scholarly journals Microsatellite Analysis and Urediniospore Dispersal Simulations Support the Movement of Puccinia graminis f. sp. tritici from Southern Africa to Australia

2019 ◽  
Vol 109 (1) ◽  
pp. 133-144 ◽  
Author(s):  
Botma Visser ◽  
Marcel Meyer ◽  
Robert F. Park ◽  
Christopher A. Gilligan ◽  
Laura E. Burgin ◽  
...  

The Australian wheat stem rust (Puccinia graminis f. sp. tritici) population was shaped by the introduction of four exotic incursions into the country. It was previously hypothesized that at least two of these (races 326-1,2,3,5,6 and 194-1,2,3,5,6 first detected in 1969) had an African origin and moved across the Indian Ocean to Australia on high-altitude winds. We provide strong supportive evidence for this hypothesis by combining genetic analyses and complex atmospheric dispersion modeling. Genetic analysis of 29 Australian and South African P. graminis f. sp. tritici races using microsatellite markers confirmed the close genetic relationship between the South African and Australian populations, thereby confirming previously described phenotypic similarities. Lagrangian particle dispersion model simulations using finely resolved meteorological data showed that long distance dispersal events between southern Africa and Australia are indeed possible, albeit rare. Simulated urediniospore transmission events were most frequent from central South Africa (viable spore transmission on approximately 7% of all simulated release days) compared with other potential source regions in southern Africa. The study acts as a warning of possible future P. graminis f. sp. tritici dispersal events from southern Africa to Australia, which could include members of the Ug99 race group, emphasizing the need for continued surveillance on both continents.

2017 ◽  
Vol 107 (10) ◽  
pp. 1175-1186 ◽  
Author(s):  
M. Meyer ◽  
L. Burgin ◽  
M. C. Hort ◽  
D. P. Hodson ◽  
C. A. Gilligan

In recent years, severe wheat stem rust epidemics hit Ethiopia, sub-Saharan Africa’s largest wheat-producing country. These were caused by race TKTTF (Digalu race) of the pathogen Puccinia graminis f. sp. tritici, which, in Ethiopia, was first detected at the beginning of August 2012. We use the incursion of this new pathogen race as a case study to determine likely airborne origins of fungal spores on regional and continental scales by means of a Lagrangian particle dispersion model (LPDM). Two different techniques, LPDM simulations forward and backward in time, are compared. The effects of release altitudes in time-backward simulations and P. graminis f. sp. tritici urediniospore viability functions in time-forward simulations are analyzed. Results suggest Yemen as the most likely origin but, also, point to other possible sources in the Middle East and the East African Rift Valley. This is plausible in light of available field surveys and phylogenetic data on TKTTF isolates from Ethiopia and other countries. Independent of the case involving TKTTF, we assess long-term dispersal trends (>10 years) to obtain quantitative estimates of the risk of exotic P. graminis f. sp. tritici spore transport (of any race) into Ethiopia for different ‘what-if’ scenarios of disease outbreaks in potential source countries in different months of the wheat season.


Plant Disease ◽  
2012 ◽  
Vol 96 (4) ◽  
pp. 590-590 ◽  
Author(s):  
Z. A. Pretorius ◽  
L. J. Szabo ◽  
W. H. P. Boshoff ◽  
L. Herselman ◽  
B. Visser

Seven races have been described in the Ug99 race group of Puccinia graminis f. sp. tritici (2). Ug99-related races previously recorded in South Africa are TTKSF, TTKSP, and PTKST (4). In December 2010, severe stem rust infection of the winter wheat cv. Matlabas was observed for the first time in South Africa. Race analysis using the 20 North American (NA) stem rust differential lines and letter code system classified the race as TTKSF. In comparative infection studies in a greenhouse, cv. Matlabas seedlings were susceptible (infection type [IT] 4) to isolate UVPgt61/1 (TTKSF+) collected from Afrikaskop in the eastern Free State, whereas the cultivar was resistant (IT 1 to 2) to stem rust isolates 2013 (TTKSF), UVPgt55 (TTKSF), UVPgt59 (TTKSP), and UVPgt60 (PTKST). Isolate 2013 represents the original collection of race TTKSF in South Africa (1). In addition to the NA differentials, no variation in the IT range of seedlings of lines with Sr7a, 8b, 12, 13, 14, 16, 18, 19, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 39, 41, 42, 43, 44, Em, R, Tt2, and Satu was observed between UVPgt61/1 and UVPgt55. With the exception of cv. Matlabas, ITs of 106 South African cultivars likewise did not differentiate UVPgt61/1 and UVPgt55. Seedling IT studies were conducted at least twice. Microsatellite analysis (4) showed that all single pustule isolates established from the original Matlabas isolate formed part of the Ug99 group. When characterized with selected single nucleotide polymorphisms (SNPs), all single pustule isolates shared an identical genotype that differed from UVPgt55 (TTKSF), a foreign introduction into South Africa (1,3). SNP genotype analysis suggests that UVPgt61/1 is genetically dissimilar to UVPgt55, as is Zim1009, another TTKSF+ isolate that was collected from Birchenough in Zimbabwe. Studies are underway to determine the identity of the defeated Sr gene in Matlabas and the cultivar has been added to the South African stem rust differential set. TTKSF+ is the eighth race detected in the Ug99 group. Since no other cultivars or advanced lines were found to carry the Matlabas gene, it is unlikely that race TTKSF+ will threaten wheat production in South Africa. However, the occurrence of a new Ug99-related race emphasizes the variability within this internationally important group. References: (1) W. H. P. Boshoff et al. Plant Dis. 86:922, 2002. (2) R. F. Park et al. Euphytica 179:109, 2011. (3) B. Visser et al. Mol. Plant Pathol. 10:213, 2009. (4) B. Visser et al. Euphytica 179:119, 2011.


2020 ◽  
Author(s):  
Mariëlle Mulder ◽  
Delia Arnold ◽  
Christian Maurer ◽  
Marcus Hirtl

<p>An operational framework is developed to provide timely and frequent source term updates for volcanic emissions (ash and SO<sub>2</sub>). The procedure includes running the Lagrangian particle dispersion model FLEXPART with an initial (a priori) source term, and combining the output with observations (from satellite, ground-based, etc. sources) to obtain an a posteriori source term. This work was part of the EUNADICS-AV (eunadics-av.eu), which is a continuation of the work developed in the VAST project (vast.nilu.no). The aim is to ensuring that at certain time intervals when new observational and meteorological data is available during an event, an updated source term is provided to analysis and forecasting groups. The system is tested with the Grimsvötn eruption of 2011. Based on a source term sensitivity test, one can find the optimum between a sufficiently detailed source term and computational resources. Because satellite and radar data from different sources is available at different times, the source term is generated with the data that is available the earliest after the eruption started and data that is available later is used for evaluation.</p>


2020 ◽  
Vol 13 (11) ◽  
pp. 5277-5310
Author(s):  
Anne Tipka ◽  
Leopold Haimberger ◽  
Petra Seibert

Abstract. Flex_extract is an open-source software package to efficiently retrieve and prepare meteorological data from the European Centre for Medium-Range Weather Forecasts (ECMWF) as input for the widely used Lagrangian particle dispersion model FLEXPART and the related trajectory model FLEXTRA. ECMWF provides a variety of data sets which differ in a number of parameters (available fields, spatial and temporal resolution, forecast start times, level types etc.). Therefore, the selection of the right data for a specific application and the settings needed to obtain them are not trivial. Consequently, the data sets which can be retrieved through flex_extract by both member-state users and public users as well as their properties are explained. Flex_extract 7.1.2 is a substantially revised version with completely restructured code, mainly written in Python 3, which is introduced with all its input and output files and an explanation of the four application modes. Software dependencies and the methods for calculating the native vertical velocity η˙, the handling of flux data and the preparation of the final FLEXPART input files are documented. Considerations for applications give guidance with respect to the selection of data sets, caveats related to the land–sea mask and orography, etc. Formal software quality-assurance methods have been applied to flex_extract. A set of unit and regression tests as well as code metric data are also supplied. A short description of the installation and usage of flex_extract is provided in the Appendix. The paper points also to an online documentation which will be kept up to date with respect to future versions.


2019 ◽  
Vol 19 (7) ◽  
pp. 4193-4210 ◽  
Author(s):  
Andrew C. Martin ◽  
Gavin Cornwell ◽  
Charlotte M. Beall ◽  
Forest Cannon ◽  
Sean Reilly ◽  
...  

Abstract. Ice-nucleating particles (INPs) have been found to influence the amount, phase and efficiency of precipitation from winter storms, including atmospheric rivers. Warm INPs, those that initiate freezing at temperatures warmer than −10 ∘C, are thought to be particularly impactful because they can create primary ice in mixed-phase clouds, enhancing precipitation efficiency. The dominant sources of warm INPs during atmospheric rivers, the role of meteorology in modulating transport and injection of warm INPs into atmospheric river clouds, and the impact of warm INPs on mixed-phase cloud properties are not well-understood. In this case study, time-resolved precipitation samples were collected during an atmospheric river in northern California, USA, during winter 2016. Precipitation samples were collected at two sites, one coastal and one inland, which are separated by about 35 km. The sites are sufficiently close that air mass sources during this storm were almost identical, but the inland site was exposed to terrestrial sources of warm INPs while the coastal site was not. Warm INPs were more numerous in precipitation at the inland site by an order of magnitude. Using FLEXPART (FLEXible PARTicle dispersion model) dispersion modeling and radar-derived cloud vertical structure, we detected influence from terrestrial INP sources at the inland site but did not find clear evidence of marine warm INPs at either site. We episodically detected warm INPs from long-range-transported sources at both sites. By extending the FLEXPART modeling using a meteorological reanalysis, we demonstrate that long-range-transported warm INPs were observed only when the upper tropospheric jet provided transport to cloud tops. Using radar-derived hydrometeor classifications, we demonstrate that hydrometeors over the terrestrially influenced inland site were more likely to be in the ice phase for cloud temperatures between 0 and −10 ∘C. We thus conclude that terrestrial and long-range-transported aerosol were important sources of warm INPs during this atmospheric river. Meteorological details such as transport mechanism and cloud structure were important in determining (i) warm INP source and injection temperature and (ii) ultimately the impact of warm INPs on mixed-phase cloud properties.


Plant Disease ◽  
2000 ◽  
Vol 84 (2) ◽  
pp. 203-203 ◽  
Author(s):  
Z. A. Pretorius ◽  
R. P. Singh ◽  
W. W. Wagoire ◽  
T. S. Payne

In much of the world, resistance to stem rust in wheat, caused by Puccinia graminis f. sp. tritici, is based at least in part on the gene Sr31. During February 1999, high levels of stem rust infection were observed on entries in wheat (Triticum aestivum) grown in a nursery at Kalengyere Research Station in Uganda. Because several of the rusted entries were known to carry the 1BL-1RS chromosome translocation containing the Sr31, Lr26, and Yr9 genes for rust resistance, virulence to Sr31 was suspected. Urediniospores, collected in bulk from rusted stems of seven entries containing Sr31, were suspended in light mineral oil and sprayed on primary leaves of 7-day-old seedlings of South African wheat cv. Gamtoos (=Veery #3, pedigree: Kvz/Buho‘S’//Kal/BB). Plants were kept overnight at 19 to 21°C in a dew chamber before placement in a greenhouse at 18 to 25°C. After ≈14 days, urediniospores were collected from large, susceptible-type stem rust pustules and subsequently increased on Gamtoos, which served as a selective host for the new rust culture, designated Pgt-Ug99. Pathogenicity of Pgt-Ug99 was studied in seedling tests of available wheats containing Sr31, as well as other stem rust differential lines. All seedling tests were conducted at least three times in independent inoculations. Isolate Pgt-Ug99 was not virulent to Avocet‘S’/Yr9 (Australian line containing Sr26) or Oom Charl (South African cultivar) but was virulent to the other Sr31 testers: Alondra ‘S’, Bobwhite, Chokka, Clement, Federation/Kavkaz, Gamtoos, Grebe, Kavkaz, Letaba, Line E/Kavkaz, RL6078, and Veery ‘S’. Virulence to Sr31 (infection types [ITs] 3-3 to 3++4) was clearly contrasted by the low reactions (ITs 0; to 1) produced by UVPgt53, a South African pathotype avirulent to Sr31. According to the reactions of the differential lines, Pgt-Ug99 is avirulent to Sr21, -22, -24, -25, -26, -27, -29, -32, -33, -34, -35, -36, -39, -40, -42, and -43, Agi, and Em and virulent to Sr5, -6, -7b, -8a, -8b, -9b, -9e, -9g, -11, -15, -17, -30, -31, and -38. Virulence to the T. ventricosum-derived gene Sr38, which is linked to Lr37 and Yr17 and occurs in cultivars from Australia, the United Kingdom, and the United States, was not known previously (1). Both Pgt-Ug99 and UVPgt53 produced a continuum of ITs (; to 2+3) on Petkus rye (obtained from the USDA-ARS National Small Grains Collection, Aberdeen, ID), the original Sr31 donor source. Pgt-Ug99 did not appear more virulent than UVPgt53 on Petkus. All triticales tested, as well as oat cv. Overberg, were highly resistant to Pgt-Ug99. According to McIntosh et al. (1), Huerta-Espino mentioned a Sr31-virulent culture from Turkey, but this could not be confirmed. Should the Sr31-virulent pathotype migrate out of Uganda, it poses a major threat to wheat production in countries where the leading cultivars have resistance based on this gene. Reference: (1) R. A. McIntosh et al. 1995. Wheat Rusts: An Atlas of Resistance Genes. Kluwer Academic Publishers, Dordrecht, the Netherlands.


2019 ◽  
Vol 58 (3) ◽  
pp. 551-568 ◽  
Author(s):  
Michael T. Kiefer ◽  
Joseph J. Charney ◽  
Shiyuan Zhong ◽  
Warren E. Heilman ◽  
Xindi Bian ◽  
...  

AbstractIn this study, the Flexible Particle (FLEXPART)-WRF, a Lagrangian particle dispersion model, is employed to simulate pollutant dispersion in and near the Lehigh Gap, a gap in a prominent ridgeline in eastern Pennsylvania. FLEXPART-WRF is used to evaluate the diagnostic value of the ventilation index (VI), an index that describes the potential for smoke or other pollutants to ventilate away from a source, for indicating dispersion potential in complex terrain. Little is known about the effectiveness of the ventilation index in diagnosing dispersion potential in complex terrain. The modeling approach used in this study is to release a dense cloud of particles across a portion of the model domain and evaluate particle behavior and VI diagnostic value in areas of the domain with differing terrain characteristics. Although both horizontal and vertical dispersion are examined, the study focuses primarily on horizontal dispersion, assessed quantitatively by calculating horizontal residence time (HRT) within a 1-km-radius circle surrounding the particle release point. Analysis of HRT across the domain reveals horizontal dispersion patterns that are influenced by the ridgeline and the Lehigh Gap. Comparison of VI and HRT in different areas of the domain reveals a robust relationship windward of the ridgeline and a weak relationship leeward of the ridgeline and in the vicinity of the Lehigh Gap. The results of this study suggest that VI users should consider whether they are windward or leeward of topographic features, and highlight the need for an alternative metric that better takes into account the influence of the terrain on dispersion.


Plant Disease ◽  
2013 ◽  
Vol 97 (4) ◽  
pp. 479-484 ◽  
Author(s):  
P. D. Olivera ◽  
Z. A. Pretorius ◽  
A. Badebo ◽  
Y. Jin

Triticale (×Triticosecale), an amphiploid of wheat (mainly Triticum turgidum) and cereal rye (Secale cereale), is an excellent source of resistance to wheat stem rust, caused by Puccinia graminis f. sp. tritici. A collection of 567 triticale accessions originating from 21 countries was evaluated at the seedling stage for reaction to races of P. graminis f. sp. tritici with broad virulence, including TTKSK, TRTTF, and TTTTF. A high frequency (78.4%) of accessions was resistant to race TTKSK, with low infection types ranging from 0; to X. A selection of 353 TTKSK-resistant accessions was evaluated for reaction to three South African isolates of P. graminis f. sp. tritici with single and/or combined virulences to stem rust resistance genes SrSatu, Sr27, and SrKw present in triticale. Genes SrSatu, Sr27, and SrKw were postulated to be present in 141 accessions and contributed to TTKSK resistance. The remaining 212 resistant accessions may possess uncharacterized genes or combinations of known genes that could not be determined with these isolates. These accessions were further evaluated for resistance to races TTKST, TPMKC, RKQQC, RCRSC, QTHJC, QCCSM, and MCCFC. Resistance remained effective across the entire set of races in the majority of the accessions (n = 200), suggesting that the resistances are effective against a broad spectrum of virulence. In all, 129 (79.6%) resistant accessions with noncharacterized genes were resistant to moderately resistant in field stem rust nurseries at Debre Zeit (Ethiopia) and St. Paul (Minnesota). Results from evaluating F2 populations derived from resistant–susceptible crosses revealed that resistance to TTKSK in triticale was conferred mostly by single genes with dominant effects.


2017 ◽  
Vol 56 (10) ◽  
pp. 2845-2867 ◽  
Author(s):  
Derek V. Mallia ◽  
Adam Kochanski ◽  
Dien Wu ◽  
Chris Pennell ◽  
Whitney Oswald ◽  
...  

AbstractPresented here is a new dust modeling framework that uses a backward-Lagrangian particle dispersion model coupled with a dust emission model, both driven by meteorological data from the Weather Research and Forecasting (WRF) Model. This new modeling framework was tested for the spring of 2010 at multiple sites across northern Utah. Initial model results for March–April 2010 showed that the model was able to replicate the 27–28 April 2010 dust event; however, it was unable to reproduce a significant wind-blown dust event on 30 March 2010. During this event, the model significantly underestimated PM2.5 concentrations (4.7 vs 38.7 μg m−3) along the Wasatch Front. The backward-Lagrangian approach presented here allowed for the easy identification of dust source regions with misrepresented land cover and soil types, which required an update to WRF. In addition, changes were also applied to the dust emission model to better account for dust emitted from dry lake basins. These updates significantly improved dust model simulations, with the modeled PM2.5 comparing much more favorably to observations (average of 30.3 μg m−3). In addition, these updates also improved the timing of the frontal passage within WRF. The dust model was also applied in a forecasting setting, with the model able to replicate the magnitude of a large dust event, albeit with a 2-h lag. These results suggest that the dust modeling framework presented here has potential to replicate past dust events, identify source regions of dust, and be used for short-term forecasting applications.


Author(s):  
J. Moussafir ◽  
C. Olry ◽  
M. Nibart ◽  
A. Albergel ◽  
P. Armand ◽  
...  

The AIRCITY project, partly funded by the European Union, is now successfully achieved. It aimed at developing a 4D innovative numerical simulation tool dedicated to the dispersion of traffic-induced air pollution at local scale on the whole urban area of PARIS. AIRCITY modeling system is based on PMSS (Parallel-Micro-SWIFT-SPRAY) software, which has been developed by ARIA Technologies in close collaboration with CEA and MOKILI. PMSS is a simplified CFD solution which is an alternative to micro-scale simulations usually carried out with full-CFD. Yet, AIRCITY challenge was to model the flow and pollutant dispersion with a 3 m resolution over the whole city of Paris covering a 14 km × 11,5 km domain. Thus, the choice was to run a mass-consistent diagnostic flow model (SWIFT) associated with a Lagrangian Particle Dispersion Model (SPRAY) on a massively parallel architecture. With a 3 m resolution on this huge domain, parallelization was applied to the computation of both the flow (by domain splitting) and the Lagrangian dispersion (management of particles is split over several processors). This MPI parallelization is more complex but gives a large flexibility to optimize the number of CPU, the available RAM and the CPU time. So, it makes possible to process arbitrarily large domains (only limited by the memory of the available nodes). As CEA operates the largest computing center in Europe, with parallel machines ranging from a few hundred to several thousand cores, the modeling system was tested on huge parallel clusters. More usual and affordable computers with a few tens of cores were also utilized during the project by ARIA Technologies and by AIRPARIF, the Regional Air Quality Management Board of Paris region, whose role was also to build the end-users requirements. These computations were performed on a simulation domain restricted to the hypercenter of Paris with dimensions around 2 km × 2 km (at the same resolution of 3 m). The focus was on the improvements needed to adapt simulation codes initially designed for emergency response to urban air quality applications: • Coupling with the MM5 / CHIMERE operational photochemical model at AIRPARIF (as the forecast background), • Turbulence generated by traffic / coupling with traffic model, • Inclusion of chemical reactions / Interaction with background substances (especially NO / NO2). Finally, in-depth validation of the modeling system was undertaken using both the routine air quality measurements in Paris (at four stations influenced by the road traffic) and a field experiment specially arranged for the project, with LIDARs provided by LEOSPHERE Inc. Comparison of PMSS and measurements gave excellent results concerning NO / NO2 and PM10 hourly concentrations for a monthly period of time while the LIDAR campaign results were also promising. In the paper, more details are given regarding the modeling system principles and developments and its validation. Perspectives of the project will also be discussed as AIRCITY system. The TRL must now be elevated from a demonstration to a robust and systematically validated modeling tool that could be used to predict routinely the air quality in Paris and in other large cities around the world.


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