Biology subjects

Moscou, M. J.

Publications and source records attributed to Moscou, M. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Rye stem rust is a reservoir of diversity and virulence for wheat stem rust

Sexual populations of the stem rust pathogen (Puccinia graminis or Pg) are producing new race types globally. An analysis of 385 Pg genomes (204 from this study) illuminated international migration and admixture events. Within Kazakhstan, a novel and diverse sexual clade of P. graminis is described. An analysis of the highly divergent mating type homeodomain (HD) locus found that the 75 Kazakhstan isolates had 41 different HD haplotypes, out of a total of 99 P. graminis HD haplotypes found globally. Kazakh isolates share HD haplotypes with isolates in clade 1 (Ug99), 3-B (TTRTF), and 4 (TKTTF). There are 148 unique combinations of HD locus haplotypes within the 385 isolates. Rye (Pgs) and wheat (Pgt) stem rust share multiple HD locus haplotypes and have conserved pheromone receptors and precursors, while oat stem rust (Pga) does not. Virulent alleles for AvrSr13, AvrSr22, and AvrSr50 in Pgt are frequently derived from admixture with Pgs. Pgs also contains virulent effectors for AvrSr33, AvrSr62, and AvrSr27. Pgt isolates virulent on Sr31, such as Ug99 and isolates from Spain, have genetic links to North American Pgs isolates which are present in regions of the United States where barberry is common.

plant biology↗

bioRxiv2026

Effector-host networks in the barley powdery mildew pathosystem reveal significant targeting of ubiquitin-associated proteins and transcriptional regulators

- The ascomycete fungal pathogen Blumeria hordei (Bh) is predicted to secrete over 530 effector proteins to infect barley and cause powdery mildew disease, yet their individual and collective functions are largely unexplored. We used yeast two-hybrid next-generation interaction screening (Y2H-NGIS) to probe the host targets of 48 Bh candidate secreted effectors (CSEPs), including multiple AVRA effectors that are recognized by MLA nucleotide-binding leucine-rich repeat (NLR) receptors. - Y2H-NGIS and subsequent binary retesting identified 356 high-confidence protein-protein interactions (PPI) among Bh CSEPs, MLA NLR fragments, and barley proteins. We uncovered unique and shared host targets, including numerous proteins involved in ubiquitin-associated processes, gene expression, immune and kinase signaling, metabolism, and vesicle trafficking. - We identified a host protein (HvCAP2) that interacts with MLA and at least five Bh effectors, as well as additional effector-host PPI that correlate with loss of recognition of AVRA13 and AVRA6 by MLA13 and MLA6, respectively. - Results were integrated with an interolog-based barley interactome (HvInt) to assemble a host-pathogen network of 1248 proteins and 1701 interactions. This PPI resource can serve as a platform for functional investigations into the molecular basis of powdery mildew pathogenesis and host recognition.

plant biology↗

bioRxiv2026

Engineering quantitative root disease resistance in barley by targeting conserved SCAR susceptibility genes without compromising seed yield or mycorrhizal symbiosis

Durable resistance to soil-borne pathogens remains elusive in cereals, partly because susceptibility (S) genes that facilitate root infection have not been identified in monocots. In the model legume Medicago truncatula, the SCAR/WAVE complex member MtAPI functions as a root S-gene for microbial invasion. Whether SCAR gene associated susceptibility function is conserved in monocots, and whether SCAR gene inactivation can enhance root resistance in cereals, remains unknown. Here, we identify and characterize three SCAR genes in barley: HvSCAR-A, HvSCAR-B, and HvSCAR-C. Cross-species complementation assays indicate that HvSCAR-B and HvSCAR-C are functionally similar to MtAPI. While hscar-b and hvscar-c single mutants exhibited no major growth defects, hvscar-a mutants showed strongly reduced seed production, and a hvscar-b/c double mutant displayed shorter root hairs. Notably, the hvscar-b/c double mutant exhibited increased resistance to the hemibiotrophic pathogen Phytophthora palmivora but greater colonization by the symbiotic arbuscular mycorrhizal fungus Funneliformis mosseae, underscoring a complex role in plant root - microbe interactions. Our findings reveal a conserved susceptibility function of SCAR genes in monocots and identify api monocot homologs as promising targets for engineering disease resistance in cereals. This study offers new insights into SCAR protein functional diversification and its potential for improving root health in crop plants.

plant biology↗

bioRxiv2026

Haplotype-phased genomes of the barley leaf rust pathogen reveal evidence of repeat element expansion and somatic hybridization

Barley leaf rust disease, caused by Puccinia hordei, leads to substantial yield losses and diminished malting quality of barley across temperate growing regions worldwide. To address the paucity of high-resolution genomic resources for this pathogen, we generated haplotype-phased, chromosome-scale assemblies for ten globally distributed isolates using PacBio HiFi and Hi-C sequencing. Phylogenomic analysis revealed seven distinct lineages of P. hordei, including evidence of nuclear exchange, with a shared nuclear haplotype detected between two US lineages. Nuclear genome sizes ranged from [~]140-147Mbp, with the exception of isolate 90ISR03 from Israel ([~]163Mbp), which also harbored a 6.2Mbp supernumerary scaffold in one nucleus exhibiting chromosomal characteristics. Consistent with its larger genome, P. hordei had a higher repeat content ([~]70%) than related cereal rust fungi, driven primarily by the proliferation of LTR retroelements and DNA transposons. Across the global pan-genome of 13 unique nuclear haplotypes, approximately one-third of all protein orthogroups were conserved across all isolates. Only 18% of predicted effector orthogroups were shared between all haplotypes, reflecting the highly dynamic and variable nature of the effector repertoire. The long-term propagation of clonal P. hordei lineages is apparent both within the US and globally, and nuclear exchange is important for generating novel diversity and virulence profiles. The high degree of genome plasticity is evident in extensive structural variation, including large-scale translocations and inversions as well as a putative accessory chromosome. These chromosome-level, haplotype-resolved genomes provide a foundational resource for exploring the evolution, diversity, and avirulence gene repertoire of P. hordei.

genomics↗

bioRxiv2026

Mapping Pc94-Mediated Crown Rust Resistance in Oat Reveals a zfBED NLR and Introgression Variation

Host resistance is a critical component of oat crown rust disease management. Pc94 is a qualitative resistance locus derived from diploid Avena strigosa with several independent introgressions into A. sativa that have been used in cultivar deployment. Quantitative trait locus (QTL) analysis combining previously published data for a historic A. strigosa population segregating for Pc94 revealed a large effect QTL on the distal end of A. strigosa chromosome 7A. Genome assembly of the parents identified a cluster of five nucleotide binding site leucine-rich repeat receptor (NLR) candidate genes within the QTL region. A single candidate NLR with an integrated zinc finger BED domain, AstNLR94, was determined as necessary for Pc94 resistance based on map-based cloning and forward mutagenesis. A presence/absence allele specific PCR marker was designed in AstNLR94 and verified for accuracy and specificity in a diverse panel of A. strigosa and A. sativa. Pc94 introgressions in A. sativa ranged in size from 1.7-71 Mbp and two different introgression locations appear to have occurred. In A. sativa Leggett, a 6.3 Mbp Pc94 introgression is located at the end of chromosome 2A, and the same sized introgression was discovered in the OT3098 v2 genome. Finally, a QTL analysis identified an additional minor resistance locus on A. strigosa chromosome 4A, which has complicated previous efforts to characterize the Pc94 locus. This is the first report of an NLR gene underlying disease resistance in Avena spp. and delivers a Pc94 marker for marker assisted selection to produce disease resistant cultivars. Key messageWe mapped a zfBED-NLR encoding gene necessary for Pc94 resistance, developed a diagnostic marker, and revealed diverse introgression sizes, clarifying Pc94s history and utility for durable oat crown rust resistance.

plant biology↗

bioRxiv2025

Starch synthesis in Brachypodium distachyon endosperm occurs in dynamic, connected amyloplast compartments

The morphology of starch granules is a major determinant of the functional and nutritional properties of starch and is highly variable among cereal species. Much of this morphological variation stems from differences in the spatial and temporal patterns of starch granule initiation in amyloplasts during grain development. Simple granules are thought to arise from a single initiation per amyloplast (e.g., in Brachypodium distachyon), whereas compound granules develop from multiple initiations per amyloplast (e.g., in rice). Using live-cell imaging in transgenic Brachypodium lines expressing a fluorescent amyloplast reporter construct, we discovered that simple-type starch granules in Brachypodium can arise from multiple initiations per amyloplast. The amyloplasts showed dynamic changes in their structure, the formation of stromules, and the movement of both the amyloplast within the cell and the starch granules within the amyloplasts. Our results suggest complex and pleiomorphic amyloplast organisation and mobility that can influence starch granule formation and morphology. This goes beyond the existing one granule, one amyloplast model for simple-type granules, and advances our understanding of both amyloplast biogenesis and granule formation.

plant biology↗

bioRxiv2025

Haplotype-resolved genomes of diverse oat crown rust isolates reveal both global dispersion of long-lived clonal haplotypes and limited recombination between haplotypes.

Genetic diversity of pathogen populations plays an important role in host adaptation. While single high quality genome references are a valuable resource, a compilation of genome references from individuals increases the breadth of genetic variation within a species that is captured. Puccinia coronata f. sp. avenae (Pca), a fungal pathogen causing crown rust of oat, demonstrates rapid virulence evolution and adaptation to newly released cultivars. To broaden the geographic and temporal distribution of available Pca genomes, we generated nuclear haplotype-resolved genome references for ten isolates from Europe, Africa and the Middle East and compared these with existing references for USA and Australian isolates. Of the full collection of 52 haplotypes, 40 were unique. Importantly, the presence of a nearly identical haplotype in a UK isolate collected in 1984 and in USA isolates from 1990 and 2017 supports the existence of long-lived clonal haplotypes in the global population that have been exchanged between lineages. Taken together with the identification of infrequent recombination between haplotypes from geographically dispersed isolates, this evidence reflects a globally mobile population of Pca that is mostly comprised of persistent clonal lineages with some influence from rare recombination events. Analysis of the core and non-core proteome suggests that while the core proteome is enriched for predicted secreted and effector proteins, sequence and expression variation are most prevalent in non-core orthogroups. We anticipate that this expanded collection of haplotypes will facilitate the development of new surveillance technologies and identification of virulence loci.

genomics↗

bioRxiv2024

Engineering an Exo70 integrated domain of a barley NLR for improved blast resistance

Intracellular immune receptors protect plants from microbial invasion by detecting and responding to pathogen-derived effector molecules, often triggering cell death responses. However, pathogen effectors can evolve to avoid immune recognition, resulting in devastating diseases that threaten global agriculture. Here, we show that an integrated Exo70 domain from the barley NLR RGH2 can interact with both the rice blast pathogen effector AVR-Pii and a closely related wheat blast variant. We used structure-led engineering to develop RGH2+ that shows increased binding affinity towards AVR-Pii variants and increased cell death responses on heterologous expression in Nicotiana benthamiana. Infection assays in transgenic barley lines carrying RGH2+ with the paired NLR RGH3 indicate a reduced susceptibility to blast strains expressing AVR-Pii variants. These results demonstrate the potential of engineering NLR receptors as an effective strategy for improving resistance towards one of the most destructive diseases affecting cereal production.

plant biology↗

bioRxiv2024

Putative neofunctionalization of a Poales-specific EXO70 clade

EXO70s are uniquely expanded in land plants compared to all other eukaryotic lineages. The functional implications of this expansion and diversification on the conserved role of EXO70 as a subunit of the octameric exocyst complex have remained unresolved. We previously demonstrated barley (Hordeum vulgare) EXO70FX12, a member of the monocot-specific EXO70FX clade, is required for resistance to wheat stripe rust in conjunction with the leucine-rich repeat receptor kinase (LRR-RK) HvPUR1. Through phylogenetic analysis, we identified unique features of the EXO70FX clade, leading us to hypothesize that this clade experienced neofunctionalization. Using structural predictions and protein-protein interaction assays, we demonstrate that HvEXO70FX12 lost the ability to serve as a subunit within the exocyst complex. We predict that the EXO70FX clade has largely lost exocyst association and represents a novel acquisition that emerged during Poales diversification for immunity.

plant biology↗

bioRxiv2024

Genomes of Poaceae sisters reveal key metabolic innovations preceding the emergence of grasses

The grass family (Poaceae, Poales) holds immense economic and ecological significance, exhibiting unique metabolic traits, including dual starch and lignin biosynthetic pathways. To investigate when and how the metabolic innovations known in grasses evolved, we sequenced the genomes of four Poales species, including Joinvillea ascendens and Ecdeiocolea monostachya representing the sister clade to Poaceae. The rho whole genome duplication ({rho}WGD) in the ancestral lineage for all grasses contributed to the gene family expansions underlying cytosolic starch biosynthesis, whereas an earlier tandem duplication of phenylalanine ammonia lyase (PAL) gave rise to phenylalanine/tyrosine ammonia lyase (PTAL) responsible for the dual lignin biosynthesis. Integrated functional genomic and biochemical analyses of grass relatives further revealed the molecular basis of key metabolic innovations predating the evolution of grasses. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/622220v2_ufig1.gif" ALT="Figure 1"> View larger version (108K): org.highwire.dtl.DTLVardef@117dd71org.highwire.dtl.DTLVardef@1cb5daborg.highwire.dtl.DTLVardef@72a331org.highwire.dtl.DTLVardef@38124e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

VRS5 (HvTB1) binds to the promoter of tillering and floral homeotic genes to regulate their expression

Variation in shoot architecture, or tillering, is an important adaptive trait targeted during the domestication of crops. A well-known regulatory factor in shoot architecture is TEOSINTE BRANCHED 1 (TB1). TB1 and its orthologs have a conserved function in integrating environmental signals to regulate axillary branching, or tillering in cereals. The barley ortholog of TB1, VULGARE ROW-TYPE SIX 5 (VRS5) does not only regulate tillering, but is also involved in regulating row-type by inhibiting lateral spikelet development. These discoveries predominantly come from genetic studies, but how VRS5 regulates these processes on a molecular level remains largely unknown. By combining transcriptome analysis between vrs5 and wild type at different developmental stages and DAP-sequencing to locate the genome-wide DNA binding sites of VRS5, we identified bona fide targets of VRS5. We found that VRS5 targets abscisic acid related genes, potentially to inhibit tillering in a conserved way. While later in inflorescence development, row-type gene VRS1 and several known floral development genes, like MIKCc type MADS-box genes, are targeted. This study identifies several significant genes for mutational analysis, representing a selection of bona fide targets that will contribute to a deeper understanding of the VRS5 network and its role in shaping barley development.

plant biology↗

bioRxiv2024

Rpt5 encodes a receptor-like protein that provides broad and effective net form net blotch (Pyrenophora teres f. teres) resistance in barley

The foliar disease net form net blotch (NFNB), caused by the necrotrophic fungal pathogen Pyrenophora teres f. teres (Ptt), causes significant yield and quality losses of barley worldwide. Dominant resistance conferred by the Resistance to Pyrenophora teres 5(Rpt5) gene from barley line CI5791 is the broadest and most effective resistance reported in this pathosystem. The Rpt5 locus was identified in multiple independent genetic studies utilizing diverse host populations and Ptt isolates, and harbors both dominant Rpt5 resistance and isolate-specific susceptibility genes/alleles that are dominant in the absence of Rpt5, designated susceptibility to Pyrenophora teres 1 (Spt1). Ptt virulence and avirulence effectors from diverse pathogen isolates genetically interact with the Rpt5/Spt1 locus, suggesting a complex locus with a function targeted by the evolution of a diversity of pathogen effectors. High-resolution mapping utilizing 1,920 recombinant gametes from a CI5791 x Tifang biparental population, identified 12 candidate genes in an [~]4.6 Mb delimited region in the cv Morex V3 genome assembly, but is 1.1 - 2.2 Mb in the pangenome assemblies, containing 5-12 genes. Analysis revealed a strong correlation between the CI5791 allele of a receptor-like protein (RLP), provisionally designated Rpt5 candidate gene 1, (Rcg1), and broad Rpt5-mediated resistance. Two independent transformants of the CI5791 Rcg1 allele in the susceptible cv Golden Promise background showed significantly increased resistance when challenged with Rpt5 avirulent Ptt isolates 6A, 15A, and 0-1 compared to the Golden Promise wildtype. Thus, Rpt5, encodes an RLP and is the first net blotch resistance gene cloned in barley. Significance StatementNet form net blotch (NFNB) causes substantial yield and quality losses of barley worldwide. Despite decades of ongoing research into genetic resistance to Pyrenophora teres f. teres, the causal agent of NFNB, no host resistance or susceptibility genes in this pathosystem had been previously identified. We present the identification and validation of Rpt5, which confers the broadest and most effective resistance against NFNB. To our knowledge Rpt5 is the first genetically defined resistance gene in a monocot to encode an RLP.

plant biology↗

bioRxiv2024

Molecular mimicry of a pathogen virulence target by a plant immune receptor

Plants and animals respond to pathogen attack by mounting innate immune responses that require intracellular nucleotide binding leucine-rich repeat (NLR) proteins. These immune receptors detect pathogen infection by sensing virulence effector proteins. However, the mechanisms by which receptors evolve new recognition specificities remain poorly understood. Here we report that a plant NLR has evolved the capacity to bind to a pathogen effector by acting as a molecular mimic of a virulence target of the effector, thereby triggering an immune response. The barley NLR Mildew Locus A 3 (MLA3) confers resistance to the blast fungus Magnaporthe oryzae by recognizing the effector Pwl2. Using structural analysis, we show that MLA3 has acquired the capacity to bind and respond to Pwl2 through molecular mimicry of the effector host target HIPP43. We demonstrate that the amino acids at the binding interface of MLA3 and Pwl2 are highly conserved in interface of HIPP43 with Pwl2, and are required to trigger an immune response. We used this discovery to bioengineer SR50--an MLA ortholog in rye that confers resistance to wheat stem rust--by introducing the Pwl2 binding interface of MLA3. This chimeric receptor has dual recognition activities, binding and responding to effectors from two major cereal pathogens. Collectively, these results provide evidence that plant immune receptors have evolved sophisticated mimicry strategies to counteract pathogen attack.

plant biology↗

bioRxiv2024

Discovery of functional NLRs using expression level, high-throughput transformation, and large-scale phenotyping

Protecting crops from pests and diseases is vital for the sustainable agricultural systems needed for food security. Introducing functional resistance genes to enhance the plant immune system is an effective method of disease control, but identifying new immune receptors is time-consuming and resource intensive. We observed that functional immune receptors of the NLR class show a signature of high expression in uninfected plants across both monocot and dicot species. Here we show that this signature, combined with high throughput crop transformation, can be used to rapidly identify candidate NLRs from diverse plant species and validate pathogen resistance directly in crop plants. As a proof of concept, we generated a wheat transgenic library carrying 995 NLRs from 18 grass species. Screening the collection with the stem rust pathogen Puccinia graminis, which is a major threat to wheat production, we confirm 19 new resistance genes. This pipeline facilitates resistance gene discovery, unlocking a large gene pool of diverse and non-domesticated plant species and providing in-planta gene validation of disease resistance directly in crops.

plant biology↗

bioRxiv2024

The blast effector Pwl2 is a virulence factor that modifies the cellular localisation of host protein HIPP43 to suppress immunity.

The rice blast fungus Magnaporthe oryzae secretes a battery of effector proteins to facilitate host infection. Among these effectors, Pwl2 was first identified as a host specificity determinant for infection of weeping lovegrass (Eragrostis curvula) and is also recognised by the barley Mla3 resistance gene. However, its biological activity is not known. Here we show that PWL2 expression is regulated by the Pmk1 MAP kinase during cell-to-cell movement by M. oryzae at plasmodesmata (PD)-containing pit field sites. Consistent with its regulation, we provide evidence that Pwl2 binds to a barley heavy metal-binding isoprenylated protein HIPP43, which results in its displacement from plasmodesmata. Transgenic barley lines overexpressing either PWL2 or HIPP43 exhibit attenuated immune responses and increased disease susceptibility. By contrast, a Pwl2SNDEYWY mutant that does not interact with HIPP43, fails to alter the PD localisation of HIPP43. Targeted deletion of three copies of PWL2 in M. oryzae results in a{Delta} pwl2 mutant showing gain-of-virulence to weeping lovegrass and barley Mla3 lines, but also a reduction in severity of blast disease on susceptible host plants. Taken together, our results provide evidence that Pwl2 is a virulence factor that acts by suppressing host immunity through perturbing the plasmodesmatal deployment of HIPP43.

plant biology↗

bioRxiv2023

A barley MLA receptor is targeted by a non-ribosomal peptide effector of the necrotrophic spot blotch fungus for disease susceptibility

The evolutionary history of plant interactions with necrotrophic pathogens that feed on dying host cells and their virulence mechanisms remains fragmentary. We have isolated the barley gene Scs6, which is required for the necrotrophic fungus Bipolaris sorokiniana isolate ND90Pr to cause spot blotch disease. Scs6 is located at the disease resistance gene locus Mildew locus a (Mla) and encodes an intracellular nucleotide-binding leucine-rich repeat receptor (NLR). In transgenic barley, Scs6 is sufficient to confer susceptibility to ND90Pr in accessions naturally lacking the receptor, resulting in infection-associated host cell death. Expression of Scs6 in evolutionarily distant Nicotiana benthamiana reconstitutes a cell death response to an uncharacterized non-ribosomal peptide effector produced by ND90Pr-specific non-ribosomal peptide synthetases (NRPSs) encoded at the VHv1 virulence locus. Our data suggest that the heat-resistant effector directly activates the SCS6 receptor. Scs6 is an allelic variant of functionally diversified Mla resistance genes each conferring strain-specific immunity to barley powdery mildew isolates with a matching proteinaceous pathogen effector. Domain swaps between MLA and SCS6 NLRs and expression of the resulting hybrid proteins in N. benthamiana reveal that the SCS6 leucine-rich repeat domain is a specificity determinant for the NRPS-derived effector to activate the receptor. Scs6 evolved after the divergence of barley from wheat and is maintained in several wild barley populations with an incidence of 8%, suggesting a beneficial function for the host. Evolution of the bona fide immune receptor SCS6 targeted by the NRPS-derived effector was key for the emergence of strain-specific spot blotch disease in domesticated barley.

plant biology↗

bioRxiv2022

Barley MLA3 recognizes the host-specificity determinant PWL2 from rice blast (M. oryzae)

Plant nucleotide-binding leucine-rich repeat immune receptors (NLRs) directly or indirectly recognize pathogen-secreted effector molecules to initiate plant defense. Recognition of multiple pathogens by a single NLR is rare and usually occurs via monitoring for changes to host proteins; few characterized NLRs have been shown to recognize multiple effectors. The barley NLR Mla has undergone functional diversification and Mla alleles recognize host-adapted isolates of barley powdery mildew (Blumeria graminis f. sp. hordei; Bgh). Here, we show that Mla3 also confers resistance to rice blast (Magnaporthe oryzae) in a dosage dependent manner. Using a forward genetic screen, we discovered that the recognized effector from M. oryzae is PWL2, a host range determinant factor that prevents M. oryzae from infecting weeping lovegrass (Eragrostis curvula). Mla3 has therefore convergently evolved the capacity to recognize effectors from diverse pathogens.

plant biology↗

bioRxiv2021

A lineage-specific Exo70 is required for receptor kinase-mediated immunity in barley

In the evolution of land plants, the plant immune system has experienced expansion in immune receptor and signaling pathways. Lineage-specific expansions have been observed in diverse gene families that are potentially involved in immunity, but lack causal association. Here, we show that Rps8-mediated resistance in barley to the fungal pathogen Puccinia striiformis f. sp. tritici (wheat stripe rust) is conferred by a genetic module: LRR-RK and Exo70FX12, which are together necessary and sufficient. The Rps8 LRR-RK is the ortholog of rice extracellular immune receptor Xa21 and Exo70FX12 is a member of the Poales-specific Exo70FX clade. The Exo70FX clade emerged after the divergence of the Bromeliaceae and Poaceae, and comprises from 2 to 75 members in sequenced grasses. These results demonstrate the requirement of a lineage-specific Exo70FX12 in Rps8 LRR-RK immunity and suggest that the Exo70FX clade may have evolved a specialized role in receptor kinase signaling.

plant biology↗