Analyses of large-scale population structure of pathogens enable the identification of migration patterns, diversity reservoirs or longevity of populations, the understanding of current evolutionary trajectories and the anticipation of future ones. This is particularly important for long-distance migrating fungal pathogens such as Puccinia striiformis f.sp. tritici (PST), capable of rapid spread to new regions and crop varieties. Although a range of recent PST invasions at continental scales are well documented, the worldwide population structure and the center of origin of the pathogen were still unknown. In this study, we used multilocus microsatellite genotyping to infer worldwide population structure of PST and the origin of new invasions based on 409 isolates representative of distribution of the fungus on six continents. Bayesian and multivariate clustering methods partitioned the set of multilocus genotypes into six distinct genetic groups associated with their geographical origin. Analyses of linkage disequilibrium and genotypic diversity indicated a strong regional heterogeneity in levels of recombination, with clear signatures of recombination in the Himalayan (Nepal and Pakistan) and near-Himalayan regions (China) and a predominant clonal population structure in other regions. The higher genotypic diversity, recombinant population structure and high sexual reproduction ability in the Himalayan and neighboring regions suggests this area as the putative center of origin of PST. We used clustering methods and approximate Bayesian computation (ABC) to compare different competing scenarios describing ancestral relationship among ancestral populations and more recently founded populations. Our analyses confirmed the Middle East-East Africa as the most likely source of newly spreading, high-temperature-adapted strains; Europe as the source of South American, North American and Australian populations; and Mediterranean-Central Asian populations as the origin of South African populations. Although most geographic populations are not markedly affected by recent dispersal events, this study emphasizes the influence of human activities on recent long-distance spread of the pathogen.

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Origin, migration routes and worldwide population genetic structure of the wheat yellow rust pathogen Puccinia striiformis f.sp. tritici.

We investigated whether the recent worldwide epidemics of wheat yellow rust were driven by races of few clonal lineage(s) or populations of divergent races. Race phenotyping of 887 genetically diverse Puccinia striiformis isolates sampled in 35 countries during 2009-2015, revealed that these epidemics were often driven by races from few but highly divergent genetic lineages. PstS1 was predominant in North America; PstS2 in West Asia and North Africa; and both PstS1 and PstS2 in East Africa. PstS4 was prevalent in Northern Europe on triticale; PstS5 and PstS9 were prevalent in Central Asia; whereas PstS6 was prevalent in epidemics in East Africa. PstS7, PstS8 and PstS10 represented three genetic lineages prevalent in Europe. Races from other lineages were in low frequencies. Virulence to Yr9 and Yr27 was common in epidemics in Africa and Asia, while virulence to Yr17 and Yr32 were prevalent in Europe, corresponding to widely deployed resistance genes. The highest diversity was observed in South Asian populations, where frequent recombination has been reported, and no particular race was predominant in this area. The results are discussed in light of the role of invasions in shaping pathogen population across geographical regions. The results emphasized the lack of predictability of emergence of new races with high epidemic potential, which stresses the need for additional investments in population biology and surveillance activities of pathogens on global food crops, and assessments of disease vulnerability of host varieties prior to their deployment at larger scales.

/pdf/yellow-rust-epidemics-worldwide-were-caused-by-pathogen-1exxhjs616.pdf

Yellow Rust Epidemics Worldwide Were Caused by Pathogen Races from Divergent Genetic Lineages.

Understanding of long-term virulence dynamics of pathogen populations in response to host resistance gene deployment is of major importance for disease management and evolutionary biology. We monitored the virulence dynamics of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust, over 25 years in France. Virulence dynamics was explained by estimates of area associated with resistance genes carried by farmers' cultivars. The epidemics assessed through disease severity significantly correlated with the number of P. striiformis f. sp. tritici isolates collected each year, used to describe virulence dynamics. In the south, the dominance of the Mediterranean pathotype 6E16 and the cultivation of a susceptible cultivar were associated with an epidemic from 1997 to 1999. In the north, five epidemics occurred due to successive acquisition of virulence to the resistance genes Yr7, Yr6, Yr9, Yr17, and Yr32, either by acquisition of the virulence in the previous dominant pathotype or by incursion or selection of one or two new pathotypes. Frequency of pathotypes with Vr7 and Vr6 declined with the reduction in the cultivation of corresponding Yr gene cultivars, whereas the virulence Vr9 persisted longer than the cultivation of Yr9 cultivars. Although the first pathotypes carrying Vr9 decreased, this virulence persisted in other pathotypes even in the absence of Yr9 cultivars. At the regional level, Yr9 cultivars in the north caused a shift from high Vr6 frequency to high Vr9 frequency whereas, in the central region, where Yr9 cultivars were rare, Vr6 remained prevalent.

https://apsjournals.apsnet.org/doi/pdf/10.1094/PDIS-02-11-0078

Virulence Dynamics and Regional Structuring of Puccinia striiformis f. sp. tritici in France Between 1984 and 2009

Information on the pathogen virulence profile and diversity across locations is crucial for host germplasm improvement and deployment. The rapid acquisition of virulence to host resistance by the wheat yellow/stripe rust pathogen (Puccinia striiformis f.sp. tritici: PST), makes it crucial to know about its virulence and pathotype diversity. Recent studies have shown the plausible centre of origin of the pathogen in the Himalayan region, with Pakistan being the most ancestral to all other worldwide populations. To assess the status of virulence and pathotype diversity in the Himalayan region of Pakistan, a set of 127 PST infected wheat samples from eight locations were collected, multiplied and pathotyped using a set of 36 differential lines from the world set, European and Chinese sets, and 9 Avocet Yr isolines. Virulence (Vr) was recorded to 18 out of 24 tested yellow rust resistance (Yr) genes, while a total of 53 pathotypes were detected out of 127 isolates tested. Virulence was found to the resistance genes rarely deployed in Pakistan (Vr8) or even worldwide level (Vr5), while virulence to Vilmorin 23 (Yr3+) was absent in Pakistan, which is common in Europe. None of the pathotypes was dominant across all locations, however, no clear spatial structuring was observed for the studied locations. Our results suggested a high virulence and pathotype diversity in line with the previously proposed potential role of sexual recombination in the temporal maintenance of PST in the Himalayan region of Pakistan. This information should be useful in host resistance gene improvement and deployment.

A high virulence and pathotype diversity of Puccinia striiformis f.sp. tritici at its centre of diversity, the Himalayan region of Pakistan

Wheat yield of 37 wheat varieties along with a susceptible check, Morocco, was studied under yellow rust pressure across 3 locations of North West Frontier Province (NWFP), Pakistan during 2007. Considerable high disease pressure, as revealed by yellow rust severity, was observed at all locations with the maximum (100%) at Cereal Crop Research Institute (CCRI), Nowshera. Disease severity ranged from 0% to 70% for the tested varieties while reached 100% for Morocco with S type of host response. We report the presence of sufficient variability across locations for both yield potential and yellow rust severity. Locations with maximum disease pressure had lower mean grain yield and vice versa. NIFA followed by AUP had higher mean grain yield (5533 kg ha-1 and 4292 kg ha-1, respectively) with lower maximum disease severity values (70% and 80%, respectively). CCRI had higher disease pressure (100% severity for Morocco) with lower mean grain yield (3676 kg ha-1). Bahawalpur-95, Suleman-96, Kohsar-93, Fakhre-Sarhad, Tatara, and Frontana had relatively stable severity across locations in a range of 0% to 10%. Based on overall traits, Kohsar-93, Bakhtawar-92, Saleem-2000, Fakhre-Sarhad, Tatara, and Karwan had better yield and lower yellow rust severity and is recommended for cultivation and further breeding exploitation.

https://journals.tubitak.gov.tr/agriculture/issues/tar-09-33-6/tar-33-6-2-0812-27.pdf

Variability in wheat yield under yellow rust pressure in Pakistan.

Thirty-seven winter wheat lines introduced from Oklahoma State University, along with local check were studied to assess their partial resistance level, at Hazara Agricultural Research Station (HARS), Abbottabad. Pathotypes of Puccinia striiformis West. tritici (Pst) prevalent at the site were found virulent on all of the introduced winter wheat lines. Partial resistance level was assessed through final rust severity (FRS), area under rust progress curve (AURPC) and coefficient of infection (CI). A considerably high disease pressure was observed with a maximum FRS up to 95% recorded for line F5-34. Six lines were having FRS value more than 70%, while remaining 24 lines along with local check were having FRS value less than 70%. Seventeen lines were having higher AURPC values while remaining 21 lines were having AURPC values ranging from 300 to 1100, marked to be partially resistant. Based on CI value, four lines (F5-64, F5-71, F5-15 and OK00611W) were marked as highly partially resistant, having CI value up to 20; F5-4, F5-21, F5-69, F5-78, F5-103, F5-122, F5-141, OK99212, OK00608W, Intrada and Ghaznavi, with CI value 21-40, were marked as moderately resistant; and F5-5, F5-9, F55-38, F5-70, F5-83, F5-99, F5-110, F5139, OK95616-56, OK98G508W, OK00421, OK00514 and OK00618W, with CI value 41-60, were designated to have low level of partial resistance. Line OK00611W performed better, producing maximum grain yield with an increase of 2736 kg ha -1 over the local check as well as having better level of partial resistance. Cluster analysis of the OSU introduced winter wheat lines revealed four major groups/cluster, based on partial resistance parameters and grain yield. Considerable diversity was observed for level of partial resistance of these introduced winter wheat breeding lines, which may be advanced further for manipulation in breeding or inheritance studies.

Waseem Ullah

Papers

Partial resistance to yellow rust in introduced winter wheat germplasm at north of Pakistan.