QTL Mapping of Stem Rust Resistance in Populations of Durum Wheat

Stem rinfectionust, caused by the fungus Puccinia graminis f. sp. tritici (Pgt), is one of the most devastating fungal diseases of durum and common wheat worldwide. The identification of sources of resistance and the validation of QTLs identified through genome-wide association studies is of paramount importance for reducing the losses caused by this disease to wheat grain yield and quality. Four segregating populations whose parents showed contrasting reactions to some Pgt races were assessed in the present study, and 14 QTLs were identified on chromosomes 3A, 4A, 6A, and 6B, with some regions in common between different segregating populations. Several QTLs were mapped to chromosomal regions coincident with previously mapped stem rust resistance loci; however, their reaction to different Pgt races suggest that novel genes or alleles could be present on chromosomes 3A and 6B. Putative candidate genes with a disease-related functional annotation have been identified in the QTL regions based on information available from the reference genome of durum cv. 'Svevo'

Identification of QTLs Associated with Fusarium Head Blight Resistance in Barley Accession CIho 4196

Fusarium head blight (FHB), incited by Fusarium graminearum Schwabe [teleomorph Gibberella zea (Schwein)], reduces quality of harvested barley (Hordeum vulgare L.) because of blighted kernels and the presence of deoxynivalenol (DON), a mycotoxin produced by the pathogen. CIho 4196, a two-rowed type, is one of the most resistant accessions known in barley; however, it possesses many undesirable agronomic traits. To better understand the genetics of reduced FHB severity and DON accumulation conferred by CIho 4196, a genetic map was generated using a population of recombinant inbred lines derived from a cross between Foster (a six-rowed malting cultivar) and CIho 4196. Quantitative trait loci (QTL) analyses were performed using data obtained from 10 field environments. The possible associations of resistance QTLs and various agronomic and morphological traits in barley also were investigated. The centromeric region of chromosome 2H flanked by the markers ABG461C and MWG882A (bins 6–10) likely (P\u3c0.001) contains two QTLs contributing to lower FHB severity and plant height, and one QTL each for DON accumulation, days to heading, and rachis node number. The QTL for low FHB severity in the bin 8 region explained from 3 to 9% of the variation, while the QTL in the bin 10 region explained from 17 to 60% of the variation. A QTL for DON accumulation that explained 9 to 14% of the variation was found in the bin 2 region of chromosome 4H. This may represent a new QTL not present in other FHB resistant sources. Resistance QTLs in the bin 8 region and bin 10 region of chromosome 2HL were provisionally designated Qrgz-2H-8 and Qrgz-2H-10, respectively. The QTL for DON accumulation in chromosome 4H was provisionally named QDON-4H-2

Genetic mapping of loci for resistance to stem rust in a tetraploid wheat collection

Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a major biotic constraint to wheat production worldwide. Disease resistant cultivars are a sustainable means for the efficient control of this disease. To identify quantitative trait loci (QTLs) conferring resistance to stem rust at the seedling stage, an association mapping panel consisting of 230 tetraploid wheat accessions were evaluated for reaction to five Pgt races under greenhouse conditions. A high level of phenotypic variation was observed in the panel in response to all of the races, allowing for genome-wide association mapping of resistance QTLs in wild, landrace, and cultivated tetraploid wheats. Twenty-two resistance QTLs were identified, which were characterized by at least two marker-trait associations. Most of the identified resistance loci were coincident with previously identified rust resistance genes/QTLs; however, six regions detected on chromosomes 1B, 5A, 5B, 6B, and 7B may be novel. Availability of the reference genome sequence of wild emmer wheat accession Zavitan facilitated the search for candidate resistance genes in the regions where QTLs were identified, and many of them were annotated as NOD (nucleotide binding oligomerization domain)-like receptor (NLR) genes or genes related to broad spectrum resistance

Genome-wide association study of common resistance to rust species in tetraploid wheat

Rusts of the genus Puccinia are wheat pathogens. Stem (black; Sr), leaf (brown; Lr), and stripe (yellow; Yr) rust, caused by Puccinia graminis f. sp. tritici (Pgt), Puccinia triticina (Pt), and Puccinia striiformis f. sp. tritici (Pst), can occur singularly or in mixed infections and pose a threat to wheat production globally in terms of the wide dispersal of their urediniospores. The development of durable resistant cultivars is the most sustainable method for controlling them. Many resistance genes have been identified, characterized, genetically mapped, and cloned; several quantitative trait loci (QTLs) for resistance have also been described. However, few studies have considered resistance to all three rust pathogens in a given germplasm. A genome-wide association study (GWAS) was carried out to identify loci associated with resistance to the three rusts in a collection of 230 inbred lines of tetraploid wheat (128 of which were Triticum turgidum ssp. durum) genotyped with SNPs. The wheat panel was phenotyped in the field and subjected to growth chamber experiments across different countries (USA, Mexico, Morocco, Italy, and Spain); then, a mixed linear model (MLM) GWAS was performed. In total, 9, 34, and 5 QTLs were identified in the A and B genomes for resistance to Pgt, Pt, and Pst, respectively, at both the seedling and adult plant stages. Only one QTL on chromosome 4A was found to be effective against all three rusts at the seedling stage. Six QTLs conferring resistance to two rust species at the adult plant stage were mapped: three on chromosome 1B and one each on 5B, 7A, and 7B. Fifteen QTLs conferring seedling resistance to two rusts were mapped: five on chromosome 2B, three on 7B, two each on 5B and 6A, and one each on 1B, 2A, and 7A. Most of the QTLs identified were specific for a single rust species or race of a species. Candidate genes were identified within the confidence intervals of a QTL conferring resistance against at least two rust species by using the annotations of the durum (cv. 'Svevo') and wild emmer wheat ('Zavitan') reference genomes. The 22 identified loci conferring resistance to two or three rust species may be useful for breeding new and potentially durable resistant wheat cultivars

Potential for re-emergence of wheat stem rust in the United Kingdom

This is the final version. Available on open access from Springer Nature via the DOI in this recordWheat 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.This project was funded by an institute development grant from the EI (Norwich, UK), an Industrial Partnership Award (BB/M025519/1) from the BBSRC, a European Research Council Starting Grant awarded to D.G.O.S. (number 715638), H2020 project EMPHASIS (number 634179), by the BBSRC Institute Strategic Programmes BB/J004553/1 and BB/P012574/1, the John Innes Foundation, and an African Women in Agricultural Research and Development (AWARD) fellowship to R.N.K

Mutagenesis of Puccinia graminis f. sp. tritici and selection of gain-of-virulence mutants

Wheat stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt), is regaining prominence due to the recent emergence of virulent isolates and epidemics in Africa, Europe and Central Asia. The development and deployment of wheat cultivars with multiple stem rust resistance (Sr) genes stacked together will provide durable resistance. However, certain disease resistance genes can suppress each other or fail in particular genetic backgrounds. Therefore, the function of each Sr gene must be confirmed after incorporation into an Sr-gene stack. This is difficult when using pathogen disease assays due to epistasis from recognition of multiple avirulence (Avr) effectors. Heterologous delivery of single Avr effectors can circumvent this limitation, but this strategy is currently limited by the paucity of cloned Pgt Avrs. To accelerate Avr gene cloning, we outline a procedure to develop a mutant population of Pgt spores and select for gain-of-virulence mutants. We used ethyl methanesulphonate (EMS) to mutagenize urediniospores and create a library of > 10,000 independent mutant isolates that were combined into 16 bulks of ~658 pustules each. We sequenced random mutants and determined the average mutation density to be 1 single nucleotide variant (SNV) per 258 kb. From this, we calculated that a minimum of three independently derived gain-of-virulence mutants is required to identify a given Avr gene. We inoculated the mutant library onto plants containing Sr43, Sr44, or Sr45 and obtained 9, 4, and 14 mutants with virulence toward Sr43, Sr44, or Sr45, respectively. However, only mutants identified on Sr43 and Sr45 maintained their virulence when reinolculated onto the lines from which they were identified. We further characterized 8 mutants with virulence toward Sr43. These also maintained their virulence profile on the stem rust international differential set containing 20 Sr genes, indicating that they were most likely not accidental contaminants. In conclusion, our method allows selecting for virulent mutants toward targeted resistance (R) genes. The development of a mutant library from as little as 320 mg spores creates a resource that enables screening against several R genes without the need for multiple rounds of spore multiplication and mutagenesis

Using virulence mutants to identify Avr genes in the wheat stem rust fungus, Puccinia graminis f. sp. tritici

The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. Resistance of host lines is often governed by recognition of fungal effector proteins (avirulence/virulence proteins) by plant resistance proteins (R proteins). We have taken a mutational genomics approach to identify Avr genes in Pgt. We isolated spontaneous mutants with virulence for Sr50, Sr5, Sr27, Sr21 or Sr45 by selection on resistant host lines. Sequence analysis of the Sr50 virulent mutant revealed that virulence resulted from the exchange of a whole chromosome between the two haploid nuclei of this dikaryotic organism, resulting in loss of the avirulence allele. This confirms the important role of somatic exchange events in virulence evolution in Pgt. The AvrSr50 gene was identified from the 25 candidate effector genes from this chromosome by transient co-expression with the cloned Sr50 gene in N. benthamiana. AvrSr50 recognition was confirmed in wheat by viral expression. Recognition of the AvrSr50 protein by the host Sr50 immune receptor is based on direct interaction and we have identified critical amino acid polymorphisms contributing to the escape from recognition in virulent isolates. Identification of AvrSr50 has enabled development of tools for testing effector function in wheat including viral overexpression and wheat protoplast transient expression assays. Spontaneous mutants for several other Avr loci have also been sequenced and a new Pacbio-based genome assembly for the Australian parental Pgt isolate has facilitated the delineation of these loci. Three mutants with virulence for Sr27 contain overlapping deletions and a single candidate gene for AvrSr27 has been identified. Likewise, AvrSr5 mutants contain large deletions spanning several candidate effector genes

Quantitative and Qualitative Stem Rust Resistance Factors in Barley Are Associated with Transcriptional Suppression of Defense Regulons

Stem rust (Puccinia graminis f. sp. tritici; Pgt) is a devastating fungal disease of wheat and barley. Pgt race TTKSK (isolate Ug99) is a serious threat to these Triticeae grain crops because resistance is rare. In barley, the complex Rpg-TTKSK locus on chromosome 5H is presently the only known source of qualitative resistance to this aggressive Pgt race. Segregation for resistance observed on seedlings of the Q21861 × SM89010 (QSM) doubled-haploid (DH) population was found to be predominantly qualitative, with little of the remaining variance explained by loci other than Rpg-TTKSK. In contrast, analysis of adult QSM DH plants infected by field inoculum of Pgt race TTKSK in Njoro, Kenya, revealed several additional quantitative trait loci that contribute to resistance. To molecularly characterize these loci, Barley1 GeneChips were used to measure the expression of 22,792 genes in the QSM population after inoculation with Pgt race TTKSK or mock-inoculation. Comparison of expression Quantitative Trait Loci (eQTL) between treatments revealed an inoculation-dependent expression polymorphism implicating Actin depolymerizing factor3 (within the Rpg-TTKSK locus) as a candidate susceptibility gene. In parallel, we identified a chromosome 2H trans-eQTL hotspot that co-segregates with an enhancer of Rpg-TTKSK-mediated, adult plant resistance discovered through the Njoro field trials. Our genome-wide eQTL studies demonstrate that transcript accumulation of 25% of barley genes is altered following challenge by Pgt race TTKSK, but that few of these genes are regulated by the qualitative Rpg-TTKSK on chromosome 5H. It is instead the chromosome 2H trans-eQTL hotspot that orchestrates the largest inoculation-specific responses, where enhanced resistance is associated with transcriptional suppression of hundreds of genes scattered throughout the genome. Hence, the present study associates the early suppression of genes expressed in this host–pathogen interaction with enhancement of R-gene mediated resistance

Confounding conventional wisdom: political not principled differences in the transatlantic regulatory relationship

The transatlantic complaints over hormone-treated beef and genetically modified organisms before the World Trade Organisation (WTO) seem to confirm two separate but related conventional wisdoms about the transatlantic economic relationship: that it is highly conflictual and that many of the conflicts are rooted in profoundly different approaches to regulation. This article argues that neither of the two conventional wisdoms is accurate. Rather, it contends that they are products of two, compounding analytical shortcomings: one methodological, one empirical. The methodological shortcoming takes the form of an implicit selection bias. While WTO complaints are high profile they are rare and extreme examples; it is, therefore, unsound to generalise from them to the regulatory relationship as a whole. The empirical shortcoming has to do with neither the beef hormones nor the GMO dispute demonstrating what it is purported to. The article thus serves as a cautionary tale about the dangers of relying on obvious cases and the need to question whether evidence really does support a prevailing popular narrative

Genetic Diversity and Ecological Niche Modelling of Wild Barley:Refugia, Large-Scale Post-LGM Range Expansion and Limited Mid-Future Climate Threats?

Describing genetic diversity in wild barley (Hordeum vulgare ssp. spontaneum) in geographic and environmental space in the context of current, past and potential future climates is important for conservation and for breeding the domesticated crop (Hordeum vulgare ssp. vulgare). Spatial genetic diversity in wild barley was revealed by both nuclear- (2,505 SNP, 24 nSSR) and chloroplast-derived (5 cpSSR) markers in 256 widely-sampled geo-referenced accessions. Results were compared with MaxEnt-modelled geographic distributions under current, past (Last Glacial Maximum, LGM) and mid-term future (anthropogenic scenario A2, the 2080s) climates. Comparisons suggest large-scale post-LGM range expansion in Central Asia and relatively small, but statistically significant, reductions in range-wide genetic diversity under future climate. Our analyses support the utility of ecological niche modelling for locating genetic diversity hotspots and determine priority geographic areas for wild barley conservation under anthropogenic climate change. Similar research on other cereal crop progenitors could play an important role in tailoring conservation and crop improvement strategies to support future human food security