Molecular genetics and evolution of disease resistance in cereals

Uncovering the Mechanisms: The Role of Biotrophic Fungi in Activating or Suppressing Plant Defense Responses

This paper discusses the mechanisms by which fungi manipulate plant physiology and suppress plant defense responses by producing effectors that can target various host proteins. Effector-triggered immunity and effector-triggered susceptibility are pivotal elements in the complex molecular dialogue underlying plant-pathogen interactions. Pathogen-produced effector molecules possess the ability to mimic pathogen-associated molecular patterns or hinder the binding of pattern recognition receptors. Effectors can directly target nucleotide-binding domain, leucine-rich repeat receptors, or manipulate downstream signaling components to suppress plant defense. Interactions between these effectors and receptor-like kinases in host plants are critical in this process. Biotrophic fungi adeptly exploit the signaling networks of key plant hormones, including salicylic acid, jasmonic acid, abscisic acid, and ethylene, to establish a compatible interaction with their plant hosts. Overall, the paper highlights the importance of understanding the complex interplay between plant defense mechanisms and fungal effectors to develop effective strategies for plant disease management.

Genome-wide atlas of rust resistance loci in wheat

Rust diseases, including leaf rust, stripe/yellow rust, and stem rust, significantly impact wheat (Triticum aestivum L.) yields, causing substantial economic losses every year. Breeding and deployment of cultivars with genetic resistance is the most effective and sustainable approach to control these diseases. The genetic toolkit for wheat breeders to select for rust resistance has rapidly expanded with a multitude of genetic loci identified using the latest advances in genomics, mapping and cloning strategies. The goal of this review was to establish a wheat genome atlas that provides a comprehensive summary of reported loci associated with rust resistance. Our atlas provides a summary of mapped quantitative trait loci (QTL) and characterised genes for the three rusts from 170 publications over the past two decades. A total of 920 QTL or resistance genes were positioned across the 21 chromosomes of wheat based on the latest wheat reference genome (IWGSC RefSeq v2.1). Interestingly, 26 genomic regions contained multiple rust loci suggesting they could have pleiotropic effects on two or more rust diseases. We discuss a range of strategies to exploit this wealth of genetic information to efficiently utilise sources of resistance, including genomic information to stack desirable and multiple QTL to develop wheat cultivars with enhanced resistance to rust disease.

The Zymoseptoria tritici Avirulence Factor AvrStb6 Accumulates in Hyphae Close to Stomata and Triggers a Wheat Defense Response Hindering Fungal Penetration

Zymoseptoria tritici, the causal agent of Septoria tritici blotch, is one of Europe's most damaging wheat pathogens, causing significant economic losses. Genetic resistance is a common strategy to control the disease, Stb6 being a resistance gene used for more than 100 years in Europe. This study investigates the molecular mechanisms underlying Stb6-mediated resistance. Utilizing confocal microscopy imaging, we determined that Z. tritici epiphytic hyphae mainly accumulate the corresponding avirulence factor AvrStb6 in close proximity to stomata. Consequently, the progression of AvrStb6-expressing avirulent strains is hampered during penetration. The fungal growth inhibition co-occurs with a transcriptional reprogramming in wheat characterized by an induction of immune responses, genes involved in stomatal regulation, and cell wall-related genes. Overall, we shed light on the gene-for-gene resistance mechanisms in the wheat-Z. tritici pathosystem at the cytological and transcriptomic level, and our results highlight that stomatal penetration is a critical process for pathogenicity and resistance. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Suppression of ZEAXANTHIN EPOXIDASE 1 restricts stripe rust growth in wheat

Reducing losses caused by pathogens is an effective strategy for stabilizing crop yields. Daunting challenges remain in cloning and characterizing genes that inhibit stripe rust, a devastating disease of wheat (Triticum aestivum) caused by Puccinia striiformis f. sp. tritici (Pst). We found that suppression of wheat zeaxanthin epoxidase 1 (ZEP1) increased wheat defense against Pst. We isolated the yellow rust slower 1 (yrs1) mutant of tetraploid wheat in which a premature stop mutation in ZEP1-B underpins the phenotype. Genetic analyses revealed increased H2O2 accumulation in zep1 mutants and demonstrated a correlation between ZEP1 dysfunction and slower Pst growth in wheat. Moreover, wheat kinase START 1.1 (WKS1.1, Yr36) bound, phosphorylated, and suppressed the biochemical activity of ZEP1. A rare natural allele in the hexaploid wheat ZEP1-B promoter reduced its transcription and Pst growth. Our study thus identified a novel suppressor of Pst, characterized its mechanism of action, and revealed beneficial variants for wheat disease control. This work opens the door to stacking wheat ZEP1 variants with other known Pst resistance genes in future breeding programs to enhance wheat tolerance to pathogens.

Plant and pathogen genomics: essential approaches for stem rust resistance gene stacks in wheat

The deployment of disease resistance genes is currently the most economical and environmentally sustainable method of crop protection. However, disease resistance genes can rapidly break down because of constant pathogen evolution, particularly when they are deployed singularly. Polygenic resistance is, therefore, considered the most durable, but combining and maintaining these genes by breeding is a laborious process as effective genes are usually unlinked. The deployment of polygenic resistance with single-locus inheritance is a promising innovation that overcomes these difficulties while enhancing resistance durability. Because of major advances in genomic technologies, increasing numbers of plant resistance genes have been cloned, enabling the development of resistance transgene stacks (RTGSs) that encode multiple genes all located at a single genetic locus. Gene stacks encoding five stem rust resistance genes have now been developed in transgenic wheat and offer both breeding simplicity and potential resistance durability. The development of similar genomic resources in phytopathogens has advanced effector gene isolation and, in some instances, enabled functional validation of individual resistance genes in RTGS. Here, the wheat stem rust pathosystem is used as an illustrative example of how host and pathogen genomic advances have been instrumental in the development of RTGS, which is a strategy applicable to many other agricultural crop species.

Genetic analysis of stripe rust resistance in the common wheat line Kfa/2*Kachu under a Chinese rust environment

KEY MESSAGE

We mapped a new race-specific seedling stripe rust resistance gene on wheat chromosome 5BL and a new APR locus QYr.hazu-2BS from CIMMYT wheat line Kfa/2*Kachu. Breeding resistant wheat (Triticum aestivum) varieties is the most economical and efficient way to manage wheat stripe rust, but requires the prior identification of new resistance genes and development of associated molecular markers for marker-assisted selection. To map stripe rust resistance loci in wheat, we used a recombinant inbred line population generated by crossing the stripe rust-resistant parent 'Kfa/2*Kachu' and the susceptible parent 'Apav#1'. We employed genotyping-by-sequencing and bulked segregant RNA sequencing to map a new race-specific seedling stripe rust resistance gene, which we designated YrK, to wheat chromosome arm 5BL. TraesCS5B02G330700 encodes a receptor-like kinase and is a high-confidence candidate gene for YrK based on virus-induced gene silencing results and the significant induction of its expression 24 h after inoculation with wheat stripe rust. To assist breeding, we developed functional molecular markers based on the polymorphic single nucleotide polymorphisms in the coding sequence region of YrK. We also mapped four adult plant resistance (APR) loci to wheat chromosome arms 1BL, 2AS, 2BS and 4AL. Among these APR loci, we determined that QYr.hazu-1BL and QYr.hazu-2AS are allelic to the known pleiotropic resistance gene Lr46/Yr29/Pm39 and the race-specific gene Yr17, respectively. However, QYr.hazu-2BS is likely a new APR locus, for which we converted closely linked SNP polymorphisms into breeder-friendly Kompetitive allele-specific PCR (KASP) markers. In the present study, we provided new stripe rust resistance locus/gene and molecular markers for wheat breeder to develop rust-resistant wheat variety.

Exploring genomic regions involved in bread wheat resistance to leaf rust at seedling/adult stages by using GWAS analysis

BACKGROUND

Global wheat productivity is seriously challenged by a range of rust pathogens, especially leaf rust derived from Puccinia triticina. Since the most efficient approach to control leaf rust is genetic resistance, many efforts have been made to uncover resistance genes; however, it demands an ongoing exploration for effective resistance sources because of the advent of novel virulent races. Thus, the current study was focused on detecting leaf rust resistance-related genomic loci against the P. triticina prevalent races by GWAS in a set of Iranian cultivars and landraces.

RESULTS

Evaluation of 320 Iranian bread wheat cultivars and landraces against four prevalent rust pathotypes of P. triticina (LR-99-2, LR-98-12, LR-98-22, and LR-97-12) indicated the diversity in wheat accessions responses to P. triticina. From GWAS results, 80 leaf rust resistance QTLs were located in the surrounding known QTLs/genes on almost chromosomes, except for 1D, 3D, 4D, and 7D. Of these, six MTAs (rs20781/rs20782 associated with resistance to LR-97-12; rs49543/rs52026 for LR-98-22; rs44885/rs44886 for LR-98-22/LR-98-1/LR-99-2) were found on genomic regions where no resistance genes previously reported, suggesting new loci conferring resistance to leaf rust. The GBLUP genomic prediction model appeared better than RR-BLUP and BRR, reflecting that GBLUP is a potent model for genomic selection in wheat accessions.

CONCLUSIONS

Overall, the newly identified MTAs as well as the highly resistant accessions in the recent work provide an opportunity towards improving leaf rust resistance.

Managing spot blotch disease in wheat: Conventional to molecular aspects

Spot blotch (SB) caused by Bipolaris sorokiniana (teleomorph Cochliobolus sativus) is one of the devastating diseases of wheat in the warm and humid growing areas around the world. B. sorokiniana can infect leaves, stem, roots, rachis and seeds, and is able to produce toxins like helminthosporol and sorokinianin. No wheat variety is immune to SB; hence, an integrated disease management strategy is indispensable in disease prone areas. A range of fungicides, especially the triazole group, have shown good effects in reducing the disease, and crop-rotation, tillage and early sowing are among the favorable cultural management methods. Resistance is mostly quantitative, being governed by QTLs with minor effects, mapped on all the wheat chromosomes. Only four QTLs with major effects have been designated as Sb1 through Sb4. Despite, marker assisted breeding for SB resistance in wheat is scarce. Better understanding of wheat genome assemblies, functional genomics and cloning of resistance genes will further accelerate breeding for SB resistance in wheat.

Ribonucleoprotein (RNP)-Mediated Allele Replacement in Barley (Hordeum vulgare L.) Leaves

Varietal differences within a species with agronomic importance are often based on minor changes in the genomic sequence. For example, fungus-resistant and fungus-susceptible wheat varieties may vary in only one amino acid. The situation is similar with the reporter genes Gfp and Yfp where two base pairs cause a shift in the emission spectrum from green to yellow. Methods of targeted double-strand break induction now allow this exchange precisely with the simultaneous transfer of the desired repair template. However, these changes rarely lead to a selective advantage that can be used in generating such mutant plants. The protocol presented here allows a corresponding allele replacement at the cellular level using ribonucleoprotein complexes in combination with an appropriate repair template. The efficiencies achieved are comparable to other methods with direct DNA transfer or integration of the corresponding building blocks in the host genome. They are in the range of 35 percent, considering one allele in a diploid organism as barley and using Cas9 RNP complexes.

A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes

BACKGROUND

Melaleuca quinquenervia (broad-leaved paperbark) is a coastal wetland tree species that serves as a foundation species in eastern Australia, Indonesia, Papua New Guinea, and New Caledonia. While extensively cultivated for its ornamental value, it has also become invasive in regions like Florida, USA. Long-lived trees face diverse pest and pathogen pressures, and plant stress responses rely on immune receptors encoded by the nucleotide-binding leucine-rich repeat (NLR) gene family. However, the comprehensive annotation of NLR encoding genes has been challenging due to their clustering arrangement on chromosomes and highly repetitive domain structure; expansion of the NLR gene family is driven largely by tandem duplication. Additionally, the allelic diversity of the NLR gene family remains largely unexplored in outcrossing tree species, as many genomes are presented in their haploid, collapsed state.

RESULTS

We assembled a chromosome-level pseudo-phased genome for M. quinquenervia and described the allelic diversity of plant NLRs using the novel FindPlantNLRs pipeline. Analysis reveals variation in the number of NLR genes on each haplotype, distinct clustering patterns, and differences in the types and numbers of novel integrated domains.

CONCLUSIONS

The high-quality M. quinquenervia genome assembly establishes a new framework for functional and evolutionary studies of this significant tree species. Our findings suggest that maintaining allelic diversity within the NLR gene family is crucial for enabling responses to environmental stress, particularly in long-lived plants.

Negative Interactions Balance Growth and Defense in Plants Confronted with Herbivores or Pathogens

Plants have evolved a series of defensive mechanisms against pathogens and herbivores, but the defense response always leads to decreases in growth or reproduction, which has serious implications for agricultural production. Growth and defense are negatively regulated not only through metabolic consumption but also through the antagonism of different phytohormones, such as jasmonic acid (JA) and salicylic acid (SA). Meanwhile, plants can limit the expression of defensive metabolites to reduce the costs of defense by producing constitutive defenses such as glandular trichomes or latex and accumulating specific metabolites, determining the activation of plant defense or the maintenance of plant growth. Interestingly, plant defense pathways might be prepared in advance which may be transmitted to descendants. Plants can also use external organisms to protect themselves, thus minimizing the costs of defense. In addition, plant relatives exhibit cooperation to deal with pathogens and herbivores, which is also a way to regulate growth and defense.

Genetic Resources of Cereal Crops for Aphid Resistance

The genetic resources of cereal crops in terms of resistance to aphids are reviewed. Phytosanitary destabilization led to a significant increase in the harmfulness of this group of insects. The breeding of resistant plant genotypes is a radical, the cheapest, and environmentally safe way of pest control. The genetic homogeneity of crops hastens the adaptive microevolution of harmful organisms. Both major and minor aphid resistance genes of cereal plants interact with insects differentially. Therefore, rational breeding envisages the expansion of the genetic diversity of cultivated varieties. The possibilities of replenishing the stock of effective resistance genes by studying the collection of cultivated cereals, introgression, and creating mutant forms are considered. The interaction of insects with plants is subject to the gene-for-gene relationship. Plant resistance genes are characterized by close linkage and multiple allelism. The realizing plant genotype depends on the phytophage biotype. Information about the mechanisms of constitutional and induced plant resistance is discussed. Resistance genes differ in terms of stability of expression. The duration of the period when varieties remain resistant is not related either to its phenotypic manifestation or to the number of resistance genes. One explanation for the phenomenon of durable resistance is the association of the virulence mutation with pest viability.

An interolog-based barley interactome as an integration framework for immune signaling

The barley MLA nucleotide-binding leucine-rich-repeat (NLR) receptor and its orthologs confer recognition specificity to many fungal diseases, including powdery mildew, stem-, and stripe rust. We used interolog inference to construct a barley protein interactome (Hordeum vulgare predicted interactome, HvInt) comprising 66,133 edges and 7,181 nodes, as a foundation to explore signaling networks associated with MLA. HvInt was compared with the experimentally validated Arabidopsis interactome of 11,253 proteins and 73,960 interactions, verifying that the 2 networks share scale-free properties, including a power-law distribution and small-world network. Then, by successive layering of defense-specific "omics" datasets, HvInt was customized to model cellular response to powdery mildew infection. Integration of HvInt with expression quantitative trait loci (eQTL) enabled us to infer disease modules and responses associated with fungal penetration and haustorial development. Next, using HvInt and infection-time-course RNA sequencing of immune signaling mutants, we assembled resistant and susceptible subnetworks. The resulting differentially coexpressed (resistant - susceptible) interactome is essential to barley immunity, facilitates the flow of signaling pathways and is linked to mildew resistance locus a (Mla) through trans eQTL associations. Lastly, we anchored HvInt with new and previously identified interactors of the MLA coiled coli + nucleotide-binding domains and extended these to additional MLA alleles, orthologs, and NLR outgroups to predict receptor localization and conservation of signaling response. These results link genomic, transcriptomic, and physical interactions during MLA-specified immunity.

Evolution of resistance (R) gene specificity

Plant resistance (R) genes are members of large gene families with significant within and between species variation. It has been hypothesised that a variety of processes have shaped R gene evolution and the evolution of R gene specificity. In this review, we illustrate the main mechanisms that generate R gene diversity and provide examples of how they can change R gene specificity. Next, we explain which evolutionary mechanisms are at play and how they determine the fate of new R gene alleles and R genes. Finally, we place this in a larger context by comparing the diversity and evolution of R gene specificity within and between species scales.

Pathogen-induced biosynthetic pathways encode defense-related molecules in bread wheat

Wheat is a widely grown food crop that suffers major yield losses due to attack by pests and pathogens. A better understanding of biotic stress responses in wheat is thus of major importance. The recently assembled bread wheat genome coupled with extensive transcriptomic resources provides unprecedented new opportunities to investigate responses to pathogen challenge. Here, we analyze gene coexpression networks to identify modules showing consistent induction in response to pathogen exposure. Within the top pathogen-induced modules, we identify multiple clusters of physically adjacent genes that correspond to six pathogen-induced biosynthetic pathways that share a common regulatory network. Functional analysis reveals that these pathways, all of which are encoded by biosynthetic gene clusters, produce various different classes of compounds—namely, flavonoids, diterpenes, and triterpenes, including the defense-related compound ellarinacin. Through comparative genomics, we also identify associations with the known rice phytoalexins momilactones, as well as with a defense-related gene cluster in the grass model plant Brachypodium distachyon. Our results significantly advance the understanding of chemical defenses in wheat and open up avenues for enhancing disease resistance in this agriculturally important crop. They also exemplify the power of transcriptional networks to discover the biosynthesis of chemical defenses in plants with large, complex genomes.

Genomic sequencing of Thinopyrum elongatum chromosome arm 7EL, carrying fusarium head blight resistance, and characterization of its impact on the transcriptome of the introgressed line CS-7EL

Background

The tall wheatgrass species Thinopyrum elongatum carries a strong fusarium head blight (FHB) resistance locus located on the long arm of chromosome 7 (7EL) as well as resistance to leaf and stem rusts, all diseases with a significant impact on wheat production. Towards understanding the contribution of Th. elongatum 7EL to improvement of disease resistance in wheat, the genomic sequence of the 7EL fragment present in the wheat Chinese Spring (CS) telosomic addition line CS-7EL was determined and the contribution and impact of 7EL on the rachis transcriptome during FHB infection was compared between CS and CS-7EL.

Results

We assembled the Th. elongatum 7EL chromosome arm using a reference-guided approach. Combining this assembly with the available reference sequence for CS hexaploid wheat provided a reliable reference for interrogating the transcriptomic differences in response to infection conferred by the 7EL fragment. Comparison of the transcriptomes of rachis tissues from CS and CS-7EL showed expression of Th. elongatum transcripts as well as modulation of wheat transcript expression profiles in the CS-7EL line. Expression profiles at 4 days after infection with Fusarium graminearum, the causal agent of FHB, showed an increased in expression of genes associated with an effective defense response, in particular glucan endo-1,3-beta-glucosidases and chitinases, in the FHB-resistant line CS-7EL while there was a larger increase in differential expression for genes associated with the level of fungal infection in the FHB-susceptible line CS. One hundred and seven 7EL transcripts were expressed in the smallest 7EL region defined to carry FHB resistance.

Conclusion

7EL contributed to CS-7EL transcriptome by direct expression and through alteration of wheat transcript profiles. FHB resistance in CS-7EL was associated with transcriptome changes suggesting a more effective defense response. A list of candidate genes for the FHB resistance locus on 7EL has been established.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08433-8.

SGT1-Specific Domain Mutations Impair Interactions with the Barley MLA6 Immune Receptor in Association with Loss of NLR Protein

The Mla (Mildew resistance locus a) of barley (Hordeum vulgare L.) is an effective model for cereal immunity against fungal pathogens. Like many resistance proteins, variants of the MLA coiled-coil nucleotide-binding leucine-rich repeat (CC-NLR) receptor often require the HRS complex (HSP90, RAR1, and SGT1) to function. However, functional analysis of Sgt1 has been particularly difficult, as deletions are often lethal. Recently, we identified rar3 (required for Mla6 resistance 3), an in-frame Sgt1_ΔKL308-309 mutation in the SGT1-specific domain, that alters resistance conferred by MLA but without lethality. Here, we use autoactive MLA6 and recombinant yeast-two-hybrid strains with stably integrated HvRar1 and HvHsp90 to determine that this mutation weakens but does not entirely disrupt the interaction between SGT1 and MLA. This causes a concomitant reduction in MLA6 protein accumulation below the apparent threshold required for effective resistance. The ΔKL308-309 deletion had a lesser effect on intramolecular interactions than alanine or arginine substitutions, and MLA variants that display diminished interactions with SGT1 appear to be disproportionately affected by the SGT1_ΔKL308-309 mutation. We hypothesize that those dimeric plant CC-NLRs that appear unaffected by Sgt1 silencing are those with the strongest intermolecular interactions with it. Combining our data with recent work in CC-NLRs, we propose a cyclical model of the MLA-HRS resistosome interactions.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.

Expanding Gene-Editing Potential in Crop Improvement with Pangenomes

Pangenomes aim to represent the complete repertoire of the genome diversity present within a species or cohort of species, capturing the genomic structural variance between individuals. This genomic information coupled with phenotypic data can be applied to identify genes and alleles involved with abiotic stress tolerance, disease resistance, and other desirable traits. The characterisation of novel structural variants from pangenomes can support genome editing approaches such as Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR associated protein Cas (CRISPR-Cas), providing functional information on gene sequences and new target sites in variant-specific genes with increased efficiency. This review discusses the application of pangenomes in genome editing and crop improvement, focusing on the potential of pangenomes to accurately identify target genes for CRISPR-Cas editing of plant genomes while avoiding adverse off-target effects. We consider the limitations of applying CRISPR-Cas editing with pangenome references and potential solutions to overcome these limitations.

A truncated CC-NB-ARC gene TaRPP13L1-3D positively regulates powdery mildew resistance in wheat via the RanGAP-WPP complex-mediated nucleocytoplasmic shuttle

A wheat RPP13-like isoform interacting with WPP1 contributes to quantitative and/or basal resistance to powdery mildew (Blumeria graminis f. sp. tritici) by restricting the development of Bgt conidia. Plant disease resistance (R) genes confer an ability to resist infection by pathogens expressing specific avirulence genes. Recognition of Peronospora parasitica 13-like (RPP13-like) genes belong to the nucleotide-binding site and leucine-rich repeat (NBS-LRR) superfamily and play important roles in resistance to various plant diseases. Previously, we detected a TaRPP13-like gene located on chromosome 3D (TaRPP13L1-3D) in the TaSpl1 resided region, which is strongly induced by the cell death phenotype (Zhang et al. 2021). Here, we investigated the expression and functional role of TaRPP13L1-3D in wheat responding to fungal stress. TaRPP13L1-3D encoded a typical NB-ARC structure characterized by Rx-N and P-loop NTPase domains. TaRPP13L1-3D transcripts were strongly upregulated in wheat by powdery mildew (Blumeria graminis f. sp. tritici; Bgt) and stripe rust (Puccinia striiformis f. sp. tritici; Pst) infection although opposing expression patterns were observed in response to wheat-Bgt in incompatible and compatible backgrounds. Overexpression of TaRPP13L1-3D enhanced disease resistance to Bgt, accompanied by upregulation of the defense-related marker genes encoding phytoalexin-deficient4 (PAD4), thaumatin-like protein (TLP) and chitinase 8-like protein (Chi8L), while silencing of TaRPP13L1-3D disrupted the resistance to Bgt infection. Subcellular localization studies showed that TaRPP13L1-3D is located in both the plasma membrane and nucleus, while yeast-two-hybrid (Y2H) assays indicated that TaRPP13L1-3D interacts with WPP domain-containing protein 1 (TaWPP1). This indicates that TaRPP13L1-3D shuttles between the nucleus and cytoplasm membrane via a mechanism that is mediated by the RanGAP-WPP complex in nuclear pores. This insight into TaRPP13L1-3D will be useful in dissecting the mechanism of fungal resistance in wheat, and understanding the interaction between R gene expression and pathogen defense.

Quantitative Trait Loci Mapping of Adult Plant and Seedling Resistance to Stripe Rust (Puccinia striiformis Westend.) in a Multiparent Advanced Generation Intercross Wheat Population

Stripe rust caused by the biotrophic fungus Puccinia striiformis Westend. is one of the most important diseases of wheat worldwide, causing high yield and quality losses. Growing resistant cultivars is the most efficient way to control stripe rust, both economically and ecologically. Known resistance genes are already present in numerous cultivars worldwide. However, their effectiveness is limited to certain races within a rust population and the emergence of stripe rust races being virulent against common resistance genes forces the demand for new sources of resistance. Multiparent advanced generation intercross (MAGIC) populations have proven to be a powerful tool to carry out genetic studies on economically important traits. In this study, interval mapping was performed to map quantitative trait loci (QTL) for stripe rust resistance in the Bavarian MAGIC wheat population, comprising 394 F6 : 8 recombinant inbred lines (RILs). Phenotypic evaluation of the RILs was carried out for adult plant resistance in field trials at three locations across three years and for seedling resistance in a growth chamber. In total, 21 QTL for stripe rust resistance corresponding to 13 distinct chromosomal regions were detected, of which two may represent putatively new QTL located on wheat chromosomes 3D and 7D.

Review: The multiple roles of plant lectins

For decades, the biological roles of plant lectins remained obscure and subject to speculation. With the advent of technological and scientific progress, researchers have compiled a vast amount of information regarding the structure, biological activities and functionality of hundreds of plant lectins. Data mining of genomes and transcriptome sequencing and high-throughput analyses have resulted in new insights. This review aims to provide an overview of what is presently known about plant lectins, highlighting their versatility and the importance of plant lectins for a multitude of biological processes, such as plant development, immunity, stress signaling and regulation of gene expression. Though lectins primarily act as readers of the glycocode, the multiple roles of plant lectins suggest that their functionality goes beyond carbohydrate-recognition.

Genomic variation within the maize stiff-stalk heterotic germplasm pool

The stiff-stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four expired Plant Variety Protection (ex-PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi-Bred International (PHI) early stiff-stalk type. Sequence was generated using long-read sequencing achieving highly contiguous assemblies of 2.13-2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred-specific gene annotations were generated using a core five-tissue gene expression atlas, whereas transposable element (TE) annotation was conducted using de novo and homology-directed methodologies. Compared with the reference inbred B73, synteny analyses revealed extensive collinearity across the five stiff-stalk genomes, although unique components of the maize pangenome were detected. Comparison of this set of stiff-stalk inbreds with the original Iowa Stiff Stalk Synthetic breeding population revealed that these inbreds represent only a proportion of variation in the original stiff-stalk pool and there are highly conserved haplotypes in released public and ex-Plant Variety Protection inbreds. Despite the reduction in variation from the original stiff-stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent stiff-stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pangenome.

Molecular Cytogenetic Analysis of the Introgression between Agropyron cristatum P Genome and Wheat Genome

Agropyron cristatum (2n = 4x = 28, PPPP) is an important wild relative of common wheat (Triticum aestivum L., 2n = 6x = 42). A previous report showed that the wheat-A. cristatum 6P translocation line WAT655 carrying A. cristatum 6PS (0.81-1.00) exhibited high resistance to prevalent physiological races of stripe rust (CYR32 and CYR33). In this study, three disease resistance-related transcripts, which were mapped to A. cristatum 6PS (0.81-1.00) through the analysis of specific molecular markers, were acquired from among A. cristatum full-length transcripts. The BC₅F₂ and BC₅F_2:3 genetic populations of the translocation line WAT655 were analyzed by using three disease resistance-related gene markers, A. cristatum P genome-specific markers, and fluorescence in situ hybridization (FISH). The results revealed that the introgression between A. cristatum P genome and wheat genome was observed in progenies of the genetic populations of the translocation line WAT655 and the physical positions of the three genes were considerably adjacent on A. cristatum 6PS (0.81-1.00) according to the FISH results. Additionally, kompetitive allele-specific PCR (KASP) markers of the three genes were developed to detect and acquire 24 breeding lines selected from the progenies of the distant hybridization of wheat and A. cristatum, which showed resistance to physiological races of stripe rust (CYR32 and CYR33) and other desirable agronomic traits according to the field investigation. In conclusion, this study not only provides new insights into the introgression between A. cristatum P genome and wheat genome but also provides the desirable germplasms for breeding practice.

Evolution of Fusarium Head Blight Management in Wheat: Scientific Perspectives on Biological Control Agents and Crop Genotypes Protocooperation

Over the past century, the economically devastating Fusarium Head Blight (FHB) disease has persistently ravished small grain cereal crops worldwide. Annually, losses globally are in the billions of United States dollars (USD), with common bread wheat and durum wheat accounting for a major portion of these losses. Since the unforgettable FHB epidemics of the 1990s and early 2000s in North America, different management strategies have been employed to treat this disease. However, even with some of the best practices including chemical fungicides and innovative breeding technological advances that have given rise to a spectrum of moderately resistant cultivars, FHB still remains an obstinate problem in cereal farms globally. This is in part due to several constraints such as the Fusarium complex of species and the struggle to develop and employ methods that can effectively combat more than one pathogenic line or species simultaneously. This review highlights the last 100 years of major FHB epidemics in the US and Canada, as well as the evolution of different management strategies, and recent progress in resistance and cultivar development. It also takes a look at protocooperation between specific biocontrol agents and cereal genotypes as a promising tool for combatting FHB.

Disruption of barley immunity to powdery mildew by an in-frame Lys-Leu deletion in the essential protein SGT1

Barley (Hordeum vulgare L.) Mla (Mildew resistance locus a) and its nucleotide-binding, leucine-rich-repeat receptor (NLR) orthologs protect many cereal crops from diseases caused by fungal pathogens. However, large segments of the Mla pathway and its mechanisms remain unknown. To further characterize the molecular interactions required for NLR-based immunity, we used fast-neutron mutagenesis to screen for plants compromised in MLA-mediated response to the powdery mildew fungus, Blumeria graminis f. sp. hordei. One variant, m11526, contained a novel mutation, designated rar3 (required for Mla6 resistance3), that abolishes race-specific resistance conditioned by the Mla6, Mla7, and Mla12 alleles, but does not compromise immunity mediated by Mla1, Mla9, Mla10, and Mla13. This is analogous to, but unique from, the differential requirement of Mla alleles for the co-chaperone Rar1 (required for Mla12 resistance1). We used bulked-segregant-exome capture and fine mapping to delineate the causal mutation to an in-frame Lys-Leu deletion within the SGS domain of SGT1 (Suppressor of G-two allele of Skp1, Sgt1ΔKL308-309), the structural region that interacts with MLA proteins. In nature, mutations to Sgt1 usually cause lethal phenotypes, but here we pinpoint a unique modification that delineates its requirement for some disease resistances, while unaffecting others as well as normal cell processes. Moreover, the data indicate that the requirement of SGT1 for resistance signaling by NLRs can be delimited to single sites on the protein. Further study could distinguish the regions by which pathogen effectors and host proteins interact with SGT1, facilitating precise editing of effector incompatible variants.

Powdery Mildew Resistance Phenotypes of Wheat Gene Bank Accessions

Powdery mildew (Blumeria graminis f. sp. tritici) is a common pathogen of bread wheat (Triticum aestivum L.), and genetic resistance is an effective and environmentally friendly method to reduce its adverse impact. The introgression of novel genes from wheat progenitors and related species can increase the diversity of disease resistance and accumulation of minor genes to improve the crop's resistance durability. To accomplish these two actions, host genotypes without major resistances should be preferably used. Therefore, the main aim of this study was to carry out seedling tests to detect such resistances in a set of wheat accessions from the Czech gene bank and to group the cultivars according to their phenotype. Ear progenies of 448 selected cultivars originating from 33 countries were inoculated with three isolates of the pathogen. Twenty-eight cultivars were heterogeneous, and 110 cultivars showed resistance to at least one isolate. Fifty-nine cultivars, mostly from Northwest Europe, were resistant to all three isolates were more than three times more frequently recorded in spring than in winter cultivars. Results will facilitate a rational and practical approach preferably using the set of cultivars without major resistances for both mentioned methods of breeding wheat cultivars resistant to powdery mildew.

NLR immune receptors and diverse types of non-NLR proteins control race-specific resistance in Triticeae

Recent progress in large-scale sequencing, genomics, and rapid gene isolation techniques has accelerated the identification of race-specific resistance (R) genes and their corresponding avirulence (Avr) genes in wheat, barley, rye, and their wild relatives. Here, we describe the growing repertoire of identified R and Avr genes with special emphasis on novel R gene architectures, revealing that there is a large diversity of proteins encoded by race-specific resistance genes that extends beyond the canonical nucleotide-binding domain leucine-rich repeat proteins. Immune receptors with unique domain architectures controlling race-specific resistance possibly reveal novel aspects on the biology of host-pathogen interactions. We conclude that the polyploid cereal genomes have a large evolutionary potential to generate diverse types of resistance genes.

Efficiency of a Seedling Phenotyping Strategy to Support European Wheat Breeding Focusing on Leaf Rust Resistance

Leaf rust resistance is of high importance for a sustainable European wheat production. The expression of known resistance genes starts at different developmental stages of wheat. Breeding for resistance can be supported by a fast, precise, and resource-saving phenotyping. The examination of detached leaf assays of juvenile plants inoculated under controlled conditions and phenotyped by a robotic- and computer-based, high-throughput system is a promising approach in this respect. Within this study, the validation of the phenotyping workflow was conducted based on a winter wheat set derived from Central Europe and examined at different plant developmental stages. Moderate Pearson correlations of 0.38-0.45 comparing leaf rust resistance of juvenile and adult plants were calculated and may be mainly due to different environmental conditions. Specially, the infection under controlled conditions was limited by the application of a single rust race at only one time point. Our results suggest that the diversification with respect to the applied rust race spectrum is promising to increase the consistency of detached leaf assays and the transferability of its results to the field.

Genetic dissection of maize disease resistance and its applications in molecular breeding

Disease resistance is essential for reliable maize production. In a long-term tug-of-war between maize and its pathogenic microbes, naturally occurring resistance genes gradually accumulate and play a key role in protecting maize from various destructive diseases. Recently, significant progress has been made in deciphering the genetic basis of disease resistance in maize. Enhancing disease resistance can now be explored at the molecular level, from marker-assisted selection to genomic selection, transgenesis technique, and genome editing. In view of the continuing accumulation of cloned resistance genes and in-depth understanding of their resistance mechanisms, coupled with rapid progress of biotechnology, it is expected that the large-scale commercial application of molecular breeding of resistant maize varieties will soon become a reality.

Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes

Background

Durum wheat (Triticum turgidum L. ssp. durum Desf. Husn) is the main staple crop used to make pasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays a crucial role in the successful release of new varieties with high yields and wide crop adaptation. In this study we evaluated a durum wheat collection consisting of 197 genotypes that mainly comprised a historical set of Argentinian germplasm but also included worldwide accessions.

Results

We assessed the genetic diversity, population structure and linkage disequilibrium (LD) patterns in this collection using a 35 K SNP array. The level of polymorphism was considered, taking account of the frequent and rare allelic variants. A total of 1547 polymorphic SNPs was located within annotated genes. Genetic diversity in the germplasm collection increased slightly from 1915 to 2010. However, a reduction in genetic diversity using SNPs with rare allelic variants was observed after 1979. However, larger numbers of rare private alleles were observed in the 2000–2009 period, indicating that a high reservoir of rare alleles is still present among the recent germplasm in a very low frequency. The percentage of pairwise loci in LD in the durum genome was low (13.4%) in our collection. Overall LD and the high (r² > 0.7) or complete (r² = 1) LD presented different patterns in the chromosomes. The LD increased over three main breeding periods (1915–1979, 1980–1999 and 2000–2020).

Conclusions

Our results suggest that breeding and selection have impacted differently on the A and B genomes, particularly on chromosome 6A and 2A. The collection was structured in five sub-populations and modern Argentinian accessions (cluster Q4) which were clearly differentiated. Our study contributes to the understanding of the complexity of Argentinian durum wheat germplasm and to derive future breeding strategies enhancing the use of genetic diversity in a more efficient and targeted way.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07519-z.

Possibilities for the Biological Control of Mycotoxins in Food and Feed

Seeking useful biological agents for mycotoxin detoxification has achieved success in the last twenty years thanks to the participation of many multidisciplinary teams. We have recently witnessed discoveries in the fields of bacterial genetics (inclusive of next-generation sequencing), protein encoding, and bioinformatics that have helped to shape the latest perception of how microorganisms/mycotoxins/environmental factors intertwine and interact, so the road is opened for new breakthroughs. Analysis of literature data related to the biological control of mycotoxins indicates the ability of yeast, bacteria, fungi and enzymes to degrade or adsorb mycotoxins, which increases the safety and quality of susceptible crops, animal feed and, ultimately, food of animal origin (milk, meat and eggs) by preventing the presence of residues. Microbial detoxification (transformation and adsorption) is becoming a trustworthy strategy that leaves no or less toxic compounds and contributes to food security. This review summarizes the data and highlights the importance and prospects of these methods.

The leucine-rich repeats in allelic barley MLA immune receptors define specificity towards sequence-unrelated powdery mildew avirulence effectors with a predicted common RNase-like fold

Nucleotide-binding domain leucine-rich repeat-containing receptors (NLRs) in plants can detect avirulence (AVR) effectors of pathogenic microbes. The Mildew locus a (Mla) NLR gene has been shown to confer resistance against diverse fungal pathogens in cereal crops. In barley, Mla has undergone allelic diversification in the host population and confers isolate-specific immunity against the powdery mildew-causing fungal pathogen Blumeria graminis forma specialis hordei (Bgh). We previously isolated the Bgh effectors AVRA1, AVRA7, AVRA9, AVRA13, and allelic AVRA10/AVRA22, which are recognized by matching MLA1, MLA7, MLA9, MLA13, MLA10 and MLA22, respectively. Here, we extend our knowledge of the Bgh effector repertoire by isolating the AVRA6 effector, which belongs to the family of catalytically inactive RNase-Like Proteins expressed in Haustoria (RALPHs). Using structural prediction, we also identified RNase-like folds in AVRA1, AVRA7, AVRA10/AVRA22, and AVRA13, suggesting that allelic MLA recognition specificities could detect structurally related avirulence effectors. To better understand the mechanism underlying the recognition of effectors by MLAs, we deployed chimeric MLA1 and MLA6, as well as chimeric MLA10 and MLA22 receptors in plant co-expression assays, which showed that the recognition specificity for AVRA1 and AVRA6 as well as allelic AVRA10 and AVRA22 is largely determined by the receptors' C-terminal leucine-rich repeats (LRRs). The design of avirulence effector hybrids allowed us to identify four specific AVRA10 and five specific AVRA22 aa residues that are necessary to confer MLA10- and MLA22-specific recognition, respectively. This suggests that the MLA LRR mediates isolate-specific recognition of structurally related AVRA effectors. Thus, functional diversification of multi-allelic MLA receptors may be driven by a common structural effector scaffold, which could be facilitated by proliferation of the RALPH effector family in the pathogen genome.

QTL mapping of adult plant and seedling resistance to leaf rust (Puccinia triticina Eriks.) in a multiparent advanced generation intercross (MAGIC) wheat population

The Bavarian MAGIC Wheat population, comprising 394 F6:8 recombinant inbred lines was phenotyped for Puccinia triticina resistance in multi-years' field trials at three locations and in a controlled environment seedling test. Simple intervall mapping revealed 19 QTL, corresponding to 11 distinct chromosomal regions. The biotrophic rust fungus Puccinia triticina is one of the most important wheat pathogens with the potential to cause yield losses up to 70%. Growing resistant cultivars is the most cost-effective and environmentally friendly way to encounter this problem. The emergence of leaf rust races being virulent against common resistance genes increases the demand for wheat varieties with novel resistances. In the past decade, the use of complex experimental populations, like multiparent advanced generation intercross (MAGIC) populations, has risen and offers great advantages for mapping resistances. The genetic diversity of multiple parents, which has been recombined over several generations, leads to a broad phenotypic diversity, suitable for high-resolution mapping of quantitative traits. In this study, interval mapping was performed to map quantitative trait loci (QTL) for leaf rust resistance in the Bavarian MAGIC Wheat population, comprising 394 F_6:8 recombinant inbred lines (RILs). Phenotypic evaluation of the RILs for adult plant resistance was carried out in field trials at three locations and two years, as well as in a controlled-environment seedling inoculation test. In total, interval mapping revealed 19 QTL, which corresponded to 11 distinct chromosomal regions controlling leaf rust resistance. Six of these regions may represent putative new QTL. Due to the elite parental material, RILs identified to be resistant to leaf rust can be easily introduced in breeding programs.

A novel adult plant leaf rust resistance gene Lr2K38 mapped on wheat chromosome 1AL

Soft red winter wheat (SRWW) cultivar AGS 2038 has a high level of seedling and adult plant leaf rust (LR) resistance. To map and characterize LR resistance in AGS 2038, a recombinant inbred line (RIL) population consisting of 225 lines was developed from a cross between AGS 2038 and moderately resistant line UGA 111729. The parents and RIL population were phenotyped for LR response in three field environments at Plains and Griffin, GA, in the 2017-2018 and 2018-2019 growing seasons, one greenhouse environment at the adult-plant stage, and at seedling stage. The RIL population was genotyped with the Illumina iSelect 90K SNP marker array, and a total of 7667 polymorphic markers representing 1513 unique loci were used to construct a linkage map. Quantitative trait loci (QTL) analysis detected six QTL, QLr.ags-1AL, QLr.ags-2AS, QLr.ags-2BS1, QLr.ags-2BS2, QLr.ags-2BS3, and QLr.ags-2DS, for seedling and adult plant LR resistance. Of these, the major adult plant leaf rust resistance QTL, QLr.ags-1AL, was detected on all field and greenhouse adult plant tests and explained up to 34.45% of the phenotypic variation. QLr.ags-1AL, tightly flanked by IWB20487 and IWA4022 markers, was contributed by AGS 2038. Molecular marker analysis using a diagnostic marker linked to Lr59 showed that QLr.ags-1AL was different from Lr59, the only known LR resistance gene on 1AL. Therefore, the QTL was temporarily designated as Lr2K38. Lr2K38-linked marker IWB20487 was highly polymorphic among 30 SRWW lines and should be useful for selecting the Lr2K38 in wheat breeding programs.

A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola

Rice root-knot nematode (RRKN), Meloidogyne graminicola is one of the major biotic constraints in rice-growing countries of Southeast Asia. Host plant resistance is an environmentally-friendly and cost-effective mean to mitigate RRKN damage to rice. Considering the limited availability of genetic resources in the Asian rice (Oryza sativa) cultivars, exploration of novel sources and genetic basis of RRKN resistance is necessary. We screened 272 diverse wild rice accessions (O. nivara, O. rufipogon, O. sativa f. spontanea) to identify genotypes resistant to RRKN. We dissected the genetic basis of RRKN resistance using a genome-wide association study with SNPs (single nucleotide polymorphism) genotyped by 50K "OsSNPnks" genic Affymetrix chip. Population structure analysis revealed that these accessions were stratified into three major sub-populations. Overall, 40 resistant accessions (nematode gall number and multiplication factor/MF < 2) were identified, with 17 novel SNPs being significantly associated with phenotypic traits such as number of galls, egg masses, eggs/egg mass and MF per plant. SNPs were localized to the quantitative trait loci (QTL) on chromosome 1, 2, 3, 4, 6, 10 and 11 harboring the candidate genes including NBS-LRR, Cf2/Cf5 resistance protein, MYB, bZIP, ARF, SCARECROW and WRKY transcription factors. Expression of these identified genes was significantly (P < 0.01) upregulated in RRKN-infected plants compared to mock-inoculated plants at 7 days after inoculation. The identified SNPs enrich the repository of candidate genes for future marker-assisted breeding program to alleviate the damage of RRKN in rice.

What natural variation can teach us about resistance durability

Breeding a crop variety to be resistant to a pathogen usually takes years. This is problematic because pathogens, with short generation times and fluid genomes, adapt quickly to overcome resistance. The triumph of the pathogen is not inevitable, however, as there are numerous examples of durable resistance, particularly in wild plants. Which factors then contribute to such resistance stability over millennia? We review current knowledge of wild and agricultural pathosystems, detailing the importance of genetic, species and spatial heterogeneity in the prevention of pathogen outbreaks. We also highlight challenges associated with increasing resistance diversity in crops, both in light of pathogen (co-)evolution and breeding practices. Historically it has been difficult to incorporate heterogeneity into agriculture due to reduced efficiency in harvesting. Recent advances implementing computer vision and automation in agricultural production may improve our ability to harvest mixed genotype and mixed species plantings, thereby increasing resistance durability.

Evolution of virulence in rust fungi - multiple solutions to one problem

Rust fungi are major pathogens that negatively affect crops and ecosystems. Recent rust disease epidemics driven by the emergence of strains with novel virulence profiles demand a better understanding of the evolutionary mechanisms of these organisms. Here, we review research advances in genome-scale analysis coupled with functional validation of effector candidate genes that have been instrumental to elucidate processes that contribute to changes in virulence phenotypes. We highlight how haplotype-phased genome references have paved the road to link these processes to the reproductive phases of rust fungi and have provided evidence for somatic exchange between strains as an important mechanism for generating diversity in asexual populations. With increasing data availability, we envision the future development of molecular virulence diagnostic tools.

Variation Patterns of NLR Clusters in Arabidopsis thaliana Genomes

The nucleotide-binding domain and leucine-rich repeat (NLR) gene family is highly expanded in the plant lineage with extensive sequence and structure polymorphisms. To survey the landscape of NLR expansion, we mined the published long-read data generated by the resistance gene enrichment sequencing of 64 diverse Arabidopsis thaliana accessions. We found that the hot spots of massive multi-gene NLR cluster expansion did not typically span the whole cluster; instead, they were restricted to a handful of, or only one, dominant radiation(s). All sequences in such a radiation were distinct from other genes in the cluster but not from each other in the clade, making it difficult to assign trustworthy reference-based orthologies when multiple reference genes were present in the radiation. Consequently, NLR genes can be broadly divided into two types: radiating or high-fidelity, where high-fidelity genes are well conserved and well separated from other clades. A similar distinction could be made for NLR clusters, depending on whether cluster size was determined primarily by extensive radiation or the presence of numerous high-fidelity genes. We also identified groups of well-conserved NLR clades that were missing from the Columbia-0 reference genome. This suggests that the classification of NLRs using gene IDs from a single reference accession can rarely capture all major paralogs in a cluster accurately and representatively and that a reference-agnostic perspective is required to properly characterize these additional variations. Finally, we present a quantitative visualization method for differentiating these situations in a given clade of interest.

Fine Mapping a Broad-Spectrum Powdery Mildew Resistance Gene in Chinese Landrace Datoumai, PmDTM, and Its Relationship with Pm24

Powdery mildew, caused by the biotrophic fungal pathogen Blumeria graminis f. sp. tritici (Bgt), is a globally important wheat disease causing severe yield losses, and deployment of resistant varieties is the preferred choice for managing this disease. Chinese wheat landrace Datoumai was resistant to 22 of 23 Bgt isolates at the seedling stage. Genetic analysis based on the inoculation of Bgt isolate E09 on the F₁, F₂, and F_2:3 populations derived from the cross Datoumai × Huixianhong revealed that the powdery mildew resistance of Datoumai is controlled by a single dominant gene, temporarily designated as PmDTM. Bulked segregant analysis and simple sequence repeat mapping with 200 F₂ plants showed that PmDTM was located in the same genetic region as Pm24 on chromosome 1DS. To fine map PmDTM, 12 critical recombinants were identified from 1,192 F₂ plants and delimited PmDTM to a 0.5-cM Xhnu58800 to Xhnu59000 interval covering 180.5 Kb (38,728,125 to 38,908,656 bp) on chromosome 1DS, and only one highly confident gene, TraesCS1D02G058900, was annotated within this region. TraesCS1D02G058900 encodes a receptor-like serine/threonine-protein kinase (STK), and a 6-bp deletion in exon 5 may confer the resistance to powdery mildew. Allele frequency analysis indicated that the STK allele with 6-bp deletion was only present in three landraces (Datoumai, Chiyacao [Pm24], and Hulutou) and was absent in all of the 353 Chinese modern cultivars and 147 foreign cultivars. These results demonstrate that PmDTM is mapped to the same locus as Pm24 and can be widely used to enhance powdery mildew resistance in wheat growing regions worldwide.

A Post-Haustorial Defense Mechanism is Mediated by the Powdery Mildew Resistance Gene, PmG3M, Derived from Wild Emmer Wheat

The destructive wheat powdery mildew disease is caused by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt). PmG3M, derived from wild emmer wheat Triticum dicoccoides accession G305-3M, is a major gene providing a wide-spectrum resistance against Bgt. PmG3M was previously mapped to wheat chromosome 6B using an F₆ recombinant inbred line (RIL) mapping population generated by crossing G305-3M with the susceptible T. durum wheat cultivar Langdon (LDN). In the current study, we aimed to explore the defense mechanisms conferred by PmG3M against Bgt. Histopathology of fungal development was characterized in artificially inoculated leaves of G305-3M, LDN, and homozygous RILs using fluorescence and light microscopy. G305-3M exhibited H₂O₂ accumulation typical of a hypersensitive response, which resulted in programmed cell death (PCD) in Bgt-penetrated epidermal cells, while LDN showed well-developed colonies without PCD. In addition, we observed a post-haustorial resistance mechanism that arrested the development of fungal feeding structures and pathogen growth in both G305-3M and resistant RIL, while LDN and a susceptible RIL displayed fully developed digitated haustoria and massive accumulation of fungal biomass. In contrast, both G305-3M and LDN exhibited callose deposition in attempt to prevent fungal invasion, supporting this as a mechanism of a basal defense response not associated with PmG3M resistance mechanism per se. The presented results shed light on the resistance mechanisms conferred by PmG3M against wheat powdery mildew.

Origin and Diversity of Plant Receptor-Like Kinases

Because of their high level of diversity and complex evolutionary histories, most studies on plant receptor-like kinase subfamilies have focused on their kinase domains. With the large amount of genome sequence data available today, particularly on basal land plants and Charophyta, more attention should be paid to primary events that shaped the diversity of the RLK gene family. We thus focus on the motifs and domains found in association with kinase domains to illustrate their origin, organization, and evolutionary dynamics. We discuss when these different domain associations first occurred and how they evolved, based on a literature review complemented by some of our unpublished results.

CsWAKL08, a pathogen-induced wall-associated receptor-like kinase in sweet orange, confers resistance to citrus bacterial canker via ROS control and JA signaling

Citrus bacterial canker (CBC) is a disease resulting from Xanthomonas citri subsp. citri (Xcc) infection and poses a grave threat to citrus production worldwide. Wall-associated receptor-like kinases (WAKLs) are proteins with a central role in resisting a range of fungal and bacterial diseases. The roles of WAKLs in the context of CBC resistance, however, remain unclear. Here, we explored the role of CsWAKL08, which confers resistance to CBC, and we additionally analyzed the molecular mechanisms of CsWAKL08-mediated CBC resistance. Based on systematic annotation and induced expression analysis of the CsWAKL family in Citrus sinensis, CsWAKL08 was identified as a candidate that can be upregulated by Xcc infection in the CBC-resistant variety. CsWAKL08 can also be induced by the phytohormones salicylic acid (SA) and methyl jasmonic acid (MeJA) and spans the plasma membrane. Overexpression of CsWAKL08 resulted in strong CBC resistance in transgenic sweet oranges, whereas silencing of CsWAKL08 resulted in susceptibility to CBC. The peroxidase (POD) and superoxide dismutase (SOD) activities were significantly enhanced in the CsWAKL08-overexpressing plants compared to the control plants, thereby mediating reactive oxygen species (ROS) homeostasis in the transgenic plants. Moreover, the JA levels and the expression of JA biosynthesis and JA responsive genes were substantially elevated in the CsWAKL08 overexpression plants relative to the controls upon Xcc infection. Based on these findings, we conclude that the wall-associated receptor-like kinase CsWAKL08 positively regulates CBC resistance through a mechanism involving ROS control and JA signaling. These results further highlight the importance of this kinase family in plant pathogen resistance.

Plant pangenomics: approaches, applications and advancements

With the assembly of increasing numbers of plant genomes, it is becoming accepted that a single reference assembly does not reflect the gene diversity of a species. The production of pangenomes, which reflect the structural variation and polymorphisms in genomes, enables in depth comparisons of variation within species or higher taxonomic groups. In this review, we discuss the current and emerging approaches for pangenome assembly, analysis and visualisation. In addition, we consider the potential of pangenomes for applied crop improvement, evolutionary and biodiversity studies. To fully exploit the value of pangenomes it is important to integrate broad information such as phenotypic, environmental, and expression data to gain insights into the role of variable regions within genomes.

The progress of leaf rust research in wheat

Leaf rust (also called brown rust) in wheat, caused by fungal pathogen Puccinia triticina Erikss. (Pt) is one of the major constraints in wheat production worldwide. Pt is widespread with diverse population structure and undergoes rapid evolution to produce new virulent races against resistant cultivars that are regularly developed to provide resistance against the prevailing races of the pathogen. Occasionally, the disease may also take the shape of an epidemic in some wheat-growing areas causing major economic losses. In the recent past, substantial progress has been made in characterizing the sources of leaf rust resistance including non-host resistance (NHR). Progress has also been made in elucidating the population biology of Pt and the mechanisms of wheat-Pt interaction. So far, ∼80 leaf rust resistance genes (Lr genes) have been identified and characterized; some of them have also been used for the development of resistant wheat cultivars. It has also been shown that a gene-for-gene relationship exists between individual wheat Lr genes and the corresponding Pt Avr genes so that no Lr gene can provide resistance unless the prevailing race of the pathogen carries the corresponding Avr gene. Several Lr genes have also been cloned and their products characterized, although no Avr gene corresponding a specific Lr gene has so far been identified. However, several candidate effectors for Pt have been identified and functionally characterized using genome-wide analyses, transcriptomics, RNA sequencing, bimolecular fluorescence complementation (BiFC), virus-induced gene silencing (VIGS), transient expression and other approaches. This review summarizes available information on different aspects of the pathogen Pt, genetics/genomics of leaf rust resistance in wheat including cloning and characterization of Lr genes and epigenetic regulation of disease resistance.

Wheat gene Sr60 encodes a protein with two putative kinase domains that confers resistance to stem rust

Wheat stem rust, caused by Puccinia graminis Pers. f. sp. tritici (Pgt), is a devastating fungal disease threatening global wheat production. The present paper reports the identification of stem rust resistance gene Sr60, a race-specific gene from diploid wheat Triticum monococcum L. that encodes a protein with two putative kinase domains. This gene, designated as WHEAT TANDEM KINASE 2 (WTK2), confers intermediate levels of resistance to Pgt. WTK2 was identified by map-based cloning and validated by transformation of a c.10-kb genomic sequence including WTK2 into susceptible common wheat variety Fielder (Triticum aestivum L.). Transformation of Fielder with WTK2 was sufficient to confer Pgt resistance. Sr60 transcripts were transiently upregulated 1 d post-inoculation with Pgt, but not in mock-inoculated plants. The upregulation of Sr60 was associated with stable upregulation of several pathogenesis-related genes. The Sr60-resistant haplotype found in T. monococcum was not found in polyploid wheat, suggesting an opportunity to introduce a novel resistance gene. Sr60 was successfully introgressed into hexaploid wheat, and we developed a diagnostic molecular marker to accelerate its deployment and pyramiding with other resistance genes. The cloned Sr60 also can be a useful component of transgenic cassettes including other resistance genes with complementary resistance profiles.

Distinct cellulose and callose accumulation for enhanced bioethanol production and biotic stress resistance in OsSUS3 transgenic rice

Genetic modification of plant cell walls is an effective approach to reduce lignocellulose recalcitrance in biofuel production, but it may affect plant stress response. Hence, it remains a challenge to reduce biomass recalcitrance and simultaneously enhance stress resistance. In this study, the OsSUS3-transgenic plants exhibited increased cell wall polysaccharides deposition and reduced cellulose crystallinity and xylose/arabinose proportion of hemicellulose, resulting in largely enhanced biomass saccharification and bioethanol production. Additionally, strengthening of the cell wall also contributed to plant biotic resistance. Notably, the transgenic plants increased stress-induced callose accumulation, and promoted the activation of innate immunity, leading to greatly improved multiple resistances to the most destructive diseases and a major pest. Hence, this study demonstrates a significant improvement both in bioethanol production and biotic stress resistance by regulating dynamic carbon partitioning for cellulose and callose biosynthesis in OsSUS3-transgenic plants. Meanwhile, it also provides a potential strategy for plant cell wall modification.

Identification and assessment of two major QTLs for dwarf bunt resistance in winter wheat line 'IDO835'

Two major dwarf bunt resistance QTLs were mapped to a known Bt9 locus and a novel locus. The associated KASP markers were developed and validated in other two populations. Dwarf bunt (DB), caused by Tilletia controversa J.G. Kühn, and common bunt (CB), caused by T. caries and T. foetida, are two destructive diseases that reduce grain yield and quality in wheat. Breeding for bunt-resistant cultivars is important in many wheat production areas, especially where organic wheat is grown. However, few molecular markers have been used in selection of bunt resistance. In the present study, a doubled haploid (DH) population derived from the bunt-resistant line 'IDO835' and the susceptible cultivar 'Moreland' was evaluated for DB resistance in a field nursery in Logan, Utah, for four growing seasons. The population was genotyped with the Illumina 90 K SNP iSelect marker platform. Two major QTLs were consistently identified on chromosomes 6DL (Q.DB.ui-6DL) and 7AL (Q.DB.ui-7AL), explaining up to 53% and 38% of the phenotypic variation, respectively. Comparative study suggested that Q.DB.ui-6DL was located in the same region as the CB resistance gene Bt9, and Q.DB.ui-7AL was located at a novel locus for bunt resistance. Based on Chinese Spring reference sequence and annotations (IWGSC RefSeq v1.1), both resistance QTLs were mapped to disease resistance gene-rich (NBS-LRR and kinase genes) regions. To validate the identified QTL and design user-friendly markers for MAS, five SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers and used to genotype two validation panels, including a DH population and a diverse winter wheat population from USDA-ARS National Small Grain Collection, as well as a Bt gene investigation panel, consisting of 15 bunt differential lines and 11 resistant lines.

Resistance mechanisms involved in complex immunity of wheat against rust diseases

The review is devoted to the disclosure of the modern concept of plant immunity as a hierarchical system of plant host protection, controlled by combinations of major and minor resistance genes (loci). The “zigzag” model is described in detail for discussing the molecular bases of plant immunity with key concepts: pathogen-associated molecular patterns triggering innate immunity, ambivalent effectors causing susceptibility, but when interacting with resistance genes, a hypersensitive reaction or alternative defense mechanisms. There are three types of resistance in cereals: (1) basal resistance provided by plasma membrane-localized receptors proteins; (2) racespecific resistance provided by intracellular immune R-receptors; (3) partial resistance conferred by quantitative gene loci. The system ‘wheat (Triticum aestivum) – the fungus causing leaf rust (Puccinia triticina)’ is an interesting model for observing all the resistance mechanisms listed above, since the strategy of this pathogen is aimed at the constitutive use of host resources. The review focuses on known wheat genes responsible for various types of resistance to leaf rust: race-specific genes Lr1, Lr10, Lr19, and Lr21; adult resistance genes which are hypersensitive Lr12, Lr13, Lr22a, Lr22b, Lr35, Lr48, and Lr49; nonhypersensitive genes conferring partial resistance Lr34, Lr46, Lr67, and Lr77. The involvement of some wheat R-genes in pre-haustorial resistance to leaf rust has been discovered recently: Lr1, Lr3a, Lr9, LrB, Lr19, Lr21, Lr38. The presence of these genes in the genotype ensures the interruption of early pathogenesis through the following mechanisms: disorientation and branching of the germ tube; formation of aberrant fungal penetration structures (appressorium, substomatal vesicle); accumulation of callose in mesophyll cell walls. Breeding for immunity is accelerated by implementation of data on various mechanisms of wheat resistance to rust diseases, which are summarized in this review.

Validation and delineation of a locus conferring Fusarium crown rot resistance on 1HL in barley by analysing transcriptomes from multiple pairs of near isogenic lines

BACKGROUND

Fusarium crown rot (FCR) is a chronic and severe disease in cereal production in semi-arid regions worldwide. A putative quantitative trait locus conferring FCR resistance, Qcrs.cpi-1H, had previously been mapped on the long arm of chromosome 1H in barley.

RESULTS

In this study, five pairs of near-isogenic lines (NILs) targeting the 1HL locus were developed. Analysing the NILs found that the resistant allele at Qcrs.cpi-1H significantly reduced FCR severity. Transcriptomic analysis was then conducted against three of the NIL pairs, which placed the Qcrs.cpi-1H locus in an interval spanning about 11 Mbp. A total of 56 expressed genes bearing single nucleotide polymorphisms (SNPs) were detected in this interval. Five of them contain non-synonymous SNPs. These results would facilitate detailed mapping as well as cloning gene(s) underlying the resistance locus.

CONCLUSION

NILs developed in this study and the transcriptomic sequences obtained from them did not only allow the validation of the resistance locus Qcrs.cpi-1H and the identification of candidate genes underlying its resistance, they also allowed the delineation of the resistance locus and the development of SNPs markers which formed a solid base for detailed mapping as well as cloning gene(s) underlying the locus.

Virulence Structure and Diversity of Puccinia coronata f. sp. avenae P. Syd. & Syd. in Poland During 2013 to 2015

The crown rust fungus Puccinia coronata f. sp. avenae P. Syd. & Syd. (Pca) attacks cultivated oat and its wild relatives, causing significant losses to the crop worldwide. Although understanding the origin and dynamics of the pathogen's diversity is critical to developing methods for its control, there are little relevant data on Pca virulence diversity in Europe, the global center of oat production. The goal of this study was to analyze the diversity of Pca populations in Poland in 2013 to 2015 based on their ability to overcome currently available host resistance Pc genes. Pca isolate virulence was evaluated on a panel of lines containing 26 major resistance genes of oat. The isolates were able to overcome from 1 to 16 resistance genes each, with most isolates being virulent on five to seven lines. In all years, a very high level of crown rust pathotype diversity was observed, with Simpson and Evenness indices of 0.99. In total, 156 different pathotypes were detected, with no prevalent pathotype in any of the 3 years analyzed. The results showed that the virulence level of P. coronata isolates was relatively low for each year studied (21% on average), most likely owing to the low take up of Pc genes in Polish oat cultivars, meaning that many sources of resistance are still effective against Pca races occurring in Poland. The long-range dispersal of Puccinia spores supported by the availability of wild, weedy, and cultivated Avena species makes it likely that the virulence profile seen in Poland is representative of much of central Europe and beyond.