Yellow rust populations can now be freely browsed on Nextstrain interface
The wheat yellow rust fungus (Puccinia striiformis f.sp. tritici) is the first plant disease to be added to an online open source platform, Nextstrain.org. The website visualises differences in sequenced genetic information of bacterial, viral and fungal diseases to investigate how strains spread and develop. The recent addition of the yellow rust pathogen grants researchers worldwide access to study the disease and plan control strategies to protect wheat crops.
When you have a cold, you usually suspect where it came from – maybe even down the person. This might make you avoid a place, signs of symptoms in another or take extra precautions in the future to avoid falling ill again.
In a similar way, when epidemics like Ebola occur, we work out how they spread and use this to inform control strategies to prevent the disease infecting more people. By knowing how diseases move and change we can work out how to reduce the likelihood of infection or how to stop them as they spread. We often think of these strategies with human diseases but increasingly we do the same with crops too.
Nextstrain is an online platform to visualise the spread of infectious disease not just over space but also over time. This means you can watch a simulation of how a disease like Zika evolved and moved over the last 10 years. Genes of interest can be identified and the diversity of the disease population explored. This is the same for a number of widely known human diseases listed on the site.
For the first time however, a plant pathogen can tracked in the same system.
Wheat rusts and resistance.
Wheat yellow rust is a fungal pathogen that infects wheat crops around the world. Even with current control measures, rusts cause an estimated one billion dollars of damage to annual harvests. In fact, a driving part of the agricultural green revolution was Norman Borlaug’s success in breeding rust resistant wheat varieties to feed rising populations. Thanks to disease resistant crop varieties such as these, wheat supports a fifth of the calories eaten worldwide and is grown on more of Earth’s surface than any other crop.
The challenge is that yellow rust, just like any other disease, is constantly evolving and some of these changes to it’s genetic diversity allow it to overcome the resistance of the wheat varieties in the field. If a strain of yellow rust is able to do this, it can rapidly spread on the wind across fields causing great losses to harvest yields. This not only means less physical food but also higher prices of staples such as bread that hit the impoverished hardest.
Another part of the problem is that even with today’s technology, breeding new wheat varieties that are resistant to emerging rust strains takes many years. Our current main control to prevent yellow rust from devastating harvests is to apply fungicides to wheat fields. Even these fungicides however are becoming less effective at controlling the pathogen as the rust develops resistance to these precautions and increasingly, environmental or potential harmful impacts of fungicide use to humans are causing governments to ban their use.
With these pressures on our limited methods of rust control, our effective protection of global wheat crops depends upon on greater understanding of the fungal pathogen and how rust strains are spreading through farmers fields.
Nextstrain benefits for researchers and governments
Through knowing what genes are involved in a wheat plant’s susceptibility or ability to resist yellow rust, we can target resistance genes to breed into wheat varieties.
The nextstrain visual display shows a collection of isolates – separate genetically sequenced rust samples from the field. The isolated are connected by genetic groups and arranged by divergence from one another. This allows the user to explore the genetic population structures and often the host wheat variety they are associated with. From this, resistance genes can be compared and patterns in rust populations explored to inform future research.
Each isolate origin can be easily traced to its origins of the research group and even the field that the sample was taken from. Geographic distributions can be added to the site in real time meaning that the spread of rust strains across an area can be monitored.
While this movement in itself is useful to identify how rust stains are moving over space, the speed of this interface means information can appear online in as little as a month after being sampled. Previously these same kinds of information might only be released in research publications or through connections to specific researcher who are willing to share their data.
This swift turn around can show local to regional pathogen movement within growing season and inform government control strategies before major outbreaks can develop. When viewed over a wider period, more general movement of the rust strains can be observed which provide evidence for policy around protection measures.
Perhaps overlooked but integral to this there is a power in this data appearing online in a format that any research with internet connection can access. Traditionally this kind of information would kept locally on the computers of the researchers who are conducting the research and published in journals that are often kept behind paywalls. Publishing the information on platforms such as Nextstrain means that researchers from labs of any resource size are able to access and interpret the data.
This is important as wheat breeders across the world are constantly improving their lines protect and raise harvests. Tools like this new addition to Nextstrain mean that breeders can be more informed in the resistance they are breeding into new wheat varieties which ultimately will benefit the farmers. Keeping these tools publicly accessible means the potential benefits of this world leading research is not limited to those who can pay.
Finally, a single central hub for yellow rust strain databases means that in order to appear on the system, the data is uniformly annotated. The challenge of separate instances of data collection leads to data that records similar information but arranged and notated differently. By having a single uniform system, the information on Nextstrain is readily available for researchers to analyse and interpret without the need to spend time reorganising data. This saves both time and the chance of mistakes in later analysis.
Short savings in time might seem trivial but when it comes to disease control, this can make a great difference. The faster we can get obtain and interpret the data, the sooner we can inform control strategies. The sooner we can apply informed control, the lower the likelihood and effects of a largescale epidemic.