post-doc and then also half of a technician to do all the crossing and all the screening and everything in the greenhouse and some .

And the other thing is that this money, like most of our Grain Commission funds, is heavily leveraged from other grants that we have, so we do support them with base funds, other grants, collaborations, and everything. So, it really synergizes the money that the Grain Commission gives us to do this work.

Drew Lyon: And I think that’s one of the things the Grain Commission really looks for is that leveraging and it sounds like you do a good job of leveraging those funds to get even more money to do this work. And the work really is impossible without people.

Dr. Timothy Paulitz: Right, right.

Drew Lyon: So that’s where a lot of it goes. So, how important is Fusarium crown rot in the dryland areas of the Pacific Northwest?

Dr. Timothy Paulitz: Well, I would say of all the soilborne pathogens I’ve worked on for the last almost 25 years, this is the one that is the most widespread and chronic. In other words, I can find it in conventional seeds. I can find it in direct seed areas. I can find it in high rainfall areas, low rainfall areas. I can find it just about everywhere.

And there was research done by Richard Smiley at Oregon State University in Pendleton, who had a 30-year career working on this, and he probably did the best yield work to see what the yield losses were.  He found that an average of about 9.5% in yield loss, although in some areas can be as much as 35%. And the thing about this disease is it not only reduces yield but also reduces the test weight and the quality because the seeds are smaller because of the disease, which attacks the crown and disrupts the movement of water up to the heads.

We also had another student, Grant Poole, a Ph.D. student about 15 years ago, that did an extensive survey around eastern Washington, and he could find this disease in about 97% of the fields. And it was a mixture of two different species that we have: Fusarium pseudograminearum and Fusarium culmorum. We tended to find the culmorum more in higher rainfall areas and the pseudograminearum in lower rainfall areas. But basically, it was mixtures, and we can find it everywhere. So, this is, I would say, of all the diseases probably the most widespread and chronic of all of them.

Drew Lyon: Okay, so it’s widely spread in the Pacific Northwest. Is it a problem in other parts of the world? And can you use findings from those other parts of the world to help you with how you approach it here in the Pacific Northwest?

Dr. Timothy Paulitz: Yeah, it is a big problem in Australia, also North Africa, [and the] Middle East. We have a lot of collaborations with CIMMYT in Turkey, and especially the Australians have probably advanced this field more than anybody. And part of it is because their climate and their soils are so much marginal and it takes a greater impact on them, so they’ve done a lot of genetic work.

We’ve actually looked at a lot of their research and tried to mimic their systems of screening for a disease. They found a lot of what are called QTLs, which are minor gene resistances in some of their lines in which we have found a lot of the same things. They have, in fact, developed some tolerant varieties. Their system is more–the breeding is done from the private end, so we use a lot of their lines kind of as standards to compare them to, kind of like our most resistant check. So, we’ve certainly leveraged a lot of their research.

Drew Lyon: Okay. And do they reciprocate? [Do] they come over here?

Dr. Timothy Paulitz: We visited there quite often, I’ve been to Australia probably three or four times. Richard Smiley spent a lot of time there, [as did] Jim Cook. So, there’s a long-term collaboration that goes back 40 years between Australia and the Pacific Northwest, and that’s mainly because we share a lot of the same diseases. So, not only Fusarium crown rot but Rhizoctonia, root lesion nematode, and serial cyst nematode. So yeah, we’ve done a lot of collaboration with them on those diseases.

Drew Lyon: Okay, interesting. So, how do growers try to manage this disease?

Dr. Timothy Paulitz: Well, this is the difficulty here. There really is no chemical means of controlling this disease. There has been a lot of work done with seed treatments, but I have not seen any that are very effective, mainly because you need to protect the plant for such a long period of time. And so, crop rotation might help a bit, but it doesn’t really manage it completely, and that’s because the Fusarium produces these spores in the soil that can last for many years and it’s also a residue-borne disease. So, crop rotation doesn’t seem to do it.

About the only thing that has been established–and this is work that goes back 40 years with Jim Cook–is that they realized early on that if you over-fertilize with nitrogen, you get more disease. And that’s because this disease is a water stress. It’s exacerbated by drought. And so if you give it too much nitrogen, you run out of your water supply, the plant goes into drought stress, and you tend to see more disease. So his recommendation always was to tailor your nitrogen fertilizer to match the water that you have in the soil.

So, that leaves really resistance as, I think, the most promising means of managing this disease. And that’s been the focus of our Grain Commission research for the last two or three cycles.

Drew Lyon: Okay. So how do you go about screening for resistance?

Dr. Timothy Paulitz: Well, this is another difficulty. Unlike rust, where you can see the disease on the leaf and very easily rate it, this one you have to look at browning on the lower part of the stem. But the problem is that it’s so affected by the environment–there’s a strong genotype-environment interaction (GxE). So, one thing you could do is you could screen lines in the field, but we don’t get reproducible enough disease and there’s a high level of variability that really hasn’t worked. The other thing you can do, and this is what Richard Smiley did for many years, is he actually inoculated his field plots. He developed a system where he could put an inoculum on millet seed into a Gandy box and then drill it right next to two rows in a four-row head row–where he would have paired two rows inoculated, two rows not inoculated–and he could get better disease. But then he calculated–he did a paper one time where he calculated how many site years would you need to really determine whether something was tolerant or not. And he found with spring wheat, he could do it with 24 site years. But with winter wheat, it took like 85 or 90 site years to do, so that part really wasn’t feasible either.

So that then leaves us to the greenhouse. In the greenhouse, you can control the environment very nicely whether you’re in a greenhouse or a growth chamber. But the problem is then mimicking the conditions out in the field that will give you the best disease. And through Grain Commission funding, we had two Ph.D. students who have now graduated–one was Yvonne Thompson, and she figured out that if you fertilize the wheat early on and then at the very end, give it heat stress and cut the water back, that you could get more disease. So that also helped us develop [a] screening process.

And then Nikayla Strauss, who finished up a couple of years ago, figured out a way of standardizing the inoculum and putting it around the plant.

And then she also came up with a better method of screening. So, we had this 1-to-9 rating system where you would look at the discoloration on the stem and then try to assign it a number somewhat subjectively. But then, she figured out that you could just count the number of inner nodes that were brown/browning. And of course, the more higher level of disease, the further up it would go on the stem. So, she kind of standardized that. So, I think we’ve improved that method for screening so that we can now screen through our varieties. And our primary focus has always been screening varieties that are out there already or very close to being released to see whether we can find some that have some tolerance already. And we’ve been able to identify some.

For example, Aaron Carter’s variety called Devote has a fairly high level of tolerance. It’s a soft white wheat. So, that’s one of the aspects that we’ve done.

Drew Lyon: Okay. These ratings, are they available for growers to see? Are they in the variety selection tool?

Dr. Timothy Paulitz: No, that’s kind of been our goal. And part of it is we want to make sure that they’re really reproducible from one trial to the next before we put those ratings out.

Drew Lyon: Okay. From what you described; it sounds like the ideal solution for this disease is genetic resistance. So, can you tell us about the collaboration between you, a plant pathologist, and Kim, the wheat breeder?

Dr. Timothy Paulitz: Yeah, it’s unfortunate that Kim couldn’t be here today because she would talk about all this. So, I’m going to try to wing it in kind of my understanding.

The real effort has been to try to find adapted germplasm that we can put into the breeding program. And one of them has been through the use of what are called synthetics, and these were developed by CIMMYT–which is an international NGO that we worked with for many years–and basically, what it does is it reproduces that domestication that happened 4,000 or 5,000 years ago where you cross a tetraploid, which is the triticum durum, with a diploid that has the D genome. And based on that you can get a lot of the variation that was present during that early domestication that is not present in current varieties, but yet at the same time they’re better adapted.

So, we’ve developed crosses with that and then turned out and crossed it with a number of other varieties to develop one screening population. So, that’s one population. She’s got another double-haploid population that’s been crossed with some locally adapted ones. We also have another interesting landrace from Iran that we’ve crossed with Louise and have backcrossed it a number of times to get material that’s more closely related to our adapted varieties.

And that is an interesting parent. It actually also has resistance to root lesion nematode and also Rhizoctonia. And that was a project that we had with Alison Thompson a number of years ago. So, the idea is that we get as much material as we can, keep backcrossing them, and then move them into the breeding program so that we’re not just relying on really primitive landraces. We want to get material that’s more adapted.

Drew Lyon: Okay. You mentioned Devote earlier. Do you know where that resistance comes from?

Dr. Timothy Paulitz: No, I don’t, unfortunately. And I think the more that we screen material, the more that we’ll find things that might have tolerance. And I wouldn’t call them resistance. And that’s the other problem is that even the Australians, after all the work they’ve done, I would kind of consider it’s not complete resistance like it is with a rust or something like that.

And part of the problem with this disease is that we know that resistance or tolerance is caused by lots of different minor genes doing different things. So, it’s not like we have one major gene that gives complete immunity like we do in the rust. We just have not found that and I don’t expect that we will.

Drew Lyon: Okay. So, a very widespread problem, Fusarium crown rot, with limited means of controlling it, but genetics seems to be the best way forward–and you and Kim and others are working hard to try and find that. Is that the story?

Dr. Timothy Paulitz: That’s the story.

Drew Lyon: Alright, Tim, thanks for sharing it. We’ll ask you to keep us up to date over time to see how you advance on this because it sounds like you’re fairly early on in the process. Alright, appreciate you sharing your information with us today, Tim.

Dr. Timothy Paulitz: Okay. Thanks, Drew.

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 [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.


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