Abstract

Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is one of the most devastating disease of wheat in Ethiopia. In the past decades, many wheat varieties became out of production due to the frequent occurrence of new virulent races. In 2013, SrTmp-virulent race TKTTF caused a severe localized epidemic that resulted in devastating losses to wheat growers in the main wheat growing regions of Bale and Arsi. The current studies were carried out to determine the virulence composition and diversity of Pgt in Ethiopia after the TKTTF epidemic and to gain insight of the role of the alternate host in stem rust epidemiology. Stem rust samples were collected from major wheat-growing areas of the country and race analysis were carried out both at Ambo agricultural research center in Ethiopia and the Cereal Diseases Laboratory (CDL) Minnesota. A total of 24 Pgt races have been identified since the stem rust epidemic in 2013. Races TKTTF, TTKSK, TTTTF, JRCQC, and RRTTF were identified each year in the 2013-2018 period. The most dominant race in the past five years was TKTTF, but the frequency and area coverage of the new race TKKTF has been increasing. Races TKFTP and TTKST with virulence to Sr24 were identified in 2016 and 2017, respectively, and this virulence is significant because several major cultivars rely on Sr24 for stem rust resistance in Ethiopia. Virulence on Ug99-resistance genes such as Sr35, Sr47, Sr1RS Amigo, and Sr13b were also identified in this study. Genotypic analyses of these isolates are being carried out. Race CKGTC with low virulence to most of the wheat cultivars was identified from samples collected from wheat grown adjacent to Berberis holstii. This is likely a result of infection from aeciospores. Continuous occurrence of new virulent races and the presence of barberry plant in Ethiopia underlines the need for monitoring the pathogen population and identifying effective resistance genes that can be used in the national wheat-breeding program to control this devastating disease.

Abstract

Atmospheric transport of urediniospores is an important vector for spreading for many rust fungi. We integrated sporulation, atmospheric spore transport and infection of wheat stem rust (Puccinia graminis f. sp. tritici) into the Community Earth System Model. The model allows us to characterize how climate impacts the risks of crop damage from the disease, as well as the role that land management strategies and agricultural practices (distribution of crops, irrigation, timing of crops, crop susceptibility etc.) could play in modulating the losses.
Evaluating the model is challenging, as available data consist of voluntary reports from farmers to USDA. Not all crops are constantly monitored, so infections can stay unnoticed and not all detected infections are reported. The reports show the wheat stem rust starting in southern USA and gradually spreading northwards during spring and summer. Our model qualitatively reproduces this behavior, while showing a low level of infection in wide areas, which would not be detected and reported. The model can reasonably capture the speed of the northwards spread.
We have applied the model to quantify the impacts of changing climate to various stages in the wheat stem rust life cycle globally. Simulations were made for the modern and future (2100, RCP8.5) climate conditions. Model results indicate reduction in days with viable spore transport between Europe, Africa, Arabian Peninsula and South Asia. The number of transport days increases for eastward connections in the southern hemisphere, with the exception of South-Africa to Australia. We show conflicting impacts from raising temperatures and decreasing relative humidity – although the predicted warmer and drier climate benefits the urediniospore production and escape to free atmosphere, the same factors significantly inhibit the germination of the deposited spores.

Abstract

Wheat stem rust has been associated with crop failures throughout history. Recent increased incidence in western Europe could signify the return of this formidable foe. Accordingly, alterations in climatic conditions over the past 25 years are consistent with increasingly conducive conditions for pathogen growth and infection. We investigated whether a lack of resistance in modern European wheat varieties, increased presence of the alternate host barberry, alongside changes in climatic conditions could be brewing the perfect storm for stem rust resurgence. In 2013, we recorded wheat stem rust in the UK for the first time in over 60 years and showed that over 80% of wheat varieties were susceptible to this strain. Furthermore, the pathogens alternate host (Berberis spp.) has been increasing in popularity and increased plantings are raising concerns this could facilitate the pathogens re-establishment. In 2016, we documented stem rust for the first time in the UK in many decades on its alternate host common barberry. Since, a wider scale search in 2018 and 2019 has identified stem rust in multiple locations across the UK. Furthermore, infection assays showed that aeciospores collected from barberry at many sites are capable of infecting barley, wheat and rye. By integrating spore dispersal models and citizen science to identify barberry locations, we are developing a risk model to better guide re-planting efforts to minimize the risk new plantings could pose to escalating cereal rust diversity in the future.

Abstract

Abstract

Wheat-infecting rust fungi of the Pucciniaceae family including Puccinia striiformis f. sp. tritici (PST) and Puccinia graminis f. sp tritici (PGT) pose a significant and sustained threat to global wheat production. Previous research has shown that wheat yield losses associated with rust infection result from a reduction in the photosynthetic capacity of the plant. Additionally, it is widely understood that the chloroplasts are a hub for the synthesis of a number of pro-defence molecules including reactive oxygen species, calcium ions and salicylic acid, making them important organelles for coordinating the immune response. However, the molecular details of how chloroplast processes are manipulated during wheat infection with rust fungi remain to be elucidated. The main objective of this project is to investigate the ways in which wheat chloroplasts are targeted by rust fungi to facilitate disease progression. To this aim, RNA-sequencing carried out on PST-infected wheat tissue over an infection time-course has been used to identify a number of nuclear-encoded chloroplast genes (NECGs) with conserved expression patterns that correlate with resistance to PST. To characterise the function of these proteins in wheat during rust infection we have obtained loss-of-function mutants from a tetraploid Targeted Induced Local Lesions In Genomes (TILLING) population. Infection of these mutants with PST and PGT will enable us to determine whether these chloroplast proteins are important for infection progression. Candidate genes which show an alteration in infection severity will be taken forward for further molecular characterisation. This analysis will enable us to gain an understanding of the ways in which the chloroplasts are targeted by rust fungi during infection. This study may also help to identify novel targets for disease resistance.

Abstract

The reliance on fungicides to manage disease creates a selection pressure for the evolution of resistance in fungal and oomycete pathogens. Rust fungi (Pucciniales) are major pathogens of cereals and other crops and have been classified as low-risk organisms to develop resistance to fungicides; no cases of field failure of fungicides in a cereal rust disease has yet been recorded. Recently, the Asian soybean rust pathogen, Phakopsora pachyrhizi evolved resistance to several fungicide classes, prompting us to screen a large sample of the globally widespread wheat yellow rust pathogen, Puccinia striiformis f. sp. tritici (Pst), for mutations associated with fungicide resistance. We evaluated 363 Pst isolates collected from Europe, USA, Ethiopia, Chile, China and New Zealand for mutations in the target genes of demethylase inhibitor (DMI; Cyp51) and succinate dehydrogenase inhibitor (SDHI; SdhB, SdhC and SdhD) fungicides, the major chemical controls for wheat foliar diseases. A high proportion of Pst isolates carrying a Y134F DMI resistance-associated substitution in the Cyp51 gene was found among those from China and New Zealand. A set of geographically diverse Pst isolates were also found to display a substitution in SdhC (I85V) that is analogous to that reported recently in P. pachyrhizi and linked to SDHI resistance. The identification of these resistance-associated alleles confirms that cereal rust species are not immune to fungicide resistance and that selection for resistance evolution is operating at a high level in certain locations. It highlights the need to adopt fungicide resistance management practices and to monitor cereal rust species for development of resistance.

Abstract

Newly emerged strains of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici (Pgt), such as Ug99, are a threat to global food security. In spite of their economic importance evolutionary origin of these Pgt strains still puzzles the scientific community. Like many basidiomycetes, Pgt is a dikaryotic fungus with two haploid nuclei (karyons) during its wheat infection cycle. To better understand the genomic architecture and evolution of this pathogen we recently developed a new strategy to generate haplotype-phased genome assemblies of Pgt by coupling PacBio long reads and Hi-C data. We discovered that Ug99 shares one complete haploid genotype (haplotype) with a much older African strain, based on fully haplotype-resolved genome assemblies. The absence of recombination or chromosome reassortment in the shared haplotype indicates that Pgt Ug99 arose by a somatic hybridization and nuclear exchange event. Such nuclear exchange between dikaryotes can be an important factor in generating genetic diversity and enabling the emergence of new adapted lineages in asexual fungal populations.

Abstract

Wheat yellow (stripe) rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is an important threat to global wheat production. Ongoing work in the Saunders lab to integrate genomics-based techniques into wheat rust surveillance has generated over 1,000 RNA-Seq datasets from Pst-infected field-collected leaf samples. As part of the EU Horizon2020 RustWatch program we are creating an open access web application to allow the visualisation and exploration of transcriptomic data on a desktop computer. This will be implemented on the expression visualisation and integration platform (expVIP), developed for the wheat expression browser. This first use case of expVIP for a pathogen species demonstrates the flexibility of this platform for improving the accessibility of transcriptomic data. Users are able to visualise expression patterns for a particular gene of interest, comparing two genes or creating a heatmap of several genes, in both the host and the pathogen genomes for a large number of samples. Gene sequences can also be searched using an integrated BLAST server. This powerful resource will prove extremely valuable to the wider community of researchers working on yellow rust with the aim to expand the platform to other rust species in the future.

Abstract

Over the last decade the development of genotyping tools for Puccinia graminis f. sp. tritici has facilitated a better understanding of the phylogenetic relationship between race groups. However, the genetic variation between the haploid nuclei in this dikaryotic fungus often masks its evolutionary history. Allelic variation of genes provides a method for identification of recombination signals. As a pilot project, allelic variation of the gene encoding the Elongation Factor 1-alpha protein (Tef1) was analyzed in 59 isolates representing genetic clades I – VII. Sequencing of cloned PCR amplicons identified seven alleles and minor variants for three of these alleles. Similar results from a subset of these isolates were observed with the actin gene (Act1), which also identified seven alleles. Recently, completely phased haploid assemblies for two isolates (21-0 and Pgt-Ug99) demonstrated that the Ug99 race group (clade I) lineage was formed by somatic hybridization between an isolate of lineage “C” containing isolates of race 21-0 and a second unknown nucleus donor (Li et al. 2019). As a case study, alleles of the Tef1 and Act1 genes of the Ug99 race group (clade I) were compared to alleles found in clades II – VII. Isolates of clade I contained Tef1 A1 and B and Act1 A1 and B alleles. Isolates of lineage “C” contained Tef1 A2 and B and Act1 A2 and B alleles. The only insolates containing Tef1 A1 and Act1 A1 alleles belonged to lineage “A” (clade II) indicating that the second nucleus donor for the Ug99 race group was likely from this lineage. To test this, PCR amplicons for five additional genes were sequenced and the allelic variants determined. The data for all seven genes supported the hypothesis that the Ug99 lineage evolved through the somatic hybridization between lineages “A” and “C”. Analysis of allelic variation of genes provides a robust method for identification of recombination events and elucidating the evolutionary history of P. graminis f. sp. tritici.