Pst Races Research Articles

Triticale Improvement: Mining of Genes Related to Yellow Rust Resistance in Triticale Based on Transcriptome Sequencing.

Yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (Pst) is a major destructive fungal disease of small grain cereals, leading to large yield losses. The breeding of resistant varieties is an effective, sustainable way to control yellow rust. Elucidation of resistance mechanisms against yellow rust and identification of candidate genes associated with rust resistance are thus crucial. In this study, seedlings of two Triticosecale Wittmack cultivars, highly resistant Gannong No. 2 and susceptible Shida No. 1, were inoculated with Pst race CYR34. Transcriptome sequencing (RNA-seq) was then used to investigate their transcriptional responses against pathogen infection before and after the appearance of symptoms—10 and 20 days after inoculation, respectively. According to the RNA-seq data, the number of upregulated and downregulated differentially expressed genes (DEGs) in the resistant cultivar was greater than in the susceptible cultivar. A total of 2,560 DEGs commonly expressed in the two cultivars on two sampling dates were subjected to pathway analysis, which revealed that most DEGs were closely associated with defense and metabolic activities. Transcription factor enrichment analysis indicated that the expressions of NAC, WRKY, and FAR1 families were also significantly changed. Further in-depth analysis of resistance genes revealed that almost all serine/threonine-protein kinases were upregulated in the resistant cultivar. Other genes related to disease resistance, such as those encoding disease-resistance- and pathogenesis-related proteins were differentially regulated in the two cultivars. Our findings can serve as a resource for gene discovery and facilitate elucidation of the complex defense mechanisms involved in triticale resistance to Pst.

High-resolution mapping of Yr78, an adult plant resistance gene to wheat stripe rust.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is responsible for significant yield losses worldwide, which can be minimized by the deployment of Pst resistance genes. Yr78 is an adult plant partial-resistance gene that has remained effective against the post-2000 virulent Pst races. In this study, we generated a high-resolution map of Yr78 based on 6,124 segregating chromosomes. We mapped Yr78 within a 0.05-cM interval on the short arm of chromosome 6B, which corresponds to an 11.16 Mb region between TraesCS6B02G116200 and TraesCS6B02G118000 in the 'Chinese Spring' Ref Seq. v1.1 genome. This interval is likely larger because it includes the unassembled NOR-B2 region, which may have contributed to the low recombination rate detected in this region. The Yr78 candidate region includes 15 genes that were prioritized for future functional studies based on their annotated function and polymorphisms between susceptible and resistant genotypes. Using exome capture data, we identified five major haplotypes in the candidate gene region, with the H1 haplotype associated with Yr78. The H1 haplotype was not detected in tetraploid wheat (Triticum turgidum L.) but was found in ∼30% of the common wheat cultivars (Triticum aestivum L.), suggesting that the associated resistance to stripe rust may have favored the selection of this haplotype. We developed two diagnostic molecular markers for the H1 haplotype that will facilitate the deployment of Yr78 in wheat breeding programs.

A candidate effector protein PstCFEM1 contributes to virulence of stripe rust fungus and impairs wheat immunity

Common in Fungal Extracellular Membrane (CFEM) domain proteins are considered to be unique to fungi and closely related to pathogenicity. However, the Puccinia striiformis f. sp. tritici (Pst) effector containing the CFEM domain has not been reported. Here, we obtained an effector, PstCFEM1, containing a functional N-terminal signal peptide sequence and the CFEM domain from Pst race CYR31. qRT-PCR assay indicated that the transcript levels of PstCFEM1 were highly induced during the early stages of infection. Overexpression of PstCFEM1 suppressed Pst322 (an elicitor-like protein of Pst)-trigged cell death, reactive oxygen species (ROS) accumulation and callose deposition. Host-induced gene silencing (HIGS) experiments showed that knockdown of PstCFEM1 decreased the virulence of Pst, while ROS accumulation in silenced plants increased near the infection site. In addition, wheat containing the PstCFEM1-silenced construct increased resistance to multiple races of Pst. Our data suggest that PstCFEM1 suppresses wheat defense by inhibiting ROS accumulation and contributes to increased virulence of Pst.

Genome-Wide Association and Genomic Prediction for Stripe Rust Resistance in Synthetic-Derived Wheats.

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.

Mapping a stable adult-plant stripe rust resistance QTL on chromosome 6AL in Chinese wheat landrace Yibinzhuermai

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases threatening the yield and stability of wheat production in China and many other countries. Identification and utilization of new genes for durable stripe rust resistance are important for ongoing control of this disease. The objectives of this study were to identify quantitative trait loci (QTL) associated with adult-plant stripe rust resistance in the Chinese wheat landrace Yibinzhuermai (YBZR) and to provide wheat breeders with new sources of potentially durable resistance. A total of 117 recombinant inbred lines (RILs) (F5:8) derived from a cross between YBZR and highly susceptible cultivar Taichung 29 (TC29) were assessed for stripe rust severity in field experiments at Wenjiang in 2016 and 2017 and Chongzhou in 2016, 2017, 2018, and 2019 in Sichuan following inoculation with a mixture of current Pst races. The RILs were genotyped using the Wheat55K single nucleotide polymorphism (SNP) array. Three QTL were identified on chromosome arms 6AL, 5BL and 7DS. QYr.YBZR-6AL and QYr.YBZR-7DS conferred major effects in all field environments, explaining 10.6% to 14.7% and 11.5% to 21.2% of phenotypic variation, respectively. The QTL on 5BL and 7DS likely correspond to previously known QTL, whereas QYr.YBZR-6AL is probably novel. Haplotype analysis revealed that the resistance allele at QYr.YBZR-6AL was present in 2.8% of 324 Chinese wheat landraces. SNP markers closely linked with QYr.YBZR-6AL were converted to kompetitive allele-specific PCR markers and validated in the RIL population and a subset of 92 wheat cultivars. QYr.YBZR-6AL and its markers should be useful in breeding programs to improve the level and durability of stripe rust resistance.

Transcriptional repression of TaNOX10 by TaWRKY19 compromises ROS generation and enhances wheat susceptibility to stripe rust.

Reactive oxygen species (ROS) are vital for plant immunity and regulation of their production is crucial for plant health. While the mechanisms that elicit ROS production have been relatively well studied, those that repress ROS generation are less well understood. Here, via screening Brachypodium distachyon RNA interference mutants, we identified BdWRKY19 as a negative regulator of ROS generation whose knockdown confers elevated resistance to the rust fungus Puccinia brachypodii. The three wheat paralogous genes TaWRKY19 are induced during infection by virulent P. striiformis f. sp. tritici (Pst) and have partially redundant roles in resistance. The stable overexpression of TaWRKY19 in wheat increased susceptibility to an avirulent Pst race, while mutations in all three TaWRKY19 copies conferred strong resistance to Pst by enhancing host plant ROS accumulation. We show that TaWRKY19 is a transcriptional repressor that binds to a W-box element in the promoter of TaNOX10, which encodes an NADPH oxidase and is required for ROS generation and host resistance to Pst. Collectively, our findings reveal that TaWRKY19 compromises wheat resistance to the fungal pathogen and suggest TaWRKY19 as a potential target to improve wheat resistance to the commercially important wheat stripe rust fungus.

Warm wheat does not rust - how wheat resists stripe rust when temperatures rise.

Stripe rust is a destructive wheat disease that is estimated to cause 5.47 million tonnes of wheat loss per year (Beddow et al., 2015). The fungus that causes the disease, Puccinia striiformis f. sp. tritici (Pst), occurs in all wheat-growing regions of the world but causes more problems in cooler climates. One reason for this is that the fungus requires relatively low temperatures for spore germination, growth, and sporulation. But some wheat plants also have a defense mechanism against Pst that only operates under high temperatures. Two types of temperature-sensitive defense mechanisms are known: high-temperature seedling plant resistance and high-temperature adult plant resistance. When grown under high-temperature conditions, wheat varieties with such a defense mechanism are resistant against Pst. Because high-temperature resistance provides immunity to all Pst races, understanding the genetic basis of this defense mechanism might be valuable for breeding. Over the last decades, breeders have developed resistant cultivars by deploying race-specific resistance genes. Race-specific resistant cultivars have limited durability because pathogens evolve quickly. In the case of Pst, new races have overcome most of the known race-specific resistance genes (Fu et al., 2009). Therefore, breeding for non-race-specific resistance such as high-temperature resistance might be a more durable solution in the fight against stripe rust. Xiaoping Hu, Professor of Plant Pathology at Northwest Agricultural and Forestry University in Yangling, China, is trying to understand the molecular mechanisms involved in high-temperature resistance in seedlings. His research group performed transcriptomic analysis on the resistant cultivar Xiaoyan 6 that had been inoculated with Pst and grown under high temperatures. Among the differentially expressed genes, they found a gene encoding a cysteine-rich receptor-like kinase that they designated TaCRK10. In this issue of The Plant Journal, the researchers investigated the role of this gene (Wang et al., 2021). To investigate if TaCRK10 is involved in resistance to Pst, the authors performed virus-induced gene silencing (VIGS) in the Xiaoyan 6 cultivar and inoculated the TaCRK10-silenced plants with Pst. When plants started to show symptoms of stripe rust, they were divided into two groups. One group was placed under high-temperature conditions (20°C) for 24 h, whereas the other group was kept at normal temperatures (16°C). In the TaCRK10-silenced plants grown under high temperatures, there was abundant spore formation on the leaves, whereas non-silenced plants showed only limited sporulation. Under normal temperatures, control plants and silenced plants did not show differences. These results suggest that TaCRK10 is required for high-temperature seedling plant resistance to Pst in the Xiaoyan 6 cultivar. Furthermore, when they overexpressed TaCRK10 from Xiaoyan 6 in the susceptible wheat cultivar Fielder, then inoculated the overexpression lines with Pst, sporulation was much lower than in wild-type plants. Interestingly, the overexpression lines were resistant against Pst when grown at normal temperatures. Further analysis of these lines revealed expression of genes involved in the salicylic acid defense pathway as well as accumulation of reactive oxygen species (ROS), which are common signs of an immunity response. To deduce the molecular action of TaCRK10, the authors performed a yeast-two-hybrid assay using a library constructed from Pst-infected leaves of the Xiaoyan 6 cultivar grown at high temperature. They found that TaCRK10 interacted with the histone variant TaH2A.1. Because TaCRK10 contains a serine/threonine kinase-like domain, the authors wondered if TaCRK10 might phosphorylate histone TaH2A.1. To test this, the researchers produced recombinantly expressed proteins and mixed them in the presence of ATP. Using an electrophoresis technique that separates phosphorylated and non-phosphorylated proteins followed by Western blot analysis, they found that TaH2A.1 was indeed phosphorylated in the presence of TaCRK10. To find out if H2A.1 is involved in high-temperature seedling plant resistance to Pst, the authors used VIGS to silence the histone variant. Subsequent inoculation experiments showed that sporulation was higher on TaH2A.1-silenced plants at both normal and high temperatures than on non-silenced plants. Hence, TaH2A.1 appears to be involved in wheat resistance to Pst (Figure). Xiaoping Hu wants to better understand the TaCRK10-TaH2A.1 pathway by identifying the phosphorylation sites on H2A.1 on which CRK10 acts and to determine if phosphorylation of TaH2A.1 plays a role in high-temperature resistance to stripe rust in seedlings. He explains that the findings might be used to develop wheat varieties with a durable resistance against Pst. Overexpression of CRK10 from Xiaoyan 6 in the susceptible variety Fielder resulted in plants that were resistant to the pathogen grown at normal temperatures, showing that susceptible cultivars can become resistant in this way, but also that constitutive overexpression of the allele leads to resistance that is no longer dependent on temperature.

Wheat genetic loci conferring resistance to stripe rust in the face of genetically diverse races of the fungus Puccinia striiformis f. sp. tritici

Key messageAnalysis of a wheat multi-founder population identified 14 yellow rust resistance QTL. For three of the four most significant QTL, haplotype analysis indicated resistance alleles were rare in European wheat.Stripe rust, or yellow rust (YR), is a major fungal disease of wheat (Triticum aestivum) caused by Puccinia striiformis Westend f. sp. tritici (Pst). Since 2011, the historically clonal European Pst races have been superseded by the rapid incursion of genetically diverse lineages, reducing the resistance of varieties previously showing durable resistance. Identification of sources of genetic resistance to such races is a high priority for wheat breeding. Here we use a wheat eight-founder multi-parent population genotyped with a 90,000 feature single nucleotide polymorphism array to genetically map YR resistance to such new Pst races. Genetic analysis of five field trials at three UK sites identified 14 quantitative trait loci (QTL) conferring resistance. Of these, four highly significant loci were consistently identified across all test environments, located on chromosomes 1A (QYr.niab-1A.1), 2A (QYr.niab-2A.1), 2B (QYr.niab-2B.1) and 2D (QYr.niab-2D.1), together explaining ~ 50% of the phenotypic variation. Analysis of these four QTL in two-way and three-way combinations showed combinations conferred greater resistance than single QTL, and genetic markers were developed that distinguished resistant and susceptible alleles. Haplotype analysis in a collection of wheat varieties found that the haplotypes associated with YR resistance at three of these four major loci were rare (≤ 7%) in European wheat, highlighting their potential utility for future targeted improvement of disease resistance. Notably, the physical interval for QTL QYr.niab-2B.1 contained five nucleotide-binding leucine-rich repeat candidate genes with integrated BED domains, of which two corresponded to the cloned resistance genes Yr7 and Yr5/YrSp.Graphical abstract

Functional Verification of Two Genes Related to Stripe Rust Resistance in the Wheat-Leymus mollis Introgression Line M8664-3.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most widespread and destructive fungal diseases of wheat worldwide. The cultivation and growth of resistant wheat varieties are the most economical, effective, and environmental friendly methods to control stripe rust. Therefore, it is necessary to use new resistance genes to breed resistant wheat varieties. A single dominant gene temporarily designated as YrM8664-3, from a wheat-Leymus mollis introgression line M8664-3 highly resistant to Chinese predominant Pst races, is a potentially valuable source of stripe rust resistance for breeding. Herein, based on previous YrM8664-3 chromosome location results (bin 4AL13-0.59-0.66 close to 4AL12-0.43-0.59) and expression change information of candidate genes and bioinformatics analysis, several candidate genes with significantly different expression changes were then selected and verified by virus-induced gene silencing (VIGS). Two of the candidate genes temporarily designated as TaFBN [containing plastid lipid-associated proteins (PAP)_fibrillin domain in its protein] and Ta_Pes_BRCT [containing Pescadillo and breast cancer tumour suppressor protein C-terminus (BRCT) domain in its protein], produced the most significant resistance changes in the wheat-Pst interaction system after silencing. These two genes were further verified by Agrobacterium-mediated wheat genetic transformation technology. According to the identification of disease resistance, the resistance function of the candidate gene TaFBN was further verified. Then, the expression of TaFBN under hormone treatment indicated that TaFBN may be related to the salicylic acid (SA) and abscisic acid (ABA) signaling pathways. Combined with the expression of TaFBN in response to environmental stress stimulation, it can be reasonably speculated that TaFBN plays an important role in the resistance of wheat to Pst and is involved in abiotic stress pathways.

Mapping quantitative trait loci associated with stripe rust resistance from the Canadian wheat cultivar ‘AAC Innova’

Stripe rust, caused by Puccinia striiformis Westend. f.sp. tritici Erikss. (Pst), is one of the most devastating diseases of wheat (Triticum aestivum L.) globally. Exploring and utilizing new sources of resistance is essential for breeding resistant wheat cultivars. Thus, a doubled haploid population (n = 291) derived from the cross ‘AAC Innova’/‘AAC Proclaim’ was evaluated to dissect the genetics of resistance in the cultivar ‘AAC Innova’. This population was evaluated for stripe rust severity in disease nurseries at Creston, British Columbia (in 2016 and 2020), and Lethbridge, Alberta (in 2016, 2017 and 2020), and genotyped using the wheat 90 K SNP assay. A high-density genetic map was constructed which consisted of 7112 SNP markers with an average marker interval of 2.3 cM. Quantitative trait loci (QTL) mapping identified one major (QYr.lrdc-2A) and 10 minor effect (QYr.lrdc-2B.1, QYr.lrdc-2B.2, QYr.lrdc-2B.3, QYr.lrdc-2B.4, QYr.lrdc-2D, QYr.lrdc-3B, QYr.lrdc-5A, QYr.lrdc-5B, QYr.lrdc-5D and QYr.lrdc-7D) loci. The QTL QYr.lrdc-2A was consistently effective against Pst races across all environments and explained up to 33.0% of the phenotypic variation. Other QTLs were either less consistent or environment specific. ‘AAC Innova’ contributed stripe rust resistance alleles for most of the QTLs except for QYr.lrdc-2D, QYr.lrdc-5A and QYr.lrdc-7D. The QTLs identified in this study should be valuable for diversifying the sources of genetic resistance against current and new virulent races of Pst. In particular, the ‘AAC Innova’-derived QTL QYr.lrdc-2A could be a valuable source of resistance to incorporate into commercial cultivars and combine with other genes using the associated SNP markers identified in this study.

Novel stripe rust all-stage resistance loci identified in a worldwide collection of durum wheat using genome-wide association mapping.

Durumwheat [Triticum turgidum L. ssp. durum (Desf.)] production is constrained by fungal diseases including stripe rust caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst). Continuous mining of germplasm for the discovery and deployment of stripe rust resistance (Yr) genes is needed to counter the impact of this disease. In this study, we evaluated a worldwide collection of 432 durum wheat accessions to seven U.S. Pst races that carry diverse virulence and avirulence combinations on wheat Yr genes. We found that 47-82% of the durum wheat accessions were susceptible to each of the tested Pst races. A total of 32 accessions were resistant to all seven races. Genome-wide association studies (GWAS) using over 97,000 single-nucleotide polymorphism markers generated from genotyping-by-sequencingof 364 accessions identified 56 quantitative trait loci (QTL) associated with all-stage stripe rust resistance located on all 14 durum wheat chromosomes. Six of these QTL were associated with resistance to 2-4 Pst races, and none were associated with resistance to all seven races. The remaining 50 QTL were race specific. Eighteen of the 56 identified QTL had relatively large effects against at least one of the races. A map-based comparison of the discovered QTL in this study with previously published Yr genes and QTL showed that 29 were previously identified, whereas the remaining 27 QTL appeared to be novel. This study reports effective sources of stripe rust resistance to contemporary races in the United States and shows that this durum wheat collection is abundant in novel resistance loci that can be transferred into adapted durum cultivars.

A New Virulent Race of Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) on the Resistance Gene Yr5 in Turkey.

The gene Yr5 in wheat has generally been known to confer resistance to Puccinia striiformis f. sp. tritici races worldwide. However, a few reports indicated that some isolates of the stripe rust pathogen were virulent on the wheat genotypes with Yr5 in India, Australia, and China (Nagarajan 1986; Wellings and McIntosh 1990; Zhang et al. 2020). In April 2020, a stripe rust infection was observed on Triticum spelta 'Album' (TSA), the Yr5 donor, provided by Turkey Seed Gene Bank in a wheat breeding field at the experimental station of Akdeniz University in the Antalya province of Turkey. The sample was tested on the seedlings of the Yr single-gene lines in the Avocet S (AvS) background including Yr5 near-isogenic line (AvSYr5NIL), TSA, and susceptible bread wheat variety 'Morocco' according to the procedure reported by Wan et al. (2014), and found to be highly virulent on Morocco with infection type (IT) 9 and virulent on AvSYr5NIL and TSA with IT 7. To confirm this novel finding, single-pustule isolates derived from this sample were obtained from TSA and re-tested on the differentials and TSA. The Yr5-virulent isolate yielded similar infection types on these plants further verifying previous results. The single-pustule isolates were determined to be avirulent (Avr) (IT 0 to 6) on AvSYr1NIL, AvSYr8NIL, AvSYr9NIL, AvSYr10NIL, AvSYr32NIL, and AvSYr43NIL and virulent (Vr) (IT 7 to 9) on AvSYr5NIL, AvSYr6NIL, AvSYr7NIL, AvSYr17NIL, AvSYr24NIL, AvSYr27NIL, AvSYr44NIL, AvSYrSpNIL, and TSA. The isolates were identified as a new race and temporarily named TRVR20-5 based on its Avr/Vr pattern. Furthermore, to confirm the presence of Yr5, the genomic DNA of fresh leaves of AvSYr5NIL and TSA used in the virulence testing were isolated using NucleoSpin Plant II (Macherey-Nagel, Germany) according to the manufacturer's procedure. The genomic DNA samples were amplified with the primers STS-7 (5'-GTACAATTCACCTAGAGT-3') and STS-8 (5'-GCAAGTTTTCTCCCTATT-3') (Chen et al. 2003) using a thermal cycler (T-100, BioRad, USA), and the resulting PCR products were digested with DpnII and visualized on an agarose gel. AvSYr5NIL and TSA had the fragment linked to the resistance allele (308 bp) whereas AvS and Morocco had the fragment linked to the susceptible allele (181 bp). Thus, both wheat genotypes were confirmed to carry Yr5, and the new Pst race virulent to Yr5 was confirmed. To the best of our knowledge, this is the first report of a Pst race virulent to Yr5 in Turkey, where stripe rust epidemics have occured in 2 out of every 5 years with 1-5% crop losses in over 25% of the wheat growing areas (Chen 2020). In a nutshell, monitoring the Pst races virulent to Yr5 with a potential to cause devastating epidemics worldwide is crucial due to the fact that international wheat breeding programs have been using Yr5 to develop wheat cultivars with resistance to stripe rust.

Virulence characterization of Puccinia striiformis f. sp. tritici collections from six countries in 2013 to 2020

Puccinia striiformis f. sp. tritici (Pst) causes wheat stripe rust (also called yellow rust, Yr), one of the most important diseases worldwide. Characterization of virulence in Pst populations is essential for developing wheat cultivars with effective and durable resistance to control the disease. A total of 138 Pst races, including 120 races that were not previously reported, were identified from stripe rust collections made from Canada, China, Ecuador, Egypt, Italy and Mexico in 2013–2020 using a set of 18 Yr single-gene differentials. Virulence of the resistance gene Yr5 or Yr15 was not found in isolates from any of the countries, indicating their effectiveness against the Pst populations. Virulence to 16 Yr genes was detected, but the frequencies varied greatly among countries. On average, the frequencies of virulence to Yr6, Yr7, Yr9, Yr43, Yr44 and YrExp2 were high (81.7–90.6%), those to Yr1, Yr8, Yr17, Yr27, YrSP and Yr76 were moderate (34.0–56.8%), and those to Yr10, Yr24, Yr32 and YrTr1 were low or very low (0.4–18.5%). The same races detected in different countries and different races from different countries clustered into the same virulence groups, indicating Pst migration among different countries, especially between eastern Asia and the Mediterranean region. These results should be useful for breeding wheat cultivars with effective resistance to stripe rust in these countries as well as globally.

Pathogenomic analyses of Puccinia striiformis f. sp. tritici supports a close genetic relationship between South and East Africa

AbstractWheat stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), occurs in all major wheat‐growing regions worldwide and poses a constant threat to production. In South Africa, Pst first emerged in 1996 in the Western Cape and has since caused frequent epidemics with three further distinct races (pathotypes) recorded to date. Herein, we undertook detailed genomic‐based analyses of four Pst isolates that represent the four dominant Pst races in South Africa recorded between 1996 and 2005. This analysis identified a number of polymorphic genes with features of known effector proteins and provided additional support of the likely stepwise changes in virulence profile of these South African Pst isolates. Next, we carried out comparative genomic‐based analyses with 54 additional Pst isolates collected across wheat‐growing regions within South Africa between 1996 and 2017 and 58 Pst isolates from East Africa, Pakistan, the UK, and France. This revealed a close genetic relationship between Pst isolates in South Africa and a number from East Africa. Furthermore, we found the South African Pst isolates also grouped closely with isolates identified in the UK in 2013 that were specifically found on triticale, illustrating long‐distance transmission of Pst isolates either between these regions or from a common independent source area. This highlights the critical need for close monitoring of Pst. With wheat being the most planted winter cereal crop in South Africa, investment in continuous surveillance is essential to rapidly identify any future introductions that could quickly lead to rust epidemics.

Transcription factor BZR2 activates chitinase Cht20.2 transcription to confer resistance to wheat stripe rust.

The brassinosteroid pathway promotes a variety of physiological processes in plants and the brassinosteroid insensitive1-ethylmethane sulfonate suppressor (BES)/brassinazole-resistant (BZR) functions as one of its key regulators. We previously showed that the BES/BZR-type transcription factor TaBZR2 mediates the drought stress response in wheat (Triticum aestivum) by directly upregulating the transcriptional activity of glutathione S-transferase 1. However, the function of TaBZR2 in plants under biotic stresses is unknown. In this study, we found that transcript levels of TaBZR2 were upregulated in response to inoculation with wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, Pst) and treatment with flg22 or an elicitor-like protein of Pst, Pst322. Wheat lines overexpressing TaBZR2 conferred increased resistance, whereas TaBZR2-RNAi lines exhibited decreased resistance to multiple races of Pst. TaBZR2 targeted the promoter of the chitinase gene TaCht20.2, activating its transcription. Knockdown of TaCht20.2 in wheat resulted in enhanced susceptibility to Pst, indicating the positive role of TaCht20.2 in wheat resistance. Upon Pst infection in vivo, the overexpression of TaBZR2 increased total chitinase activity, whereas RNAi-mediated silencing of TaBZR2 reduced total chitinase activity. Taken together, our results suggest that TaBZR2 confers broad-spectrum resistance to the stripe rust fungus by increasing total chitinase activity in wheat.

Identification of a recessive gene YrZ15-1370 conferring adult plant resistance to stripe rust in wheat-Triticum boeoticum introgression line.

A novel recessive gene YrZ15-1370 derived from Triticum boeoticum confers adult-plant resistance to wheat stripe rust. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most damaging diseases of wheat globally and resistance is the effectively control strategy. Triticum boeoticum Boiss (T. monococcum L. ssp. aegilopoides, 2n = 2x = 14, AbAb) accession G52 confers a high level of adult-plant resistance against a mixture of the Chinese prevalent Pst races. To transfer the resistance to common wheat, a cross was made between G52 and susceptible common wheat genotype Crocus. A highly resistant wheat-T. boeoticum introgression line Z15-1370 (F5 generation) with 42 chromosomes was selected cytologically and by testing with Pst races. F1, F2, and F2:3 generations of the cross between Z15-1370 and stripe rust susceptible common wheat Mingxian169 were developed. Genetic analysis revealed that the resistance in Z15-1370 was controlled by a single recessive gene, tentatively designated YrZ15-1370. Using the bulked segregant RNA-Seq (BSR-Seq) analysis, YrZ15-1370 was mapped to chromosome 6AL and flanked by markers KASP1370-3 and KASP-1370-5 within a 4.3cM genetic interval corresponding to 1.8Mb physical region in the Chinese Spring genome, in which a number of disease resistance-related genes were annotated. YrZ15-1370 differed from previously Yr genes identified on chromosome 6A based on its position and/or origin. The YrZ15-1370 would be a valuable resource for wheat resistance improvement and the flanking markers developed here could be useful tools for marker-assisted selection (MAS) in breeding and further cloning the gene.

Disease Resistance and Genes in 146 Wheat Cultivars (Lines) from the Huang-Huai-Hai Region of China

Wheat stripe rust, powdery mildew, and Fusarium head blight (FHB) are the three most important diseases in wheat worldwide. Growing resistant cultivars is the most economic and effective method to control these diseases. To assess the disease resistance of commercial wheat cultivars and regional trial wheat lines in the Huang-Huai-Hai region of China, 146 wheat entries were inoculated with the Chinese prevalent Puccinia striiformis f. sp. tritici (Pst) races CYR32, CYR33, CYR34, and Blumeria graminis f. sp. tritici (Bgt) isolate E09 under controlled greenhouse conditions, respectively; these entries were also tested with the mixed Pst races, Bgt and FHB isolates at adult-plant stage in the field, respectively. The results showed that 108 (73.97%), 83 (56.85%), 99 (67.81%), and 22 (15.07%) entries were resistant to CYR32, CYR33, CYR34, and E09 at the seedling stage, respectively; 102 (69.86%), 24 (16.44%), and 2 (1.37%) entries were resistant to stripe rust, powdery mildew, and Fusarium head blight at the adult-plant stage, respectively. Additionally, the possible resistance gene(s) in these entries were postulated by the closely linked markers of stripe rust resistance genes Yr5, Yr9, Yr10, Yr15, Yr17, Yr18, Yr26, powdery mildew resistance gene Pm21, and Fusarium head blight resistance gene Fhb1. Combined with disease resistance and molecular markers tests, 62, nine, and three wheat entries were postulated to carry the Yr9, Yr17, Yr26 gene, respectively, and no entries contained Yr5, Yr10, Yr15, Yr18, Pm21, and Fhb1 gene. This study laid a theoretical foundation for rational utilization of these entries and gene in wheat breeding programs and disease control.

Seedling and Adult Plant Resistance in the Ethiopian Bread Wheat Landraces to Stripe Rust Disease

High yielding farmers’ bread wheat cultivars are threatened by emerging race(s) of stripe (yellow) rust caused by Puccinia striiformis f.sp. tritici (Pst) in the highlands of Ethiopia. In depletion of rust resistance in commercial cultivars, researchers often look for new sources from close relatives and landraces. The objective of this study was to determine stripe rust resistance in selected Ethiopian bread wheat landraces obtained from the Ethiopian Institute of Biodiversity (IBCE). In 2017, a total of 152 accessions were exposed to the prevailing stripe rust races in hot spot areas (Kulumsa and Meraro) in Arsi zone of Oromia region. In the second year (2018), only promising landraces (57) were evaluated both at seedling and adult plant growth stages. The seedling test was conducted in the greenhouse at Kulumsa research center using three (PstS2 (v32), (PstS11) and (PstS11 v25) Pst races. In field evaluations, terminal severity (TRS), coefficient of infection (CI), area under disease progress curve (AUDPC), disease progress rate (DPR) and head infection (HI) were considred. High disease pressure was noted with 100% severity on susceptible entries at both locations and seasons. Highly significant (P<0.001) differences were noted among the landraces for all disease parameters indicated above. Of the 152 landraces, 57(38%) exhibited lower or equal disease reaction compared to the resistant check(Enkoy) across locations. Overall, 18 accessions showed resistance to the prevailing Pst races both at seedling stage and field conditions whereas14 exhibited susceptible /intermediate reaction at seedling stage, but had lower disease reaction under field conditions. This study has identified potential sources of overall and adult plant resistance in the Ethiopian bread wheat landraces to the prevailing Pst races. The authors recommend further studies to determine the diversity and/or novelity of resistance genes in selected accessions. Future wheat improvement should focus on utilization of these genetic resources to minimize the re-current outbreak of rust diseases.

Emergence of new aggressive races of Puccinia striiformis f. sp. tritici causing yellow rust epiphytotic in Egypt

Yellow (stripe) rust, caused by Puccinia striiformis f. sp. tritici (Pst), has been consistently severe in the country during recent years. A survey data of the disease at five provinces in Egypt during 2018–2020 resulted in 42 physiologic races and revealed the emergence of six new aggressive races i.e., 151E80, 135E16, 160E173, 224E191, 238E143 and 72E8 that were first detected in Egypt in the current study. The new aggressive race 151E80 was detected in Kafr-Elsheikh in the first growing season (2018/19), while it occurred in Alexandria, Beheira and Kafr-Elsheikh in the second one (2019/20). The new aggressive races; 224E191 and 238E143 (Kafr-Elsheikh), 72E8 (Beheira) occurred during both growing seasons (2018/19 and 2019/20). Common genetic lineages of Pst races corresponding to respective yellow rust resistance genes (Yr,s) indicated that they belonging to six lineages represented by ten races. Seven of them were new, i.e., races PstS2v3, PstS2v10v24, PstS2v1v10, PstS4 (Triticale2006), PstS6, PstS12 (Hereford), and a new lineage termed as PstS19 (Egy19) first detected in the current study. The most aggressive race (with Yr1, Yr10 and Yr27 virulences) was a new lineage termed as PstS19 (new pathotype Egy19), while a new pathotype designed as PstS2v1v10 came in the second rank. Field response data revealed that among 15 Egyptian wheat cultivars tested to yellow rust, only four cultivars were moderately resistant i.e., Misr-3, Sakha-95, Giza-168 and Giza-171. Gene postulation revealed that these cultivars possessed effective resistance genes; Yr5 (Sakha-95), Yr15, Yr29 (Giza-168 and Giza-171), and Yr17 was present in Misr-3. Combination of durable resistance genes, Yr18 and Yr29 with broad-spectrum resistance genes Yr5 and Yr15 is the best available option to avoid disease epiphytotic on a large scale.

RNAi-mediated stable silencing of TaCSN5 confers broad-spectrum resistance to Puccinia striiformis f. sp. tritici.

The constitutive photomorphogenesis 9 (COP9) signalosome (CSN) is a versatile regulator of plant growth, development, and response to diverse pathogens. However, little research has been done to understand the function of those CSN genes in broad‐spectrum resistance to pathogens. In this study, we found that the transcript levels of wheat TaCSN5 were induced in response to inoculation with Puccinia striiformis f. sp. tritici (Pst) and treatment with salicylic acid (SA). Overexpression of TaCSN5 in Arabidopsis resulted in increased susceptibility to Pseudomonas syringae pv. tomato DC3000 infection accompanied by down‐regulation of AtPR1 expression. Overexpression of TaCSN5 in wheat lines significantly increased susceptibility to Pst accompanied by decreased SA accumulation, whereas TaCSN5‐RNAi wheat lines exhibited opposite trends. Moreover, we found that TaCSN5 negatively regulated TaG3NPR1 genes involved in the SA signalling pathway. In addition, TaCSN5‐RNAi lines showed increased resistance to multiple races of Pst. Taken together, we demonstrate that TaCSN5 contributes to negative regulation of wheat resistance to Pst in an SA‐dependent manner.