Climate change intensifies abiotic stress and disease pressure on crops, while domestication has narrowed genetic diversity. Advances in high-throughput sequencing, pangenomics and genome editing enable discovery, validation and precise deployment of beneficial alleles from landraces and wild relatives. These approaches transform plant breeding into a predictive, sustainable discipline, illustrated here on barley and wheat resistance breeding.

Hop is an essential ingredient in brewing, providing beer with its characteristic bitterness and aroma. Most modern hop cultivars are hybrids between European and North American hop lineages, but how these ancestries contribute to bitter acid content, the most important trait in hop breeding, remains unclear. Here, we report chromosome-scale, haplotype-resolved assemblies of the hybrid hop cultivar Apollo, assign European and North American ancestry across the genome, and identify varying levels of recombination suppression between chromosomes of either origin. Using this reference, we uncover genetic and chemical diversity in core bittering pathways between European and North American hops. We further show additive effects of beneficial European and North American alleles on bitter acid content, providing a foundation for genomics-assisted hop breeding.

Abstract Rye ( Secale cereale L.) is an important cereal crop known for its high yield potential and tolerance to biotic and abiotic stresses. However, its large, repeat-rich, and heterozygous genome has posed challenges for assembly compared to related species such as wheat and barley. Here, we present a high-quality, chromosome-scale genome assembly of the inbred line Lo7, generated using PacBio HiFi, Oxford Nanopore, Hi-C, and BioNano technologies with the TRITEX pipeline. The resulting Lo7_V3 assembly spans 6.76 Gb with a contig N50 of 128 Mb, correcting previous misorientations and fully assembling all seven centromeres. Repetitive clusters containing rye-specific satellite sequences (pSc200 and pSc250) are contiguously assembled. Their chromosomal positions are validated using FISH. Centromeric retrotransposon analysis reveals RLG_Abia and RLG_Abigail as abundant, recently active elements, unlike in wheat. Collectively, the Lo7_V3 genome assembly provides an improved genomic resource for future genomic research in rye and related cereal species.

Abstract Background As pangenomes approach saturation, identifying additional genomes that contribute novel sequence information becomes increasingly difficult. Current sample-selection strategies often rely on global diversity metrics or variant counts and do not explicitly account for the composition of an existing pangenome, a limitation that becomes increasingly relevant as pangenomes mature. Here, we present SelHap, a haplotype-based pipeline that uses whole-genome sequencing (WGS) data to prioritize accessions based on their contribution of novel haplotypes relative to a defined background, enabling targeted and iterative pangenome expansion. Results We applied SelHap to the barley pangenome, using 76 assembled genomes as a background to select new accessions from a large WGS panel. Using this approach, we generated chromosome-scale genome assemblies from 19 accessions selected with SelHap and from 17 elite lines selected based on their relevance in historical barley breeding. Across multiple benchmarking scenarios, SelHap-based selection consistently resulted in a greater increase in non-redundant (single-copy) pangenome sequence, demonstrating that prioritizing haplotype novelty relative to an existing background maximizes unrepresented sequence content. Conclusions By transforming complex haplotype-clustering outputs into interpretable summaries and ranked candidate lists, SelHap provides a practical framework for targeted pangenome expansion. Beyond sample selection, SelHap can facilitate ancestry and germplasm comparisons across diverse panels. As WGS data become more accessible, SelHap offers a scalable and interpretable solution for extending mature pangenomes by explicitly targeting previously unrepresented sequence space.

Background Herbarium collections are a vast but underutilized resource for ancient DNA research, containing over 400 million specimens with detailed metadata and spanning centuries of global biodiversity. Understanding patterns of DNA preservation in natural collections is crucial for optimizing ancient DNA studies and informing future curation practices. We analysed genomic data for 573 herbarium specimens from 6 plant species from the genera Hordeum and Oryza collected from the Americas and Eurasia over 220 years. Using standardized laboratory protocols and shotgun sequencing, we quantified DNA degradation and elucidated factors that accelerate it.Results We find significant age-dependent DNA fragmentation rates, indicating temporal degradation processes not detected in prehistoric samples. In our analysis, DNA decay rates in herbarium specimens were almost 8 times faster than in moa bones, reflecting fundamental differences in tissue composition and preservation environments. Environmental conditions at the time of specimen collection emerged as the major determinants of post-mortem damage rates, with the interaction term between temperature and genus being the dominant driver of cytosine deamination. We find no effect of sample storage on DNA damage and degradation.Conclusions These findings provide insights into how climatic origin, preservation environment, taxonomic identity, and age influence DNA preservation while highlighting opportunities for improving institutional preservation practices. Due to standardized preservation conditions, museum collections can provide better insights into DNA damage and degradation over time than archaeological and paleontological samples.

Abstract 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.

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.

The causal agents of yellow and leaf rust in wheat, Puccinia striiformis f. sp. tritici and Puccinia triticina , pose a serious threat to grain yield and quality worldwide. Growing durable resistant wheat cultivars is an effective protection measure contributing to sustainable agriculture. Many of the known resistance genes, however, have been overcome due to the high genetic diversity and adaptability of pathogen populations. Therefore, the present study aimed to identify novel loci associated with yellow rust and leaf rust in a genome-wide association study (GWAS) using 1,984 spring wheat accessions from the German Federal ex situ Genebank. Phenotypic data obtained from a detached leaf assay were combined with 90,283 genotyping-by-sequencing genome wide markers. Six significant peak marker-trait associations (MTA) were identified for yellow rust and leaf rust, respectively. These are located on chromosomes 1D, 2B, 3B, 4A, 4B, 4D, 5A, 6B, and 7D. Six candidate genes were identified in close proximity to the identified loci. These findings may be valuable for identifying and deploying genetic resources to broaden the genetic basis of resistance and safeguard durability of resistance against yellow and leaf rust.

Awns of wild barley (Hordeum vulgare ssp. spontaneum L.) are rough by default due to silicified upward-oriented trichomes on the awn's epidermis, forming a ratcheted surface, which is advantageous for seed dispersal and burial. Cultivated barley, however, may carry smooth awns covered by smaller barbs or lacking barbs completely. The gene Raw1 on chromosome 5H is a major factor controlling barley awn roughness and was shown to encode a LONG AND BARBED AWN1 (LABA1) homolog. Here we report, by using quantitative analysis of the barb trait, map-based cloning and Cas9-mediated gene knock-out, a second gene Raw7, located on barley chromosome 7H, encoding a putative two-component response regulator. We propose that Raw7 acts downstream of Raw1 in a cytokinin signaling pathway underlying cell cycle control in epidermal barb primordia cells. Raw1 and Raw7 show epistatic interaction, suggesting that Raw1 acts as the primary driver of barb initiation, while Raw7 modulates barb size and frequency. Our findings provide the foundation to study the selection and domestication history of the awn roughness trait in barley, and thus to dissect if awn roughness is providing an advantage in cultivated barley or if the trait persisted after domestication due to linkage drag.

Utilizing the diversity preserved in genebank collections is essential for accelerating crop improvement, yet information is often limited to selected core collections. Genome-wide prediction (GWP) offers a promising approach to large-scale phenotypic imputation, with proven utility in practical pre-breeding contexts. In this study, we leveraged GWP to expand the German Federal ex situ barley core collection (core1000) with a focus on resistance to Puccinia hordei, Blumeria graminis hordei, and Rhynchosporium commune. Using the barley core1000 collection, which was originally selected to maximize molecular diversity, we trained genomic prediction models and imputed resistance scores for 20,458 genebank accessions based on sequence data encompassing 306,049 high-quality SNPs. To empirically validate prediction accuracy, we selected 300 spring and winter barley genotypes for field evaluation across four environments, resulting in moderate-to-strong correlations between predicted and observed resistance levels. Genome-wide association mapping in this set revealed five marker–trait associations that were not detected in the original core1000 collection. These results demonstrate that prediction-informed sampling can effectively expand trait-relevant genetic diversity and increase the frequency of resistance-associated alleles, thereby improving the power to detect loci that may be overlooked in conventional panels. Accordingly, GWP supports the targeted inclusion of accessions with trait-relevant variation and enhances the value of genebank resources for trait discovery and pre-breeding applications.

Here we illuminate the evolutionary trajectory of domesticated wheat through genomic analysis of 3,000-6,000-year-old grains excavated in the southern Levant. Our results identify these specimens as an early domesticated form closely related to wheat accessions from Ethiopia, the Arabian Peninsula and India. Genomic evidence supports a multi-stage domestication model centred on the non-shattering spike, requiring mutations in both TtBtr1-A and TtBtr1-B genes. These mutations probably arose independently in northern and southern wild populations, respectively. The foundational domestication event was hybridization of these populations, uniting the required mutations to create domesticated wheat. Remarkably, this hybridization occurred at least twice, producing distinct domesticated lineages. Following this, ancient grain lineages acquired advantageous traits through gene flow from local wild emmer populations. These findings redefine wheat domestication as a prolonged, dynamic and regionally interconnected process, characterized by repeated independent hybridization events that were later diversified through human-led dispersal and local adaptation.

Integrating high-throughput phenotyping with multiple complementary GWAS models reduces method-dependent bias and enables reliable identification of novel loci and elite germplasm for durable yellow and leaf rust resistance in wheat. The causal agents of yellow and leaf rust in wheat, Puccinia striiformis f. sp. tritici and Puccinia triticina, pose a serious threat to grain yield and quality worldwide. Growing durable resistant wheat cultivars is an effective protection measure contributing to sustainable agriculture. Many of the known resistance genes, however, have been overcome due to the high genetic diversity and adaptability of pathogen populations. Therefore, the present study aimed to identify novel loci associated with yellow rust and leaf rust in a genome-wide association study using 1984 spring wheat accessions from the German Federal ex situ Genebank. Phenotypic data obtained from a detached-leaf assay were combined with 90,283 genotyping-by-sequencing genome-wide markers. Six significant peak marker-trait associations were identified for yellow rust and leaf rust, respectively. These are located on chromosomes 1D, 2B, 3B, 4A, 4B, 4D, 5A, 6B, and 7D. Six candidate genes were identified close to the identified loci. These findings may be valuable for identifying and deploying genetic resources to broaden the genetic basis of resistance and safeguard durability of resistance against yellow and leaf rust.

Wheat is the most widely cultivated crop in the world, with over 215 million hectares grown annually. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome-level the genomes of nine wheat cultivars, uncovering genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for these wheat cultivars across multiple tissues. Using the de novo annotations we identify cultivar-specific genes and define the core and dispensable genomes. Expression analysis across cultivars and tissues reveals conservation in expression between a large core set of homeologous genes, in addition to widespread changes in subgenome homeolog expression bias between cultivars and cultivar-specific expression profiles. We utilise both the newly constructed gene-based wheat pan-genome and pan-transcriptome, demonstrating variation in the prolamin superfamily and immune-reactive proteins across cultivars.

Using modern genomic tools, Feng et al. revisited Mendel's seven pea traits in a recent Nature study, uncovering the molecular genetic basis of all of them, including the three unresolved ones: pod color, pod shape, and flower position. Their work highlights the level of complexity provided by structural variation that could impact genes and their regulatory regions and thus influence the expression of plant traits. The authors demonstrate how revisiting foundational experiments with contemporary tools can manifest novel biological insights and also guide future crop improvement.

Wheat genetic resources hold the diversity required to mitigate agricultural challenges from climate change and reduced inputs. Using DArTseq, we genotype 461 wheat landraces and cultivars and evaluate them for powdery mildew resistance. By developing a k-mer-based GWAS approach with fully assembled genomes of Triticum aestivum and its progenitors, we uncover 25% more resistance-associated k-mers than single-reference methods, outperforming SNP-based GWAS in both loci detection and mapping precision. In total, we detect 34 powdery mildew resistance loci, including 27 potentially novel regions. Our approach underscores the importance of integrating multiple reference genomes to unlock the potential of wheat germplasm.

Whereas genome sequencing and assembly technologies are improving, cost can still be prohibitive for plant species with large, complex genomes. As a consequence, genomics work on some taxa in evolutionarily pivotal positions in the vascular plant tree of life has been hampered. The species-rich genus Ranunculus (Ranunculaceae) is an important angiosperm group for the study of polyploidy, apomixis, and reticulate evolution. However, neither mitochondrial nor high-quality nuclear genome sequences are available. This limits phylogenomic, functional, and taxonomic analyses thus far. Here, we tested Illumina short-read, Oxford Nanopore Technology (ONT) and PacBio (HiFi) long-read, and hybrid-read assembly strategies. We sequenced the diploid progenitor species R. cassubicifolius (R. auricomus species complex) and selected the best assemblies in terms of completeness, contiguity, and quality scores. We first assembled the plastome (156 kbp, 85 genes) and mitogenome (1.18 Mbp, 40 genes) sequences using Illumina and Illumina-PacBio-hybrid strategies, respectively. We also present an updated plastome and the first mitogenome phylogeny of Ranunculaceae, including studies of gene loss (e.g., infA, ycf15, or rps) with evolutionary implications. For the nuclear genome sequence, we favored a PacBio-based assembly polished three times with filtered short reads and subsequently scaffolded into eight pseudochromosomes by chromatin conformation data (Hi-C). We obtained a haploid genome sequence of 2.69 Gbp, with 94.1% complete BUSCO genes found and 35 482 annotated genes, and inferred ancient gene duplications compared to existing Ranunculales genomes. The genomic information presented here will enable advanced evolutionary-functional analyses for the species complex, but also for the genus and beyond Ranunculaceae.

The tetraploid genome and clonal propagation of the cultivated potato (Solanum tuberosum L.)1,2 dictate a slow, non-accumulative breeding mode of the most important tuber crop. Transitioning potato breeding to a seed-propagated hybrid system based on diploid inbred lines has the potential to greatly accelerate its improvement3. Crucially, the development of inbred lines is impeded by manifold deleterious variants; explaining their nature and finding ways to eliminate them is the current focus of hybrid potato research4-10. However, most published diploid potato genomes are unphased, concealing crucial information on haplotype diversity and heterozygosity11-13. Here we develop a phased potato pangenome graph of 60 haplotypes from cultivated diploids and the ancestral wild species, and find evidence for the prevalence of transposable elements in generating structural variants. Compared with the linear reference, the graph pangenome represents a broader diversity (3,076 Mb versus 742 Mb). Notably, we observe enhanced heterozygosity in cultivated diploids compared with wild ones (14.0% versus 9.5%), indicating extensive hybridization during potato domestication. Using conservative criteria, we identify 19,625 putatively deleterious structural variants (dSVs) and reveal a biased accumulation of deleterious single nucleotide polymorphisms (dSNPs) around dSVs in coupling phase. Based on the graph pangenome, we computationally design ideal potato haplotypes with minimal dSNPs and dSVs. These advances provide critical insights into the genomic basis of clonal propagation and will guide breeders to develop a suite of promising inbred lines.

Rye ( Secale cereale L.) is an important cereal crop known for its high yield potential and tolerance to biotic and abiotic stresses. However, its large, repeat-rich, and heterozygous genome has posed challenges for assembly compared to related species such as wheat and barley. Here, we present a high-quality, chromosome-scale genome assembly of the inbred line Lo7, generated using PacBio HiFi, Oxford Nanopore, Hi-C, and BioNano technologies using the TRITEX pipeline. The resulting Lo7_V3 assembly spans 6.76 Gb with a contig N50 of 128 Mb, correcting previous misorientations and achieving complete centromere assemblies across all seven chromosomes. Repetitive clusters containing rye-specific satellite sequences (pSc200 and pSc250) were contiguously assembled. Their chromosomal positions were validated using FISH. Centromeric retrotransposon analysis highlighted RLG_Abia as a prominent element in rye, showing signs of recent activity and high abundance, unlike in wheat. Collectively, the new Lo7_V3 genome assembly provides a highly improved resource that will support future genomic research and crop improvement efforts in rye and related cereal species.

Plant genetic resources (PGR) are a vital research infrastructure and an important asset to increase the resiliency of agri-food systems, conserve agrobiodiversity and mitigate the effects of climate change. In the current scenarios of climate change and biodiversity loss, it becomes increasingly urgent to ensure the conservation of existing crop diversity and assure its availability for research and breeding to enable the development of new, adapted crops. Throughout Europe, more than 400 collections conserve PGR of over 6,500 genera, with over 2 million accessions documented in the European Search Catalogue for Plant Genetic Resources (EURISCO). To make these resources available to breeders, more research investment in these collections is needed. Here, we analyze the participation of European genebanks in collaborative projects within the EU Horizon scheme as an indicator for the use of PGR collections in research. We highlight two Horizon projects, AGENT and G2P-SOL, and the ECPGR initiative European Evaluation Network (EVA), which have brought together genebanks and other stakeholders to create tools and knowledge on PGR. Their experience could be translated into a dedicated, large European research infrastructure for PGR (GRACE-RI), suggested in the Plant Genetic Resources Strategy for Europe and currently in the concept phase by the Horizon Europe project PRO-GRACE. GRACE-RI will connect European research institutes involved in PGR conservation and research and will be key to ensuring access to well-documented and maintained PGR and methods for their characterization and utilization, preventing further loss of plant biodiversity which is increasingly threatening European agriculture and natural landscapes.

Variegation mutants provide valuable insights into chloroplast biogenesis. We characterized a newly identified variegated barley mutant, in which the phenotype is controlled by duplicate dominant epistasis-representing, to our knowledge, the first reported case of digenic control in chloroplast-deficient mutants. The causal loci, Var4 and Var5, were mapped on chromosomes 2H and 3H. We used whole-genome resequencing to identify candidate genes. Our two top candidate genes are an NBR1-like selective autophagy receptor gene and a DNAJ-domain containing gene, respectively. Based on their homology-based functional annotation, both candidates could be implicated in chloroplast proteostasis, regulating protein import, folding, and/or degradation. We propose that mild, independent defects in proteostasis from each mutation act synergistically to surpass a functional threshold, impairing chloroplast development in early leaves while allowing partial recovery in later stages. These findings highlight a novel digenic mechanism underlying variegation and point to proteostasis as a central vulnerability in chloroplast biogenesis. ### Competing Interest Statement The authors have declared no competing interest.