Matthew James Moscou

Summary: 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 , AvrSrC2 , 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.

Summary: 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 AVR _A 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 ( Hv CAP2) that interacts with MLA and at least five Bh effectors, as well as additional effector-host PPI that correlate with loss of recognition of AVR _A13 and AVR _A6 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.

The grass family (Poaceae) has immense economic and ecological importance and exhibits distinctive metabolic traits, including dual starch and lignin biosynthetic pathways. We sequenced the genomes of Pharus , Joinvillea , Ecdeiocolea , and Typha species to investigate when and how these metabolic innovations evolved relative to the origin of the grass family. The rho whole-genome duplication (ρWGD) within the lineage that led to the last common ancestor of 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 ), which is responsible for the dual lignin biosynthesis. Integrated biochemical, functional, and structural studies, guided by phylogenomic analyses, further revealed the molecular basis of key metabolic innovations predating the evolution of grasses.

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, how receptors evolve new recognition specificities remains poorly understood. We found that the plant NLR MLA3 (Mildew locus a 3) has evolved to recognize a pathogen effector by acting as a molecular mimic of an effector virulence target, thereby triggering an immune response. By introducing the mimic’s binding interface into the wheat stem rust resistance protein SR50, we bioengineered a chimeric receptor with dual recognition activities that conferred resistance to two major cereal pathogens in barley transgenic lines. These results demonstrate that molecular mimicry by immune receptors can be harnessed to engineer multiple disease 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 intracellular nucleotide-binding leucine-rich repeat (NLR) RGH2 can interact with both the rice blast pathogen effector AVR-Pii and a closely related wheat blast causing variant. We used structure-led engineering to develop RGH2+ that shows increased binding affinity toward 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 toward one of the most destructive diseases affecting cereal production.

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.

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 further capture the genetic variation of Pca, we generated nuclear haplotype-resolved genomes for 10 isolates from Europe, Africa, and the Middle East and compared these with existing references for U.S. and Australian isolates. Of the full collection of 52 haplotypes, 40 were unique. Importantly, the presence of a nearly identical haplotype in a U.K. isolate collected in 1984 and in U.S. isolates from 1990 and 2017 supports the existence of long-lived clonal haplotypes in the global population that have been exchanged between lineages. We identified infrequent recombination between haplotypes from geographically dispersed isolates, hinting toward a globally mobile population of Pca that is mostly composed of persistent clonal lineages with some influence from rare recombination events. One isolate contained an additional scaffold with telomeric and centromeric features, suggesting the presence of a supernumerary chromosome. Whereas the core pan-proteome is enriched for predicted secreted and effector proteins, sequence and expression variation are most prevalent in non-core orthogroups, which also displayed allele-specific expression. We anticipate that this expanded collection of haplotypes will facilitate the development of new surveillance technologies and identification of virulence loci. [ ] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

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 .

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 message: We mapped a zfBED-NLR encoding gene necessary for Pc94 resistance, developed a diagnostic marker, and revealed diverse introgression sizes, clarifying Pc94 ’s history and utility for durable oat crown rust resistance.

Summary: 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). We used live‐cell imaging to visualise amyloplasts in the developing endosperm of Brachypodium , using transgenic lines expressing a fluorescent amyloplast reporter. We discovered that the simple‐type starch granules in Brachypodium can arise from multiple initiations per amyloplast. The amyloplasts showed dynamic changes in their structure and formed two types of stromules: stable stromules that formed a stromal continuum between amyloplasts, and short‐lived stromules that were more dynamic. We also observed actin‐dependent movement of amyloplasts within endosperm cells, and movement of starch granules within the amyloplasts. Our results suggest complex and pleiomorphic amyloplast organisation and mobility that could influence granule formation. 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.