The spread of exotic and aggressive strains of a plant fungus is presenting a serious threat to wheat production in the UK, according to research published in Genome Biology. The research uses a new surveillance technique that could be applied internationally to respond to the spread of a wide variety of plant diseases.
Wheat is a critical staple and provides 20% of the calories and over 25% of the protein consumed by humans. ‘Yellow rust’ caused by the fungus Puccinia striiformis f. sp. tritici (PST) is one of the plant’s major diseases and is widespread across the major wheat-producing areas of the world. Infections lead to significant reductions in both grain quality and yield, with some rare events leading to the loss of an entire crop. New fungus strains have recently emerged that adapt to warmer temperatures, are more aggressive and have overcome many of the major defensive genes in wheat.
Lead author Diane Saunders of the John Innes Centre and The Genome Analysis Centre (TGAC), UK, said: “Increased virulence, globalization, and climate change, are all increasing the scale and frequency of emerging plant diseases, and threatening global food security.
“Our research shows that in the UK we have a newly emerging population of wheat rust fungus that could be the result of an influx of more exotic and aggressive strains that are displacing the previous population. By continuing to use these new surveillance techniques, not only can we track and respond to the ongoing threat of wheat rust, but our technology opens the door for tracking other plant pathogens, including ash dieback.”
Researchers from the John Innes Centre, The Sainsbury Laboratory, TGAC and the National Institute of Agricultural Botany sequenced genetic material from 39 PST-infected samples of wheat collected from 17 UK counties in 2013.
By comparing the fungal RNA with fungal genetic information from previously prevalent populations between 1978 and 2011, they showed that there has been a rapid and dramatic shift in the PST population that could have serious implications for wheat production in the UK.
The 2013 PST samples showed more genetic variation and diversity, reflecting an increase in the evolutionary potential in the UK pathogen population that could enhance their ability to overcome disease resistance in wheat.
Of the samples, 11 were also genetically similar to a PST strain called “Warrior”. The strain emerged in 2011 as a serious threat to European wheat production due to its virulence on an array of previously resistant wheat varieties. This indicates that a diverse PST population containing the “Warrior” strain is now prevalent across the UK.
This new diagnostic technique, called “field pathogenomics”, could be applied internationally to respond to the spread of a wide variety of plant diseases. By rapidly pinpointing a fungus’s genetic make-up from field samples, the technique is able to confirm outbreaks on particular wheat varieties and provides an efficient means of confirming whether previously resistant wheat varieties have been broken by virulent strains of the pathogen. This is in contrast to current techniques which can be lengthy, costly and are only able to sample a relatively small proportion of the fungal population.
The data collection and analysis took just a few months to produce from sample collections from the field, demonstrating the potential for the method to reduce delays and transform current disease surveillance systems. The highly detailed information that is generated could help inform disease incidence predictions and agricultural practices.
To counter the threat of wheat yellow rust, breeders have developed wheat variants that incorporate resistance genes (R-genes). Yr15 is an R-gene taken from wild emmer (Triticum dicoccoides) that provides resistance to this disease. Yet it remains difficult, due to the complex hexaploid structure of wheat DNA, to accurately identify which plants should be used in breeding schemes to ensure that the next generation of wheat will have the resistance gene.
Funded by the BBSRC, the study was led by Dr Cristobal Uauy at the John Innes Centre, and Ricardo Ramirez-Gonzalez and Dr Mario Caccamo at The Genome Analysis Centre (TGAC), as part of an international team of scientists from agri-tech Institutes.
“This is a good example of how collaboration with business and public science can lead to exciting results that can be applied to industry”, said Ricardo Ramirez-Gonzalez, lead author and PhD student at TGAC.
As the global population soars, there is a heightening pressure on agriculture to produce enough food to satisfy worldwide demand. Wheat is a major crop providing over 20% of the world's calorie and 25% of its protein intake. This vital crop’s productivity is threatened by devastating diseases such as the wheat yellow rust pathogen (Puccinia striiformis f. sp. tritici) that infects bread wheat (Triticum aestivum L.).
Named after the yellow stripes that appear on the leaves of infected plants, yellow rust results in a heavily reduced or non-existent yield. Furthermore, there has been a recent upsurge in what are known as ‘Warrior’ strains of this disease that infect wheat variants that were previously believed to have resistance.
The new research provides a new mechanism to identify whether or not a variant of wheat DNA contains this resistance gene. The team sequenced the RNA of wheat plants that were known to either be susceptible or resistant to wheat yellow rust.
By comparing the results, not only against each other, but also against existing models of bread wheat gene annotation, areas of genetic divergence were identified between the plants. These differences, known as single nucleotide polymorphisms (SNPs), were used to locate an allele (number of alternative forms of the same gene) that was very frequent in the resistant plants while rare in the susceptible plants. This indicated the chromosomal arm where Yr15is located.
Further analysis identified the resistant gene out of the wheat's three closely related genomes, supported by the bioinformatics pipeline developed for the project, PolyMarker. This tool enabled the research team to select and design a set of genome specific primers to identify the genetic position of Yr15 and identify two SNPs that strongly indicate the presence of the resistance gene. Ricardo added: “This study also shows that despite the complexity of the wheat genome, it is possible to take advantage of next-generation sequencing as an addition to existing techniques, such as Bulk Segregant Analysis.”
The identification of these genetic markers facilitates a new method to ascertain if a bread wheat variant is resistant to wheat yellow rust. By checking for the presence of these markers within wheat plants, breeders will be more informed in their selection of which individuals to incorporate in their breeding strategy. In addition to this, the process used in this study may be applied to determine the location and markers for other genes within wheat and polyploid species.
