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Stripe rust caused by Puccnina striiformis (Pst) is an economically important disease attacking wheat all over the world. Identifying and deploying new genes for Pst resistance is an economical and long-term strategy for controlling Pst. A genome-wide association study (GWAS) using single nucleotide polymorphisms (SNPs) and functional haplotypes were used to identify loci associated with stripe rust resistance in synthetic-derived (SYN-DER) wheats in four environments. In total, 92 quantitative trait nucleotides (QTNs) distributed over 65 different loci were associated with resistance to Pst at seedling and adult plant stages. Nine additional loci were discovered by the linkage disequilibrium-based haplotype-GWAS approach. The durable rust-resistant gene Lr34/Yr18 provided resistance in all four environments, and against all the five Pst races used in this study. The analysis identified several SYN-DER accessions that carried major genes: either Yr24/Yr26 or Yr32. New loci were also identified on chr2B, chr5B, and chr7D, and 14 QTNs and three haplotypes identified on the D-genome possibly carry new alleles of the known genes contributed by the Ae. tauschii founders. We also evaluated eleven different models for genomic prediction of Pst resistance, and a prediction accuracy up to 0.85 was achieved for an adult plant resistance, however, genomic prediction for seedling resistance remained very low. A meta-analysis based on a large number of existing GWAS would enhance the identification of new genes and loci for stripe rust resistance in wheat. The genetic framework elucidated here for stripe rust resistance in SYN-DER identified the novel loci for resistance to Pst assembled in adapted genetic backgrounds.

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease of wheat (Triticum aestivum L.). The best economical technique for disease control is breeding for genetic resistance to stripe rust. To find resistance genes in landrace PI388222 from Pakistan, a segregating population was developed by a cross between PI388222 and susceptible Australian spring wheat line Avocet ‘S’. The F2:4 seeds were harvested and seeds were planted in the greenhouse of Washington State University Pullman, to grow F4:5 recombinant inbred lines (RIL). A variable set of seedling reactions were noted when a set of 136 F5 and parental lines were screened with four Puccinia striiformis f. sp. tritici races (PSTv-37, PSTv-40, PSTv-4 and PSTv-51). The great proportion of RILs showed resistant reaction displayed by the RILs was against PSTv-40, for which 85% of the RILs showed resistant reaction, while less resistance to the race PSTv-37 was detected against which the resistance was for only 49% of the RILs. The RIL population was further evaluated at two locations; Palouse Conservation Field Station (PCFS) and Mount Vernon (MV). In MV field, 76% of RILs displayed resistant reaction while 15% of RILs exhibited moderate reaction. About 53% of RILs exhibited resistant reaction to four P. tritici races that were used in glasshouse screening and they were also resistant in field environments at PCFS and MV. This study demonstrates that landrace comprises partial resistance in the range of resistant to moderately resistant lines.

Stripe (yellow) rust caused by Puccinia striiformis f. sp. tritici (Pst) is a major disease in many wheat growing regions. The objective of this study was to characterise stripe rust resistance in a common wheat landrace PI388231, originated from Sindh province of Pakistan, which confers high to moderate levels of resistance against Pst pathotypes prevalent in Pakistan. A recombinant inbred line (RIL) population was developed by crossing PI388231 with the susceptible parent Avocet ‘s’. Screening of this population with Pakistani Pst pathotype 574212 in glasshouse indicated the presence of a single gene and the locus was temporarily named YrPak. Bulked segregant analysis using the targeted genotyping-by-sequencing (tGBS) platform located YrPak on the short arm of chromosome 5B. YrPak-linked SNPs were converted into kompetitive-allele specific PCR (KASP) markers and were genotyped on the parents. Five KASP markers sunKASP_330, sunKASP_334, sunKASP_335, sunKASP_338 and sunKASP_341 that showed clear clustering between parents were tested on the entire RIL population. Markers sunKASP_338 and sunKASP_341 flanked YrPak. The markers sunKASP_338 and sunKASP_341 amplified alleles alternate to those linked with YrPak in 86% and 83% of wheat cultivars tested, respectively. This population segregated for two adult plant resistance genes in addition to YrPak. The presence of pleiotropic locus Yr46/Lr67/Sr55 was confirmed using the gene specific marker TM10_67T and the second gene remains unknown.

Wheat stem rust, a devastating disease of wheat and barley caused by the fungal pathogen Puccinia graminis f. sp. tritici, was largely eradicated in Western Europe during the mid-to-late twentieth century. However, isolated outbreaks have occurred in recent years. Here we investigate whether a lack of resistance in modern European varieties, increased presence of its alternate host barberry and changes in climatic conditions could be facilitating its resurgence. We report the first wheat stem rust occurrence in the United Kingdom in nearly 60 years, with only 20% of UK wheat varieties resistant to this strain. Climate changes over the past 25 years also suggest increasingly conducive conditions for infection. Furthermore, we document the first occurrence in decades of P. graminis on barberry in the UK . Our data illustrate that wheat stem rust does occur in the UK and, when climatic conditions are conducive, could severely harm wheat and barley production. Clare Lewis et al. report the first identification in nearly 60 years of a cultivated wheat plant infected with the fungal pathogen Puccinia graminis f.sp. tritici (wheat stem rust) in the United Kingdom. They find that only 20% of UK wheat varieties are resistant to this strain and urge growers to resume resistance breeding programs.