Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health ^1,2 . Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues ³ . Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales ⁴ . In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.

Powdery mildew of oats is a major threat to intensive oat farming under humid climate, and the use of resistant cultivars is the most environmentally friendly way of achieving safe yields. In this study, the genetic mapping of unexplored resistance genes from Avena byzantina accessions AVE2406 and AVE2925, designated Pm9 and Pm10, is described. Both accessions were crossed with susceptible cultivars, and monogenic segregation was established based on detached leaf segment tests. The two recombinant inbred line (RIL) populations RIL29 (with AVE2925) and RIL24 (with AVE2406) were phenotyped for powdery mildew resistance and genotyped with DArTseq. The genetic map of RIL24 had 2,516 markers in 30 linkage groups with a length of 2,641.5 cM; for RIL29, 921 markers were allocated to 30 linkage groups totalling to 1,378.2 cM. A major resistance QTL in RIL24 harbouring Pm9 was mapped to Mrg21 of the consensus map using BLASTn analysis. For RIL29, a QTL was found on Mrg03. The results support that at least Pm9 is different from the powdery mildew resistance genes mapped so far.

Key message: Three independent experiments with different genetic backgrounds mapped the resistance genePm7in the oat genome to the distal part of the long arm of chromosome 5D. Resistance of oat toBlumeria graminisDC. f. sp.avenaeis an important breeding goal in Central and Western Europe. In this study, the position of the effective and widely used resistance genePm7in the oat genome was determined based on three independent experiments with different genetic backgrounds: genome-wide association mapping in a diverse set of inbred oat lines and binary phenotype mapping in two bi-parental populations. Powdery mildew resistance was assessed in the field as well as by detached leaf tests in the laboratory. Genotyping-by-sequencing was conducted to establish comprehensive genetic fingerprints for subsequent genetic mapping experiments. All three mapping approaches located the gene to the distal part of the long arm of chromosome 5D in the hexaploid oat genome sequences of OT3098 and ‘Sang.’ Markers from this region were homologous to a region of chromosome 2Ce of the C-genome species,Avena eriantha, the donor ofPm7, which appears to be the ancestral source of a translocated region on the hexaploid chromosome 5D.

The genus Avena consists of approximately 30 wild and cultivated oat species. Cultivated oat is an important food crop, yet the broader genetic diversity within the Avena gene pool remains underexplored and underexploited. Here, we characterize over 9000 wild and cultivated hexaploid oat accessions of global origin using genotyping-by-sequencing and explore population structure using multidimensional scaling and population-based clustering methods. We also conduct analyses to reveal chromosome regions associated with local adaptation, sometimes resulting from large-scale chromosome rearrangements. We report four distinct genetic populations within the wild species A. sterilis , a distinct population of cultivated A. byzantina , and multiple populations within cultivated A. sativa . Some chromosome regions associated with local adaptation are also associated with confirmed structural rearrangements on chromosomes 1A, 1C, 3C, 4C, and 7D. This work provides evidence suggesting multiple polyploid origins, multiple domestications, and/or reproductive barriers amongst Avena populations caused by differential chromosome structure.

Over the last three decades,Fusariuminfections and related mycotoxin contamination have caused significant economic losses in oats (Avena sativaL.). Breeding for resistance is highly prioritized in oats, but infection processes and resistance components againstFusariumspecies are not fully identified. In this study, the genetic variation for flowering traits and its impact on mycotoxin accumulation in oats is described. The first experiment of this paper was focused on flowering traits in 50 oat genotypes (Panel 1) to identify cleistogamic oats. Then, two separateFusarium‐inoculated experiments in three (Panel 2 with 25 genotypes) and two environments (Panel 3 with 16 genotypes) were conducted to assess the relationship between the degree of anther retention (AR) and resistance toFusariuminfestation and mycotoxin accumulation in oats. Panel 2 was inoculated withFusarium culmorum,F. langsethiae, andF. sporotrichioides, and Panel 3 was inoculated with eitherF.graminearumorF. culmorum. The assessment of open flowering score and AR displayed a continuous variation from dominating chasmogamy to complete cleistogamy. Significant differences for deoxynivalenol and T‐2 were found, with a modest correlation between both mycotoxins. The lowest mycotoxin levels were found in two old and one modern cultivar, and the highest levels were found in a dwarf oat cultivar. Compared with plant height, AR was a rather ambiguous factor for the mycotoxin content, and it interfered with effects of other traits displaying high ranges such as earliness, lodging, or hull content. To unravel components of resistance toFusariumin oats more precisely, specific populations with lower ranges in plant height and heading date should be studied.

Powdery mildew, caused by the biotrophic fungus Blumeria graminis DC. f. sp. avenae, is a widespread disease of oats, especially in the temperate regions of Western and Central Europe, and the use of resistant varieties is the most sustainable way to ensure stable yields. Therefore, the identification of robust and effective resistance to powdery mildew is of great interest for oat breedinpg. In contrast to race‐specific resistance genes, adult plant resistance (APR) is generally considered to be more durable. The oat variety ‘Firth’, as well as related varieties such as ‘Husky’ or ‘Flämingstip’, contains an unknown APR gene, which was previously located on chromosome 1D using DArT markers. The aim of this study was to confirm and refine the chromosomal location of this resistance gene, tentatively named Pm13. To this end, two independent experiments were carried out using different genetic material under natural infection conditions in the field: genome‐wide association mapping (GWAS) in a diverse set of 250 oat lines grown in 10 environments and QTL mapping in a HuskyxAVE1284 biparental population grown in three environments. Both approaches identified a QTL for powdery mildew resistance on the distal end of chromosome 1D in the hexaploid Sang oat genome. The locus explained up to 15% of the phenotypic variance in GWAS and 64% of the phenotypic variance in QTL mapping. Comparison of field data with results from laboratory leaf segment tests confirmed that Pm13 does indeed confer APR. The sequence information of the identified linked markers may allow the development of molecular markers useful for early selection of oat lines with high levels of APR.