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Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley ( Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion. The International Barley Genome Sequencing Consortium reports sequencing and assembly of a reference genome for barley, Hordeum vulgare . Barley genome sequenced Triticeae grasses, which include barley, wheat and rye, are widely cultivated plants with particularly complex genomes and evolutionary histories. Sequencing of the barley genome has been particularly challenging owing to its large size and particular genomic features, such as an abundance of repetitive elements. Nils Stein and colleagues of the International Barley Genome Sequencing Consortium report sequencing and assembly of a reference genome for barley ( Hordeumvulgare L). They use a combined approach of hierarchical shotgun sequencing of bacterial artificial chromosomes, genome mapping on nanochannel arrays and chromosome-scale scaffolding with Hi-C sequencing. This brings the first comprehensive, completely ordered assembly of the pericentromeric regions of a Triticeae genome. The authors also sequenced and examined genetic diversity in the exomes of 96 European elite barley lines with a spring or winter growth habit, and highlight the utility of this resource for cereal genomics and breeding programs.

P an genomes are collections of annotated genome sequences of multiple individuals of a species 1 . The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants 2 . Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that are rich in gene copy number variation. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that allelic diversity at structurally complex loci may have helped crop plants to adapt to new selective regimes in agricultural ecosystems.Reliable crop yields fuelled the rise of human civilizations. As people embraced a new way of life, cultivated plants, too, had to adapt to the needs of their domesticators. There are different adaptive requirements in a wild compared with an arable habitat. Crop plants and their wild progenitors differ in how many vegetative branches they initiate or how many seeds or fruits they produce and when. A case in point is barley (Hordeum vulgare): in six-rowed forms of the crops, thrice as many grains set as in the ancestral two-rowed forms. This change was brought about by knockout mutations 3 of a recently evolved regulator 4 of inflorescence development. Consequently, six-rowed barleys came to predominate in most barley-growing regions 5 . Taking a broader view of the environment as a set of exogeneous factors that drive natural selection, barley provides another fascinating, and economically important, example. The process of malting involves the sprouting of moist barley grains, driving the release of enzymes that break down starch into fermentable sugars. In the wild, various environmental cues can trigger germination to improve the odds of the emerging seedling encountering favourable weather conditions for subsequent growth 6 . In the malt house, by contrast, germination has to be fast and uniform in modern cultivars to satisfy the desired specifications of the industry. In addition to these examples, traits such as disease resistance, plant architecture and nutrient use have been a focus for plant breeders and studied intensively by barley geneticists 7 . Although barley genetic analysis flourished during a 'classical' period 8 in the first half of the 20th century, it started to lag behind small-genome models because of difficulties in adapting molecular biology techniques to a large genome rich in repeats 9 . However, interest in barley as a diploid model for temperate cereals has surged again as DNA sequencing became more powerful. High-quality sequences of several barley genomes have been recently assembled 10 . New sequencing technologies have shifted the focus of

Summary The European Commission (EC) proposal for New Genomic Techniques (NGTs) of July 2023 specifies that Category 1 NGT (NGT1) plants, which are considered equivalent to conventional plants, that is those obtainable by conventional plant breeding or mutagenesis, may differ from the recipient or parental plant by no more than 20 insertions, which cannot be longer than 20 bp; deletions can be no more than 20 but of any size. Here, we examine the proposed 20/20 NGT1 limit against the background of the theoretical considerations and older data used to frame it and in light of recent data from highly contiguous long‐read assemblies for reference genomes and pangenomes. We find that current genomic data indicate that natural variation in germplasm used by breeders is much greater than earlier understood and that both conventional breeding and mutagenesis can introduce genomic changes that are both more extensive in size and more frequent than the NGT Category 1 ‘20 insertions of maximum 20 bp’ limit would allow. Furthermore, natural variation also scales with genome size and complexity, a factor not considered in the EC proposal. We conclude that the proposed cut‐offs under which an NGT plant is considered equivalent to conventional plants do not align with what is observed in nature, conventional breeding and mutagenesis. Updating the 20/20 rule to broader limits would facilitate breeding for climate resilience, farming sustainability and nutritional security, while ensuring that NGT1 plants are equivalent to conventional ones.

Background Mutants have had a fundamental impact upon scientific and applied genetics. They have paved the way for the molecular and genomic era, and most of today’s crop plants are derived from breeding programs involving mutagenic treatments. Results Barley ( Hordeum vulgare L.) is one of the most widely grown cereals in the world and has a long history as a crop plant. Barley breeding started more than 100 years ago and large breeding programs have collected and generated a wide range of natural and induced mutants, which often were deposited in genebanks around the world. In recent years, an increased interest in genetic diversity has brought many historic mutants into focus because the collections are regarded as valuable resources for understanding the genetic control of barley biology and barley breeding. The increased interest has been fueled also by recent advances in genomic research, which provided new tools and possibilities to analyze and reveal the genetic diversity of mutant collections. Conclusion Since detailed knowledge about phenotypic characters of the mutants is the key to success of genetic and genomic studies, we here provide a comprehensive description of mostly morphological barley mutants. The review is closely linked to the International Database for Barley Genes and Barley Genetic Stocks ( bgs.nordgen.org ) where further details and additional images of each mutant described in this review can be found.

Saltatorial locomotion is a type of hopping gait that in mammals can be found in rabbits, hares, kangaroos, and some species of rodents. The molecular mechanisms that control and fine-tune the formation of this type of gait are unknown. Here, we take advantage of one strain of domesticated rabbits, the sauteur d’Alfort , that exhibits an abnormal locomotion behavior defined by the loss of the typical jumping that characterizes wild-type rabbits. Strikingly, individuals from this strain frequently adopt a bipedal gait using their front legs. Using a combination of experimental crosses and whole genome sequencing, we show that a single locus containing the RAR related orphan receptor B gene ( RORB ) explains the atypical gait of these rabbits. We found that a splice-site mutation in an evolutionary conserved site of RORB results in several aberrant transcript isoforms incorporating intronic sequence. This mutation leads to a drastic reduction of RORB-positive neurons in the spinal cord, as well as defects in differentiation of populations of spinal cord interneurons. Our results show that RORB function is required for the performance of saltatorial locomotion in rabbits.

Peanut (Arachis hypogaea L.) is globally recognized as an important oilseed crop. Traits related to plant architecture are closely associated with yield in peanut. In this study, we focused on four specific traits related to plant architecture—first branch length (FBL), main stem height (MSH), stem diameter (SD), and the number of nodes on the main stem (NSK)—across three locations. Using whole‐genome resequencing data from a genetically diverse collection of peanut landraces, we conducted a genome‐wide association study analysis to identify genetic variants associated with these traits. Notably, a novel genomic region on Arahy.03:39916768–42652757 was associated with SD for the first time. Homology analysis suggested that two annotated genes within this region may contribute to stem elongation and seed development. For MSH, NSK, and FBL, more than half of the significantly associated single‐nucleotide polymorphisms (SNPs) were localized on chromosome Arahy.05. Two SNPs at Arahy.09:112028951 and Arahy.09:112272948 were identified as the potential diagnostic markers for MSH and FBL: one homologous gene near these SNPs encoded an E3 ubiquitin–protein ligase, while the other encodes cinnamyl alcohol dehydrogenase. Additionally, one SNP at Arahy.05:53493734 was identified as a potential diagnostic marker for MSH, FBL, and NSK and validated using the penta‐primer amplification refractory mutation system and quantitative real‐time polymerase chain reaction. A gene near this SNP belongs to the protein kinase superfamily. Enzymes are known to regulate diverse cellular and biological processes, including plant development. These findings advance our understanding of the genetic basis of peanut architecture and provide valuable markers for future yield improvement efforts. Core Ideas We identified 411 significant single‐nucleotide polymorphisms (SNPs) associated with four traits related to peanut architecture through a genome‐wide association study. For the trait of stem diameter, we identified a novel genomic region on Arahy.03:39916768–42652757, associated with this trait for the first time. Two SNPs located at Arahy.09:112028951 and Arahy.09:112272948 were identified as the potential diagnostic markers for main stem height (MSH) and first branch length (FBL). An SNP located at Arahy.05:53493734 was associated with MSH, FBL, and the number of nodes on the main stem. The genomic region surrounding this SNP has been annotated as part of the protein kinase superfamily, which plays a crucial role in plant development. Plain Language Summary The yield of peanut (Arachis hypogaea L.) is closely linked to its structural characteristics, which can significantly influence planting density and lodging resistance. Here, we examined the complete genomic sequence of the peanut to identify minor variations that may correlate with peanut architecture. We specifically analyzed the genome to uncover insights related to four specific traits: first branch length (FBL), main stem height (MSH), SD, and number of nodes on the main stem. Notably, some of these loci were associated with multiple traits, particularly MSH and FBL, corroborating findings from previous studies. One of our most exciting discoveries was three genomic loci that may serve as a reliable predictor for plant architecture. Furthermore, we identified a crucial segment and two candidate genes on Arahy.03 that appear to be linked to stem thickness. Gaining insights into these genomic loci could prove invaluable for enhancing the cultivation of more robust and productive peanut plants in the future.

Social Impact Statement: Climate change threatens millions of farmers worldwide by exposing crops to multiple concurrent or sequential environmental stresses such as drought, heat, waterlogging, and diseases. Although crops have long been selected under naturally occurring multi-stress conditions, breeding pipelines largely focus on optimal or single-stress environments, leaving complex stress combinations under-addressed. Developing crop cultivars that withstand multiple stress scenarios is essential for ensuring food security, food safety, and strengthening farmer resilience. Breeding for multi-stress resilience seems feasible but requires international collaboration among applied crop scientists, pure biologists, and policymakers to develop climate-resilient crops that sustain people and ecosystems. Summary: Climate change is increasing the frequency and intensity of combined abiotic and biotic stressors that may occur simultaneously or sequentially, dramatically reducing crop growth and yield stability. Plant breeding activities primarily target crop improvement for a single stressor, limiting crop resilience under complex environmental conditions. This opinion paper highlights the complexity of crop breeding for multi-stress growing conditions and discusses major challenges and opportunities to enable plant breeders to develop more climate-resilient crops. It also outlines the importance of integrating conventional breeding approaches with multi-omics and novel breeding technologies to develop multi-stress resilient crop cultivars. Identifying and validating key regulatory genes involved in multi-stress resilience and evaluating their performance across diverse genetic backgrounds, environments, and stress combination scenarios are needed. Although achieving complete multi-stress resilience remains an immense challenge, advances in integrative approaches and cross-disciplinary collaboration are steadily improving the potential to enhance crop resilience to multiple environmental stresses.

In an ethyl methanesulfonate oat ( Avena sativa ) mutant population we have found a mutant with striking differences to the wild-type (WT) cv. Belinda. We phenotyped the mutant and compared it to the WT. The mutant was crossed to the WT and mapping-by-sequencing was performed on a pool of F2 individuals sharing the mutant phenotype, and variants were called. The impacts of the variants on genes present in the reference genome annotation were estimated. The mutant allele frequency distribution was combined with expression data to identify which among the affected genes was likely to cause the observed phenotype. A brassinosteroid sensitivity assay was performed to validate one of the identified candidates. A literature search was performed to identify homologs of genes known to be involved in seed shape from other species. The mutant had short kernels, compact spikelets, altered plant architecture, and was found to be insensitive to brassinosteroids when compared to the WT. The segregation of WT and mutant phenotypes in the F2 population was indicative of a recessive mutation of a single locus. The causal mutation was found to be one of 123 single-nucleotide polymorphisms (SNPs) spanning the entire chromosome 3A, with further filtering narrowing this down to six candidate genes. In-depth analysis of these candidate genes and the brassinosteroid sensitivity assay suggest that a Pro303Leu substitution in AVESA.00010b.r2.3AG0419820.1 could be the causal mutation of the short kernel mutant phenotype. We identified 298 oat proteins belonging to orthogroups of previously published seed shape genes, with AVESA.00010b.r2.3AG0419820.1 being the only of these affected by a SNP in the mutant. The AVESA.00010b.r2.3AG0419820.1 candidate is functionally annotated as a GSK3/SHAGGY-like kinase with homologs in Arabidopsis, wheat, barley, rice, and maize, with several of these proteins having known mutants giving rise to brassinosteroid insensitivity and shorter seeds. The substitution in AVESA.00010b.r2.3AG0419820.1 affects a residue with a known gain-of function substitution in Arabidopsis BRASSINOSTEROID-INSENSITIVE2. We propose a gain-of-function mutation in AVESA.00010b.r2.3AG0419820.1 as the most likely cause of the observed phenotype, and name the gene AsGSK2.1 . The findings presented here provide potential targets for oat breeders, and a step on the way towards understanding brassinosteroid signaling, seed shape and nutrition in oats.

Colored potato cultivars are rich in phenolic compounds that confer high antioxidant capacity; however, these beneficial metabolites could be susceptible to oxidation by polyphenol oxidases (PPOs), leading to enzymatic browning and the loss of antioxidant potential. Despite the agronomic relevance of this trade-off, the dynamics of the PPO gene family (StPPOs) gene expression in pigmented potatoes remains poorly characterized. Here, we present an integrated biochemical and molecular analysis of two purple-fleshed Peruvian landraces (Siriñacha and Angashungo), a partially pigmented landrace (Sapa), and non-pigmented cultivars, including the commercial cultivar Desirée. We quantified the total phenolic content, antioxidant capacity, and enzymatic browning index (EBI) using colorimetric and spectrophotometric methods. We also generated gene expression profiles of ten StPPO genes using semi-quantitative and digital PCR. Purple-fleshed cultivars exhibited significantly higher phenolic content and antioxidant capacity but also displayed accelerated browning kinetics compared to non- or partially pigmented genotypes. Expression analysis revealed cultivar-specific StPPO patterns, with StPPO2 and StPPO8 being markedly upregulated in pigmented materials, particularly StPPO8. These findings provide the first integrated biochemical and transcriptional evidence linking specific StPPO isoforms to enzymatic browning in colored potatoes, and highlight their potential for biotechnological applications.

Translocation and introduction of non-native organisms can have major impacts on local populations and ecosystems. Nevertheless, translocations are common practices in agri- and aquaculture. Each year, millions of wild-caught wrasses are transported large distances to be used as cleaner fish for parasite control in marine salmon farms. Recently, it was documented that translocated cleaner fish are able to escape and reproduce with local wild populations. This is especially a challenge in Norway, which is the world's largest salmon producer. Here, a panel of 84 informative SNPs was developed to identify the presence of nonlocal corkwing wrasse (Symphodus melops) escapees and admixed individuals in wild populations in western Norway. Applying this panel to ~2000 individuals, escapees and hybrids were found to constitute up to 20% of the local population at the northern edge of the species’ distribution. The introduction of southern genetic material at the northern edge of the species distribution range has altered the local genetic composition and could obstruct local adaptation and further range expansion. Surprisingly, in other parts of the species distribution where salmon farming is also common, few escapees and hybrids were found. Why hybridization seems to be common only in the far north is discussed in the context of demographic and transport history. However, the current lack of reporting of escapes makes it difficult to evaluate possible causes for why some aquaculture-dense areas have more escapees and hybrids than others. The results obtained in this study, and the observed high genomic divergence between the main export and import regions, puts the sustainability of mass translocation of nonlocal wild wrasse into question and suggests that the current management regime needs re-evaluation.