Race-Specific Adult-Plant Resistance in Winter Wheat to Stripe Rust and Characterization of Pathogen Virulence Patterns

The genetics of Ug99 stem rust resistance in spring wheat variety 'Linkert'

Wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt) threatens wheat production worldwide. The objective of this study was to characterize wheat stem rust resistance in 'Linkert', a variety with adult plant resistance effective to emerging wheat stem rust pathogen strain Ug99. Two doubled haploid (DH) populations and one recombinant inbred line (RIL) population were developed with 'Linkert' as a stem rust resistant parent. Hard red spring wheat variety 'Forefront' and genetic stock 'LMPG' were used as stem rust susceptible parents of the DH populations. Breeding line 'MN07098-6' was used as a susceptible parent of the RIL population. Both DH and RIL populations with their parents were evaluated both at the seedling stage and in the field against Pgt races. Genotyping data of the DH populations were generated using the wheat iSelect 90k SNP assay. The RIL population was genotyped by genotyping-by-sequencing. We found QTL consistently associated with wheat stem rust resistance on chromosome 2BS for the Linkert/Forefront DH population and the Linkert/MN07098-6 RIL population both in Ethiopia and Kenya. Additional reliable QTL were detected on chromosomes 5BL (125.91 cM) and 4AL (Sr7a) for the Linkert/LMPG population in Ethiopia and Kenya. Different QTL identified in the populations reflect the importance of examining the genetics of resistance in populations derived from adapted germplasm (Forefront and MN07098-6) in addition to a genetic stock (LMPG). The associated markers in this study could be used to track and select for the identified QTL in wheat breeding programs.

Important wheat diseases in the US and their management in the 21st century

Wheat is a crop of historical significance, as it marks the turning point of human civilization 10,000 years ago with its domestication. Due to the rapid increase in population, wheat production needs to be increased by 50% by 2050 and this growth will be mainly based on yield increases, as there is strong competition for scarce productive arable land from other sectors. This increasing demand can be further achieved using sustainable approaches including integrated disease pest management, adaption to warmer climates, less use of water resources and increased frequency of abiotic stress tolerances. Out of 200 diseases of wheat, 50 cause economic losses and are widely distributed. Each year, about 20% of wheat is lost due to diseases. Some major wheat diseases are rusts, smut, tan spot, spot blotch, fusarium head blight, common root rot, septoria blotch, powdery mildew, blast, and several viral, nematode, and bacterial diseases. These diseases badly impact the yield and cause mortality of the plants. This review focuses on important diseases of the wheat present in the United States, with comprehensive information of causal organism, economic damage, symptoms and host range, favorable conditions, and disease management strategies. Furthermore, major genetic and breeding efforts to control and manage these diseases are discussed. A detailed description of all the QTLs, genes reported and cloned for these diseases are provided in this review. This study will be of utmost importance to wheat breeding programs throughout the world to breed for resistance under changing environmental conditions.

Stem rust on barberry species in Europe: Host specificities and genetic diversity

The increased emergence of cereal stem rust in southern and western Europe, caused by the pathogen Puccinia graminis, and the prevalence of alternate (sexual) host, Berberis species, have regained attention as the sexual host may serve as source of novel pathogen variability that may pose a threat to cereal supply. The main objective of the present study was to investigate the functional role of Berberis species in the current epidemiological situation of cereal stem rust in Europe. Surveys in 11 European countries were carried out from 2018 to 2020, where aecial infections from five barberry species were collected. Phylogenetic analysis of 121 single aecial clusters of diverse origin using the elongation factor 1-α gene indicated the presence of different special forms (aka formae speciales) of P. graminis adapted to different cereal and grass species. Inoculation studies using aecial clusters from Spain, United Kingdom, and Switzerland resulted in 533 stem rust isolates sampled from wheat, barley, rye, and oat, which confirmed the presence of multiple special forms of P. graminis. Microsatellite marker analysis of a subset of 192 sexually-derived isolates recovered on wheat, barley and rye from the three populations confirmed the generation of novel genetic diversity revealed by the detection of 135 multilocus genotypes. Discriminant analysis of principal components resulted in four genetic clusters, which grouped at both local and country level. Here, we demonstrated that a variety of Berberis species may serve as functional alternate hosts for cereal stem rust fungi and highlights the increased risks that the sexual cycle may pose to cereal production in Europe, which calls for new initiatives within rust surveillance, epidemiological research and resistance breeding.

Identification and molecular mapping of YrBm for adult plan resistance to stripe rust in Chinese wheat landrace Baimangmai

A new adult plan resistance gene YrBm for potentially durable resistance to stripe rust was mapped on wheat chromosome arm 4BL in landrace Baimangmai. SSR markers closely flanking YrBm were developed and validated for use in marker-assisted selection. The wheat stripe rust pathogen Puccinia striiformis f. sp. tritici (Pst) frequently acquires new virulences and rapidly adapts to environmental stress. New virulences in Pst populations can cause previously resistant varieties to become susceptible. If those varieties were widely grown, consequent epidemics can lead to yield losses. Identification and deployment of genes for durable resistance are preferred method for disease control. The Chinese winter wheat landrace Baimangmai showed a high level of adult plant resistance (APR) to stripe rust in a germplasm evaluation trial at Langfang in Hebei province in 2006 and has continued to confer high resistance over the following 15 years in field nurseries in Hebei, Sichuan and Gansu. A recombinant inbred line population of 200 F₁₀ lines developed from a cross of Baimangmai and a susceptible genotype segregated for APR at a single locus on chromosome 4BL; the resistance allele was designated YrBm. Allelism tests of known Yr genes on chromosome 4B and unique closely flanking marker alleles Xgpw7272₁₈₉ and Xwmc652₁₆₄ among a panel of Chinese wheat varieties indicated that YrBm was located at a new locus. Moreover, those markers can be used for marker-assisted selection in breeding for stripe rust resistance.

Molecular Mapping and Analysis of an Excellent Quantitative Trait Loci Conferring Adult-Plant Resistance to Stripe Rust in Chinese Wheat Landrace Gaoxianguangtoumai

The Chinese wheat landrace "Gaoxianguangtoumai" (GX) has exhibited a high level of adult-plant resistance (APR) to stripe rust in the field for more than a decade. To reveal the genetic background for APR to stripe rust in GX, a set of 249 F_6:8 (F₆, F₇, and F₈) recombinant inbred lines (RILs) was developed from a cross between GX and the susceptible cultivar "Taichung 29." The parents and RILs were evaluated for disease severity at the adult-plant stage in the field by artificial inoculation with the currently predominant Chinese Puccinia striiformis f. sp. tritici races during three cropping seasons and genotyped using the Wheat 55K single-nucleotide polymorphism (SNP) array to construct a genetic map with 1,871 SNP markers finally. Two stable APR quantitative trait loci (QTL), QYr.GX-2AS and QYr.GX-7DS in GX, were detected on chromosomes 2AS and 7DS, which explained 15.5-27.0% and 11.5-13.5% of the total phenotypic variation, respectively. Compared with published Yr genes and QTL, QYr.GX-7DS and Yr18 may be the same, whereas QYr.GX-2AS is likely to be novel. Haplotype analysis revealed that QYr.GX-2AS is likely to be rare which presents in 5.3% of the 325 surveyed Chinese wheat landraces. By analyzing a heterogeneous inbred family (HIF) population from a residual heterozygous plant in an F₈ generation of RIL, QYr.GX-2AS was further flanked by KP2A_36.85 and KP2A_38.22 with a physical distance of about 1.37Mb and co-segregated with the KP2A_37.09. Furthermore, three tightly linked Kompetitive allele-specific PCR (KASP) markers were highly polymorphic among 109 Chinese wheat cultivars. The results of this study can be used in wheat breeding for improving resistance to stripe rust.

Genome-wide association analysis of Mexican bread wheat landraces for resistance to yellow and stem rust

Deploying under-utilized landraces in wheat breeding has been advocated to accelerate genetic gains in current era of genomics assisted breeding. Mexican bread wheat landraces (Creole wheats) represent an important resource for the discovery of novel alleles including disease resistance. A core set of 1,098 Mexican landraces was subjected to multi-location testing for rust diseases in India, Mexico and Kenya. The landrace core set showed a continuous variation for yellow (YR) and stem rust (SR) disease severity. Principal component analysis differentiated Mexican landraces into three groups based on their respective collection sites. Linkage disequilibrium (LD) decay varied from 10 to 32 Mb across chromosomes with an averge of 23Mb across whole genome. Genome-wide association analysis revealed marker-trait associations for YR resistance in India and Mexico as well as for SR resistance in Kenya. In addition, significant additive-additive interaction effects were observed for both YR and SR resistance including genomic regions on chromosomes 1BL and 3BS, which co-locate with pleiotropic genes Yr29/Lr46/Sr58/Pm39/Ltn2 and Sr2/Yr30/Lr27, respectively. Study reports novel genomic associations for YR (chromosomes 1AL, 2BS, and 3BL) and SR (chromosomes 2AL, 4DS, and 5DS). The novel findings in Creole wheat landraces can be efficiently utilized for the wheat genetic improvement.

Susceptibility of Winter Wheat and Triticale to Yellow Rust Influenced by Complex Interactions between Vernalisation, Temperature, Plant Growth Stage and Pathogen Race

Environmental factors influence the disease susceptibility of crop plants. In this study, we established an experimental system to investigate the effects of vernalisation, temperature and plant growth stage on the susceptibility of winter wheat and winter triticale to Puccinia striiformis, the causal agent of yellow (stripe) rust. Two temperature regimes: standard (18 °C day/12 °C night) and low (12 °C day/6 °C night), vernalised and non-vernalised seedlings, vernalised adult plants and two pathogen races were investigated. At low temperatures, vernalisation reduced the susceptibility of seedlings exposed to the ‘Warrior’ race, while this was only the case for five out of eight varieties exposed to the ‘Kranich’ race. Changing from standard to low temperature resulted in increased susceptibility of non-vernalised seedlings of seven varieties inoculated with the ‘Warrior’ race and five varieties inoculated with the ‘Kranich’ race. Increased susceptibility at low temperature was also detected for several varieties at the adult plant growth stage. Comparisons between vernalised seedlings and adult plants revealed an effect of plant growth stage on disease susceptibility (e.g., Adult Plant Resistance) in five varieties at standard temperature for the ‘Warrior’ race and in five and four varieties at standard and low temperature respectively, for the ‘Kranich’ race. The complex and unpredictable interactions between environment and pathogen influencing yellow rust susceptibility of individual varieties stress the importance of phenotyping for disease resistance under different environmental conditions and pathogen populations. The environmental impact on rust susceptibility should also be taken into account in early-warning systems targeting wheat and triticale breeding programmes and growers.

MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

Background

Effective disease management depends on timely and accurate diagnosis to guide control measures. The capacity to distinguish between individuals in a pathogen population with specific properties such as fungicide resistance, toxin production and virulence profiles is often essential to inform disease management approaches. The genomics revolution has led to technologies that can rapidly produce high-resolution genotypic information to define individual variants of a pathogen species. However, their application to complex fungal pathogens has remained limited due to the frequent inability to culture these pathogens in the absence of their host and their large genome sizes.

Results

Here, we describe the development of Mobile And Real-time PLant disEase (MARPLE) diagnostics, a portable, genomics-based, point-of-care approach specifically tailored to identify individual strains of complex fungal plant pathogens. We used targeted sequencing to overcome limitations associated with the size of fungal genomes and their often obligately biotrophic nature. Focusing on the wheat yellow rust pathogen, Puccinia striiformis f.sp. tritici (Pst), we demonstrate that our approach can be used to rapidly define individual strains, assign strains to distinct genetic lineages that have been shown to correlate tightly with their virulence profiles and monitor genes of importance.

Conclusions

MARPLE diagnostics enables rapid identification of individual pathogen strains and has the potential to monitor those with specific properties such as fungicide resistance directly from field-collected infected plant tissue in situ. Generating results within 48 h of field sampling, this new strategy has far-reaching implications for tracking plant health threats.

Electronic supplementary material

The online version of this article (10.1186/s12915-019-0684-y) contains supplementary material, which is available to authorized users.

New Sources of Adult Plant and Seedling Resistance to Puccinia coronata f. sp. avenae Identified among Avena sativa Accessions From the National Small Grains Collection

Accessions of cultivated oat (Avena sativa L.) from the United States Department of Agriculture-Agricultural Research Service Small Grains Collection in Aberdeen, ID were characterized for adult plant resistance (APR) and seedling resistance to crown rust, caused by Puccinia coronata f. sp. avenae. Initially, 607 oat accessions with diverse geographic origins were evaluated in field tests in Baton Rouge, LA. Of those, 97 accessions were not fully susceptible and were tested in the field in St. Paul, MN against a diverse P. coronata f. sp. avenae population. Thirty-six accessions that had some level of resistance in both field tests and mean coefficients of infection of ≤20 were further evaluated for APR and seedling resistance. Among these, four accessions (PI 193040, PI 194201, PI 237090, and PI 247930) were resistant to eight P. coronata f. sp. avenae races as seedlings. Twenty-nine accessions had resistance to at least one of the P. coronata f. sp. avenae races. Three accessions (CIav 2272, CIav 3390, and PI 285583) were fully susceptible to all eight P. coronata f. sp. avenae races as seedlings. Further evaluation of the three seedling-susceptible accessions at the flag leaf stage in a growth chamber resulted in moderately susceptible to moderately resistant responses. The resistance sources presented here may contain genes not deployed in elite oat varieties, and may be useful for future crown rust resistance breeding. The adult and seedling resistance found in accessions of the cultivated oat species is especially valuable because it avoids problems associated with the transfer of genes from wild species to cultivated oat.

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

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.

Characterization of Stripe Rust Resistance in Wheat Lines with Resistance Gene Yr17 and Implications for Evaluating Resistance and Virulence

Stripe rust, caused by Puccinia striiformis f. sp. tritici, has been the most important foliar wheat disease in south central United States since 2000 when a new strain of the pathogen emerged. The resistance gene Yr17 was used by many breeding programs to develop resistant cultivars. Although Yr17 was classified as a seedling (all-stage) resistance gene conferring a low infection type, seedlings with Yr17 frequently had intermediate to high infection types when inoculated with isolates that caused little or no disease on adult plants of the same wheat lines. The objectives of this study were to determine how to best evaluate Yr17 resistance in wheat lines and to determine which factors made seedling tests involving Yr17 so variable. Stripe rust reactions on wheat seedlings with Yr17 were influenced by temperature, wheat genotype, pathogen isolate, and the leaf (first or second) used to assess the seedling reaction. The most critical factors for accurately evaluating Yr17 reactions at the seedling stage were to avoid night temperatures below 12°C, to use the first leaf to assess the seedling reaction, to use multiple differentials with Yr17 and known avirulent, partially virulent and virulent isolates as controls, and to recognize that intermediate infection types likely represent a level of partial virulence in the pathogen that is insufficient to cause disease on adult plants in the field.