Robbie Waugh

Structural variants (SVs) are abundant in plant genomes and influence agronomic traits, yet their regulatory interpretation remains challenging. Here, we combine pangenome-wide profiling of DNA methylation and chromatin accessibility across 20 barley genotypes, complemented by histone modification and chromatin interaction data in a subset of 10 genotypes. Comparative analysis of genotype-specific epigenomes reveals a globally conserved DNA methylation landscape across the barley pangenome alongside extensive regulatory variability at orthologous genes. We show that SVs do not broadly remodel global chromatin landscapes but instead act through context-dependent rewiring of local regulatory interactions. Despite this epigenomic stability, SVs may contribute to gene expression changes via chromatin contacts. Tissue-specific chromatin accessibility demonstrates that SV effects depend on developmental context. Integrating chromatin state variation with SVs at key vernalization genes explains epigenetic contributions to growth habit diversity. Together, these results provide a framework for interpreting the regulatory consequences of structural variation in crop genomes.

Heavy metals act as essential metalloprotein cofactors in numerous physiological processes but can become toxic when non-essential metals accumulate or when essential metals are in excess. As plants continuously encounter heavy metals through their roots, they have evolved complex homeostatic mechanisms to regulate metal uptake and distribution. The Heavy Metal ATPase ( HMA ) gene family encodes a group of heavy metal transporting P-type ATPases that have been linked to stress resistance and nutrient supply. Here, we used a bioinformatics approach to identify and characterise 13 HMA genes containing characteristic P _1B -type ATPase domains and motifs in the barley Morex V3 reference genome. The genes are located on five of the seven barley chromosomes. Phylogenetic analysis revealed that they cluster into five sub-clades, including one clade unique to barley. Expression profiling across multiple datasets showed distinct temporal and tissue-specific expression patterns among HvHMA s, with several members exhibiting significant transcriptional responses to specific biotic and abiotic stresses. By utilising recently available pan-transcriptomic and pan-genomic resources, we have identified substantial allelic diversity and inter-accession variation in HvHMA s. Our findings suggest that HvHMA s have functions extending beyond canonical heavy metal homeostasis and warrant further investigation for their potential roles in broader physiological and stress-related processes.

Summary: Land plants secrete a protective outer cuticular layer with diverse functions. Barley ( Hordeum vulgare L.) develops two cuticular specialisations: the β‐diketone rich wax bloom on vegetative tissues and an adherent grain surface which sticks to the hulls, leading to barley's distinctive ‘covered’ grain phenotype. Two barley SHINE transcription factors, HvWIN1 and NUD, promote the wax bloom and covered grain phenotypes, respectively, yet we know little about other genes involved. We investigated a barley mutant showing defects in both cuticular specialisations to better understand the networks and processes underlying these traits. We identified the barley BODYGUARD1 ( HvBDG1 ) gene encoding an α/β hydrolase as crucial for leaf cuticular integrity and wax‐bloom deposition. Mining tetraploid wheat ( Triticum turgidum ssp. durum ) mutant populations demonstrated that BDG1 and WIN1 orthologues also control the wax bloom in wheat. We further reveal that NUD and HvWIN1 retain functional, independent overlap in leaf cuticle integrity and hull adhesion in barley, functions which involve upregulation of HvBDG1 and other direct or indirect targets, shared and distinct, depending on the stage and tissue. Our work greatly expands our knowledge of genetic and developmental mechanisms underlying shared and distinctive cuticular features in plants.

OzBarley is a comprehensive genotype-to-phenotype resource to support research and enhance barley breeding by integrating genotypic and phenotypic data for gene discovery. This publicly available dataset comprises genotypic data from historical and modern elite barley cultivars of significance to Australian barley breeding. The phenotypic component includes high-throughput imaging and X-ray CT-based spike analysis, enabling trait measurements such as plant growth dynamics and seed morphology. Users can leverage genome-wide association studies (GWAS) and genomic selection to identify genetic variants associated with agronomically important traits in the OzBarley datasets, thereby accelerating targeted breeding strategies. The dataset is accessible for download under CC-BY 4.0 license and users are invited to contribute new data when using OzBarley plant material in their research. Through its FAIR-compliant design ( F indable, A ccessible, I nteroperable, R eusable), OzBarley represents a resource to protect genotypes of historical relevance, explore the genetic architecture of adaptation to dryland environments, and to enhance knowledge of the resilience, yield, and quality of barley cultivars under diverse environmental conditions, contributing to global food security and agricultural sustainability.

Anthropogenic selection of grain traits such as dormancy has shaped the developmental trajectories of crops. In cereals, shortening dormancy provides rapid and even postharvest germination, but increases the risk of weather-induced preharvest sprouting, with yearly harvest losses beyond 1 billion dollars. Our understanding of how, why, when, and where cereal dormancy diversification arose is fragmentary. Here, we show in the founder crop barley ( Hordeum vulgare ) that dormancy is primarily regulated through a mosaic of locus haplotypes comprising copy number variation and inherent kinase activity of Mitogen-activated protein kinase kinase 3 ( MKK3 ). We provide evidence supporting the historical selection of specific MKK3 haplotypes that shaped dormancy levels according to changing climatic pressures and outline a genetic framework for breeders to balance grain dormancy and preharvest sprouting avoidance.

Using a positional candidate-gene approach, we show that semi-sterile desynaptic8 mutants are associated with deleterious variants of the barley homolog of XRCC2 (X-Ray Repair Cross Complementing 2). In barley XRCC2 mutants, the initial meiotic progression is normal, albeit with a small delay in initiation, with completion of synapsis. However, the absence of HvXRCC2 subsequently leads to a dramatic reduction in the number of crossovers, chromosome mis-segregation, and infertility, suggesting that HvXRCC2 plays a major role in recombination. This mutant phenotype is congruent with that reported in mammalian studies but contrasts with the XRCC2 mutant in Arabidopsis which is fertile, exhibits normal chromosome pairing and correct chromosome segregation, and is associated with an increased rate of crossovers. This observation indicates that the XRCC2 mutant phenotype in Arabidopsis is not representative of all plants and that XRCC2 is not a good candidate for the modulation of recombination in barley.

Summary: This study characterizes the function of a grass‐specific E3 ubiquitin ligase, HvST1 , in regulating synapsis and crossover (CO) formation during meiosis in barley ( Hordeum vulgare ). In large‐genome cereals, COs are predominantly restricted to distal chromosomal regions, limiting genetic recombination and breeding flexibility. We aimed to identify genetic components regulating CO frequency and distribution. A frameshift mutation in HvST1 was identified in the semi‐sterile barley near‐isogenic line BW233 through fine mapping of the des12.w locus. The causal role of this mutation was validated via CRISPR/Cas9 gene editing. HvST1 function was investigated using in vitro autoubiquitination and substrate ubiquitination assays, while meiotic progression was assessed using structured illumination microscopy and immunolocalization of key axis and synaptonemal complex (SC) proteins. Loss of HvST1 function led to disrupted SC formation, persistent ASY1 signal, and aberrant ZYP1 polycomplex formation. Despite impaired synapsis, Hvst1 mutants showed a significant increase in distal CO frequency. HvST1 was shown to ubiquitinate ASY1 in vitro , linking its activity to protein turnover at the chromosome axis. HvST1 is critical for normal synapsis and CO regulation during meiosis in barley. Its loss disrupts SC progression but enhances distal CO formation, revealing a previously uncharacterized ubiquitination‐based mechanism modulating recombination in grasses.

Over the past 10,000 years, the development of civilization has been enabled by the domestication of plants and animals tailored to human needs. The Triticeae tribe, including barley and wheat, has emerged as one of the most important sources of staple foods worldwide. Here, comparing genomes of wheat and barley genotypes from around the world, we unveiled genomic footprints of convergent selection affecting genes involved in crop adaptation and productivity, as well as a lack of parallel selection for diverse genes delivering genetic diversity specific to particular geographic and associated environmental conditions. We demonstrate that studying convergent selection between crops can help to identify genes crucial for adaptation and sources of diversity for improving cultivated species—forming the basis of the proposed concept of inter-crop translational research for breeding.

To exploit allelic variation in Hordeum vulgare subsp. spontaneum, the Wild Barley Diversity Collection was subjected to paired-end Illumina sequencing at ∼9 × depth and evaluated for several agronomic traits. We discovered 240.2 million single nucleotide polymorphisms (SNPs) after alignment to the Morex V3 assembly and 24.4 million short (1 to 50 bp) insertions and deletions. A genome-wide association study of lemma color identified one marker-trait association (MTA) on chromosome 1H close to HvBlp, the cloned gene controlling black lemma. Four MTAs were identified for seedling stem rust resistance, including 2 novel loci on chromosomes 1H and 6H and one co-locating to the complex RMRL1-RMRL2 locus on 5H. The whole-genome sequence data described herein will facilitate the identification and utilization of new alleles for barley improvement.