Background: Wheat yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (PST) is one of the most devastating diseases of wheat worldwide. To design effective breeding strategies that maximize the potential for durable disease resistance it is important to understand the molecular basis of PST pathogenicity. In particular, the characterisation of the structure, function and evolutionary dynamics of secreted effector proteins that are detected by host immune receptors can help guide and prioritize breeding efforts. However, to date, our knowledge of the effector repertoire of cereal rust pathogens is limited. Results: We re-sequenced genomes of four PST isolates from the US and UK to identify effector candidates and relate them to their distinct virulence profiles. First, we assessed SNP frequencies between all isolates, with heterokaryotic SNPs being over tenfold more frequent (5.29 ± 2.23 SNPs/kb) than homokaryotic SNPs (0.41 ± 0.28 SNPs/kb). Next, we implemented a bioinformatics pipeline to integrate genomics, transcriptomics, and effector-focused annotations to identify and classify effector candidates in PST. RNAseq analysis highlighted transcripts encoding secreted proteins that were significantly enriched in haustoria compared to infected tissue. The expression of 22 candidate effector genes was characterised using qRT-PCR, revealing distinct temporal expression patterns during infection in wheat. Lastly, we identified proteins that displayed non-synonymous substitutions specifically between the two UK isolates PST-87/7 and PST-08/21, which differ in virulence to two wheat varieties. By focusing on polymorphic variants enriched in haustoria, we identified five polymorphic effector candidates between PST-87/7 and PST-08/21 among 2,999 secreted proteins. These allelic variants are now a priority for functional validation as virulence/avirulence effectors in the corresponding wheat varieties. Conclusions: Integration of genomics, transcriptomics, and effector-directed annotation of PST isolates has enabled us to move beyond the single isolate-directed catalogues of effector proteins and develop a framework for mining effector proteins in closely related isolates and relate these back to their defined virulence profiles. This should ultimately lead to more comprehensive understanding of the PST pathogenesis system, an important first step towards developing more effective surveillance and management strategies for one of the most devastating pathogens of wheat.

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most destructive diseases of wheat. The disease is mainly controlled by growing resistant cultivars and applying fungicides when necessary. To determine potential yield loss and fungicide response, major cultivars grown in the US Pacific Northwest and susceptible checks were tested in complete split-block design experiments. From 2002 to 2012, stripe rust caused yield losses ranging from 18% to more than 90% and from 5% to more than 50% with an average of 44% and 33% on susceptible winter and spring wheat checks, respectively. Without fungicide application, the commercially grown cultivars with various levels of stripe rust resistance could reduce potential yield losses to 2–21%, with an average of 8% for winter wheat, and to 0–27% with an average of 13% for spring wheat. Significant or insignificant effects of fungicide applications on yield increase were determined for each cultivar, and the results were used to guide stripe rust management by selecting resistant cultivars to grow and appropriately applying fungicides under different levels of stripe rust epidemic. The results should be useful for developing wheat cultivars with high durable resistance, and for improving chemical control in order to minimize yield losses and maximize profits while protecting the environment by reducing use of fungicides.

Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici, has been one of the most destructive diseases on wheat in the western USA since the late 1950s and has become increasingly important in the central and south-eastern USA since 2000. Stripe rust of barley, caused by P. striiformis f. sp. hordei, a relatively new disease, has established and caused severe damage in the south-central and western states since the pathogen was first reported in Texas in 1991. Stripe rusts of wheat and barley have been monitored by trap nurseries and by field surveys. Collections of stripe rust from wheat, barley, triticale, and grasses have been tested on a set of 20 wheat differential genotypes for identifying races of P. striiformis f. sp. tritici and a set of 12 barley differential genotypes for identifying races of P. striiformis f. sp. hordei. In total, 62 new races of P. striiformis f. sp. tritici and 22 new races of P. striiformis f. sp. hordei have been identified since 2000. Germplasm and breeding lines of wheat and barley have been tested every year under natural infection in the field and with selected races in the greenhouse. Combinations of durable high-temperature, adult-plant resistance with effective all-stage resistance should provide more effective stripe rust control and reduce the use of fungicides.

Puccinia striiformis f. sp. tritici causes stripe rust (yellow rust) of wheat and is highly variable in virulence toward wheat with race-specific resistance. During 2010, wheat stripe rust was the most widespread in the recorded history of the United States, resulting in large-scale application of fungicides and substantial yield loss. A new differential set with 18 yellow rust (Yr) single-gene lines was established and used to differentiate races of P. striiformis f. sp. tritici, which were named as race PSTv in distinction from the PST races identified in the past. An octal system was used to describe the virulence and avirulence patterns of the PSTv races. From 348 viable P. striiformis f. sp. tritici isolates recovered from a total of 381 wheat and grass stripe rust samples collected in 24 states, 41 races, named PSTv-1 to PSTv-41, were identified using the new set of 18 Yr single-gene differentials, and their equivalent PST race names were determined on the previous set of 20 wheat cultivar differentials. The frequencies and distributions of the races and their virulences were determined. The five most predominant races were PSTv-37 (34.5%), PSTv-11 (17.5%), PSTv-14 (7.2%), PSTv-36 (5.2%), and PSTv-34 (4.9%). PSTv-37 was distributed throughout the country while PSTv-11 and PSTv-14 were almost restricted to states west of the Rocky Mountains. The races had virulence to 0 to 13 of the 18 Yr genes. Frequencies of virulences toward resistance genes Yr6, Yr7, Yr8, Yr9, Yr17, Yr27, Yr43, Yr44, YrTr1, and YrExp2 were high (67.0 to 93.7%); those to Yr1 (32.8%) and YrTye (31.3%) were moderate; and those to Yr10, Yr24, Yr32, and YrSP were low (3.4 to 5.7%). All of the isolates were avirulent to Yr5 and Yr15.