Introduction

The genus Avena contains approximately 30 recognized oat species, including diploids, tetraploids and hexaploids1,2,3. Among them, the common oat (Avena sativa L., 2n = 6x = 42, AACCDD), a globally important cereal crop, was domesticated from the wild hexaploid Avena sterilis L. (2n = 6x = 42, AACCDD) more than 3000 years ago4. Closely related to both is Avena fatua L. (2n = 6x = 42, AACCDD), a weedy hexaploid oat that frequently invades agricultural fields alongside A. sativa. Unlike typical wild oats, A. fatua lacks a distinct natural geographic range and is predominantly associated with human-disturbed habitats. Its taxonomic status remains contentious: Ladizhinski and Zohary (1971) argued that A. fatua should be classified as a morphological type of a single biological species encompassing A. sativa and A. sterilis, given the absence of reproductive isolation5,6. However, this view is not universally accepted7, as many researchers maintain A. fatua as a separate species due to its unique ecological impact and invasive behavior.

Regardless of its taxonomic placement, A. fatua is well-known as one of the worst annual weeds worldwide, causing enormous problems in agriculture and its infection keeps rapidly increasing8,9 (Fig. 1a, b). Depending on plant density and relative time of emergence, A. fatua can reduce annual crop yields by as much as 70%10. In western Canada, over $500 million are expended on herbicides to control A. fatua annually10, and A. fatua also infests over 11 million ha of cropland in the Great Plains and Pacific Northwest regions causing over $1 billion in annual crop losses10. Despite its significant damage as a weed, the weedy oat (A. fatua) harbors valuable alleles that can be utilized to enhance disease resistance and stresses resistance in cultivated oats, such as resistance to crown rust and powdery mildew8,11,12. One successful example is the cultivar “Bayou18”13, which exhibits strong resistance to disease, drought, and barrenness, along with high yield and quality. This cultivar was developed through interspecific hybridization between A. fatua and the cultivated varieties “Jizhangyou4” and “Bayou9”. Therefore, genomic studies of A. fatua have the potential to further our understanding of its evolution and provide a valuable resource for the genetic improvement of cultivated oats.

Fig. 1: Phenotypes of Avena fatua and overview of the A. fatua accession W1004 assembly.

a The morphological features of A. fatua (W1004) and A. sativa, including the plant, seeds and spike type. The herbicide tolerance of A. fatua and A. sativa. The photo shows A. fatua and A. sativa after treatment with 340 g/hm2 fenoxaprop-P-ethyl for 9 days. b A. fatua plants growing in crop fileds. The arrow indicates the plant A. fatua. c Syntenic blocks shared between A. fatua (W1004) and A. sterilis (W038)/A. sativa (Sanfensan). Gray lines connect matched gene pairs. Inversion blocks are highlighted in orange. The translocation and duplication blocks are highlighted in light green and blue, respectively.

As a cosmopolitan grass weed, A. fatua can be well adapted to changing environmental conditions, and grow not only in various climatic zones from tropics to polar circle, but also on nearly all types of soil8 (Fig. 1b; Supplementary Fig. 1a, b). A. fatua also exhibits strong phenotypic plasticity in morphological characteristics, including plant height, leaf size, tiller number and length, in response to the changes in photoperiod and temperature under controlled environment conditions14. In addition to the excellent adaptation to diverse extreme environments, the consistently high abundance of A. fatua in cropland may also be assisted by its seed shattering and relatively long persistence in the soil seed bank15,16 (Supplementary Fig. 1b). A. fatua exhibits strong competitive ability, high resistance to various abiotic and biotic stresses as well as herbicide tolerance10,17,18 (Supplementary Fig. 1c), making it become a good model for understanding plant adaptation to diverse environments and the genomic basis of A. fatua’s success.

Herbicide resistance in weeds is a global problem threatening crop production19,20. The continuous and rapid increase in herbicide resistance among weeds, driven by intensive herbicide use, has caused substantial crop yield losses and increased production costs21. Many herbicide-resistant weed species are polyploids22, such as the hexaploid wild oat and Barnyard grass, but little is known about its molecular evolution in polyploids. Previous studies have demonstrated that metabolic tolerance often involves multiple detoxification enzyme families23,24, such as glutathione S-transferases (GSTs), which can conjugate glutathione to herbicide molecule, rendering them nontoxic25. Numerous studies have provided evidence for the important roles of enhanced GST activity or increased GST expression in herbicide resistance mechanisms26,27,28,29. Although numerous enzymes and related mechanisms associated with herbicide-resistance have been identified and elucidated in weeds, the availability of genome sequences could accelerate research on these processes. Due to the relatively limited genetic information, few enzymes and related mechanisms associated with herbicide-resistance have been identified and elucidated in A. fauta30,31,32. Exploring herbicide-tolerance mechanisms and identifying the key loci responsible for strong herbicide resistance in A. fatua could aid in the development of new herbicides and the breeding of cultivated oats with strong herbicide resistance.

Here, we report a near-complete genome assembly for A. fatua (W1004) through the integration of HiFi, Nanopore, and Hi-C sequencing techniques. Additionally, we construct a comprehensive genomic variation map consisting of 768 wild and cultivated oats worldwide (288 cultivated oats from A. sativa, 443 wild oats from A. fatua, and 37 previously released33 wild oats data from A. sterilis). Population genetic analysis reveals the evolutionary history of A. sterilis, A. fatua and A. sativa. It also aids in the identification of highly divergent genomic regions between A. fatua and A. sativa, and the genes in these regions are largely associated with responses to diverse extreme environments. One highly divergent genomic locus on chromosome 4D with expanded GST genes in A. fatua is identified. By combining transcriptome and chromatin accessibility profiling with functional validation using knock-down and over-expression transgenic lines in oat, we demonstrate the crucial role of a recently expanded cluster of GST genes in conferring strong herbicide resistance in A. fatua. Our study provides resources for elucidating oat genome evolution and understanding the genetic basis of A. fatua’s adaptation to diverse and extreme environmental conditions.

Results

High-quality genome assembly, annotation and comparative genomics of A. fatua

To uncover the genome architecture of A. fatua, we obtained 306.43 Gb of Pacbio HiFi long reads with a N50 length of 19.61 kb, 317.73 Gb ONT ultra-long reads with N50 of 74.51 kb and 196.64 Gb of high-throughput chromosome conformation capture (Hi-C) data (Supplementary Table 1). The HiFi reads and ONT ultra-long reads were used to construct a preliminary assembly comprising 145 contigs with the contig N50 of 473.48 Mb. Utilizing Hi-C data, the assembled contigs were further anchored onto 21 pseudochromosomes (Supplementary Fig. 2; Supplementary Fig. 3a). As a result, we achieved a final assembly of 10.98 Gb with a contig N50 length of 473.48 Mb. More than 99.79% of sequences were anchored to the 21 chromosomes with only 22 gaps, and among them, 10 chromosomes were gap-free (Supplementary Fig. 2; Table 1; Supplementary Table 2-4). These chromosomes were further assigned to A, C, and D subgenomes based on synteny with previously published hexaploid oat genomes3, and subgenome-specific k-mers34 (Supplementary Fig. 3b, c).

This highly contiguous assembly enabled us to identify all telomere regions at 42 chromosomal ends (Supplementary Table 5). The Benchmarking Universal Single-Copy Orthologs (BUSCO) evaluation with the embryophyta_odb10 database demonstrated high genome completeness, with 98.50% of conserved orthologs successfully detected under the genome mode (Table 1; Supplementary Fig. 3d). To further evaluate its quality, we remapped all primary sequencing data to the A. fatua (W1004) genome assembly, achieving mapping rates of 99.94% for HiFi reads, 99.97% for ONT reads and 99.94% for Hi-C reads. Moreover, the consensus Quality Value (QV) of k-mer-based estimates reached 72.42, exceeding all of the published oat genomes (Supplementary Fig. 3e). These metrics showed that we have obtained a high-quality and near-complete A. fatua (W1004) genome assembly (Supplementary Fig. 2).

For genome annotation, we first characterized repetitive sequences, which comprise 9.70 Gb (88.38%) of the assembled genome (Table 1), consistent with other oat genomes. The majority (87.26-89.64%) of these repeats were transposons distributed across all three subgenomes (A: 87.83%, 3.02 Gb; C: 89.64%, 3.78 Gb; D: 87.26%, 2.85 Gb; Supplementary Table 6). Retrotransposons dominated the transposable element landscape, with Gypsy-type LTR retrotransposons representing the most abundant class (35.17% of total transposon length; Supplementary Fig. 3f). For protein-coding gene annotation, we integrated evidence from five tissue-specific RNA-seq datasets with ab initio predictions and homology-based searches. This comprehensive approach identified 135,470 high-confidence protein-coding genes (Table 1; Supplementary Table 7), establishing A. fatua (W1004) as having one of the most extensively annotated oat genomes. We also applied the same annotation procedure to other related oats genomes, including Sang2, SanfenSan3, and OT3098, identifying 135,528, 131,864, and 131,157 genes, respectively, to further facilitate their comparison (Supplementary Table 7).

To identify the closest extant relatives of each subgenome and to verify the allopolyploid origin of A. fatua, we conducted a phylogenetic analysis using 4709 single-copy orthologs from 19 (sub) genomes representing 10 Pooideae species (Fig. 2a; Supplementary Table 8). The result indicated that the divergence between A. fatua (W1004) and hulled oat (Sang) as well as naked oat (Sanfensan3) occurred more recently, at 0.79 ~ 1.13 Mya, and A. fatua was identified as the closest outgroup to cultivated oats (Fig. 2a). To better capture the genomic features of A. fatua (W1004) genome, we performed a comparative analysis of large-scale structural variations among A. fatua (W1004), cultivated oat genomes (Sanfensan) and A. sterilis (Fig. 1c; Supplementary Fig. 4). This analysis revealed numerous large-scale inversions specific to A. fatua (W1004), particularly on chromosomes 4 A and 4 C, which are absent in both A. sterilis and cultivated oats (Supplementary Fig 4d–f).

Fig. 2: Phylogeny of Avena genomes and gene family analysis in A. fatua accession W1004.

a Phylogenetic relationship of 19 subgenomes from 10 species based on single-copy orthologs. Numbers in black represent the divergence time of each node (MYA, million years ago). The numbers of gene family expansion and contraction are enumerated below the species names in red and green, respectively. b Cluster analysis of gene families in four oat genomes. c Gene ontology enrichment analyses of expanded gene families in A. fatua (W1004). d The number of different types of GSTs in four oat genomes. e The number of Tau genes in the A, C and D subgenomes of four oat genomes. f GSTs located on the 1D and 4D chromosomes in A. fatua (W1004), Sang, Sanfensan, and OT3098. Red lines indicate GST genes. Source data are provided as a Source Data file.

Comparative genomic analysis revealed 472 expanded gene families in A. fatua (W1004) versus cultivated oats, including stress-related ‘Gibberellin-insensitive, Repressor of gal-3 and Scarecrow (GRAS)’, ‘Glutathione-S transferase (GST)’, and ‘UDP-Glycosyltransferase (UGT)’ families (Fig. 2b, c; Supplementary Fig. 5a). GRAS, an important gene family in plant development and response to multiple stresses35, showed notable expansion (187 vs. 162-179 in cultivars), particularly on the A subgenome (Supplementary Fig. 5a, b). And homologs of many cloned disease resistance genes co-localized with R gene-rich regions in A. fatua (W1004) (Supplementary Note 1; Supplementary Fig. 5c–e; Supplementary Table 9). We also found that GSTs exhibited dramatic expansion (266 vs. 236-248 in cultivars), with Tau-class genes specifically amplified on chromosome 4D (13 genes vs. 9–11 in cultivars) (Fig. 2d–f; Supplementary Fig. 6). RNA-seq analysis demonstrated tissue-specific expression of these GSTs, with preferential accumulation in root and leaf (Supplementary Fig. 6e), consistent with their roles in detoxification and herbicide tolerance36,37. These expansions likely underlie A. fatua’s unique environmental adaptability.

Genetic relationship and evolutionary history of A. sterilis, A. fatua and A. sativa

To reveal the evolutionary relationships among wild, weedy and cultivated oats, we performed whole-genome resequencing for 443 A. fatua accessions collected from roadsides and fields. The sampled A. fatua accessions cover three representative ecological niches in northern China, including 267 accessions from the Tibet Plateau (AFT, average altitude ~3800 m), 71 accessions from Xinjiang (AFXJ, average altitude ~1006 m), and 105 accessions from Zhangjiakou (AFZJK, average altitude ~1416 m) (Fig. 3a; Supplementary Fig. 7a, b; Supplementary Data 1). We further sequenced a diverse collection of cultivated oats (A. sativa) consisting of 288 globally distributed accessions (Fig. 3b; Supplementary Table 10; Supplementary Data 1). In total, 58.16 Tb of resequencing data were generated, with an average depth of 7.29 (79.56 Gb per accession) (Supplementary Data 2). By combining the previously released genomic data of 37 wild (A. sterilis) accessions from different regions of Israel33 and taking the A. fatua (W1004) genome as the reference, we obtained 76,205,385 high-quality single-nucleotide polymorphisms (SNPs) across the genome, with 84.65% in intergenic and 1.97% in coding regions, respectively (Supplementary Tables 11 and 12). Subgenome D exhibited elevated SNP density, particularly on chromosomes 1D and 4D (Supplementary Fig. 7c; Supplementary Table 12).

Fig. 3: Population genetic analysis of A. sterilis, A. fatua and A. sativa.

a Geographic distribution of A. fatua accessions in China. The red dots represent A. fatua accessions in the Zhangjiakou (Hebei province); The green dots represent A. fatua accessions in Xinjiang province; The blue dots represent A. fatua accessions in Tibet. DEM data were obtained from the NASA SRTM global DEM (https://lpdaac.usgs.gov/) and the study area was extracted using ArcGIS 10.8. b Worldwide distribution of A. sterilis and A. sativa. The radius of each pie chart represents the sample size in each country and the colors indicate the proportions of the A. sativa (CSA, dark blue), the A. sativa (CNU, yellow), and the wild relatives A. sterilis (WST, red) respectively. c Model-based clustering analysis with different numbers of ancestry kinship (K = 2-4). Species names are indicated by the colored bar at the bottom. WST is A. sterilis, AFT, AFXJ, and AFZJK are A. fatua from Tibet, Xinjiang and Zhangjiakou; CSA is hulled oat of A. sativa, and CNU is naked oat of A. sativa. The world map was constructed using the R package ggplot2 with the Natural Earth dataset (http://www.naturalearthdata.com). d PCA plot of A. sterilis, A. fatua and A. sativa accessions. Different colors represent different groups as follows: red, WST (A. sterilis); green, AFT (A. fatua); orange, AFXJ (A. fatua); pink, AFZJK (A. fatua); dark blue, CSA (A. sativa) and yellow, CNU (A. sativa). e Summary of nucleotide diversity (π) and population divergence (F**ST) among A. sterilis, A. fata and A. sativa (CSA and CNU). f Linkage disequilibrium was measured as the squared correlation coefficient between genotypes (r2) in the WST, CSA, CNU and A. fatua groups. g Genome-wide screening and annotation of selected sweeps. The XP-CLR value between the A. fatua and the A. sativa was plotted across the 21 chromosomes. The orthologs of known adaptation-related genes are shown above the XP-XLR value. Source data are provided as a Source Data file.

To reveal the population structure of these oat populations, we performed principal components analysis (PCA) and ADMIXTURE analysis. To mitigate sample size bias among the three oat species, we performed SNP ascertainment using a balanced panel consisting of 30 randomly selected samples per species and used this SNP panel for subsequent analyses (Supplementary Fig. 8; see Methods). PCA revealed a clear separation of A. sterilis (WST) accessions from other populations along the first principal component, with hulled oats (CSA) forming an intermediate cline and naked oats (CNU) clustering at the opposite end, which is consistent with the notion that A. sativa was domesticated from A. sterilis4 (Fig. 3d). Along the second principal component, A. fatua accessions were distinctly separated from cultivated oats. Within A. fatua, accessions from different regions formed overlapping clusters, with Xinjiang accessions positioned intermediately between those from Zhangjiakou and Tibet, reflecting their geographic distribution (Fig. 3d). The ADMIXTURE analysis closely mirrored PCA results (Fig. 3c; Supplementary Fig. 7d), identifying A. sterilis as harboring a distinct genetic component at K = 2. At K = 3, A. sativa and A. fatua were modeled with predominantly different ancestral components. The lowest cross-validation error occurred at K = 4 (Supplementary Fig. 8b), where cultivated oats split into two components corresponding to hulled and naked varieties. Phylogenetic analysis further supported these patterns (Supplementary Fig. 7e), with oat accessions clustering into three major clades representing the three species, and naked oats forming a distinct subclade within cultivated oats. These results demonstrate that A. fatua accessions from northern China are genetically distinct from both cultivated and wild oats, consistent with their unique ecological niche and morphological characteristics. In PCA, A. fatua accessions clustered closer to naked oats than to hulled oats, forming a cline that suggests closer genetic affinity with naked oats (Fig. 3d; Supplementary Fig. 8c). The pattern on PCA is also supported by D-statistics as A. fatua populations positioned closer to naked oat share more alleles with it than others (D (AFT/AFXJ, AFZJK; CNU, A. sterilis) <0, 7 <|Z | <31) (Supplementary Fig. 7f). Together, these results demonstrate a genetic connection between northern Chinese A. fatua and the widely cultivated naked oats, potentially reflecting either a direct evolutionary origin from naked oats or extensive historical gene flow between these groups. Moreover, ADMIXTURE analysis consistently detected a minor A. sterilis-related component in A. fatua populations that is absent in naked oats, indicating additional hybridization occurred between A. fatua and A. sterilis.

To investigate genetic diversity and divergence among the four groups, we calculated the nucleotide diversity (π) for each group and conducted a pairwise analysis of genetic distances (F**ST). The naked oat population (CNU) exhibited the lowest nucleotide diversity (π = 0.61 × 10−3), while the A. fatua population showed the highest genetic diversity (π = 1.06 × 10−3) among the four groups. Within A. fatua, genetic diversity decreased from high altitude (AFT) to low (AFXJ and AFZJK), with the highest π in Tibet province of China (Supplementary Table 13). The genetic differentiation between A. fatua and CNU (0.272) is lower than the comparisons between A. fatua and CSA/WST (0.337/0.345), further supporting their genetic connection (Fig. 3e). The lowest level of linkage disequilibrium (LD) decay distance was observed for WST and highest level of LD was observed for CNU (Fig. 3f), suggesting a substantial decrease in genetic diversity of CNU during its unique process of evolution and domestication history in China. Together, our results demonstrated the close relationship between A. fatua and A. sativa, and shed light on the genetic relationships and evolutionary history of A. sterilis, A. fatua from various geographical regions in China, and A. sativa worldwide.

Genomic signatures of selection underlying A. fauta’s environmental adaptability

A. fatua has long been noted for being adaptable to a wide range of extreme environments38. To uncover the genetic basis, we compared the population genomes of A. fatua and its closely related, A. sativa, using six complementary methods to identify genomic regions with selection signatures in A. fatua population (Fig. 4a; Supplementary Fig. 9a). (I) Top 10% genomic regions with the greatest differences in the average reads coverage of the whole-genome resequencing data from A. fatua and A. sativa accessions; (II) Top 10% genomic regions with highest structural variations (SVs) frequencies between A. fatua and all cultivated oat genomes (Supplementary Note 2; Supplementary Tables 14 and 15); (III) Cross-population extended haplotype homozygosity (XP-EHH) for the top 10% haplotypes; (IV) Cross-population composite likelihood ratio (XP-CLR) for the top 10% genomic regions (Supplementary Note 3); (V) Fixation statistics (F**ST) for top 10% genomic regions; (VI) Nucleotide diversity PI (π A. sativa/π A. fatua) for top 10% genomic regions. Specifically, methods I and II searches for differentiated genomic regions between the two species based on the pattern of large sequence alterations, while methods III to VI focused on SNP patterns. Collectively, these approaches identified 1.11–1.71 Gb of regions (spanning 12,896–22,051 genes) (Figs. 3g, 4b, c; Supplementary Fig. 9b; Supplementary Note 3; Supplementary Data 3). Among them, we identified 2,417 candidate genes detected by at least five methods (Fig. 4d), suggesting strong divergence between A. sativa and A. fatua with potential selection in A. fatua. We focused on these genes to investigate the genomic basis of their differences in environmental adaptation and phenotypic traits. Functional enrichment analysis revealed strong associations with stress responses (e.g., oxidative stress, auxin signaling) and growth/development (Supplementary Fig. 10a). A total of 105 candidate genes are homologs of known stress-tolerance genes in rice and wheat (Fig. 4e; Supplementary Data 4), linked to heavy metal resistance (8), salt tolerance (22), heat resistance (4), cold resistance (13), drought resistance (14), disease resistant (41) and herbicide resistance (3). Another 51 genes were homologs of genes conferring for important agronomic traits (Fig. 4e; Supplementary Data 4), including yield and quality (16), growth and development (25), sterility (9) and shattering (1). Besides, we found stress-related genes exhibited lower sequence similarity between A. fatua and A. sativa than agronomic-related genes (Fig. 4e), suggesting significant divergence in environmental adaptation between A. fatua and A. sativa.

Fig. 4: Genome-wide scan for regions of genetic divergence between A. fatua and A. sativa.

a Whole-genome signatures screening for signatures of divergent regions in the D subgenome between A. fatua and A. sativa using multi methods. The tracks show (I) SNP density along the chromosomes in 1 Mb windows; (II) Top 10% genomic regions with the greatest differences in the average reads coverage of the whole-genome resequencing data from A. fatua and A. sativa accessions; (III) Top 10% genomic regions with highest structural variations (SVs) frequencies between A. fatua and all cultivated oat genomes; (IV) Cross-population Supplementary haplotype homozygosity (XP-EHH) for the top 10% haplotypes; (V) Cross-population composite likelihood ratio (XP-CLR) for the top 10% genomic regions; (VI) Fixation statistics (F**ST) for top 10% genomic regions; (VII) Nucleotide diversity PI (π A. sativa/π A. fatua) for top 10% genomic regions; (VIII) Regions considered as highly differentiated common candidate regions were identified by more than five methods. The area box in black represents the highly differentiated region. b Statistics of total length of divergent regions identified by different methods in the A, C, and D subgenomes. c Number of genes in divergent regions identified by different methods in the A, C, and D subgenomes. d UpSet plot showing the number of genes identified by the four, five, and six methods. Pie charts showing the total number and proportion of genes identified by four, five and six methods. e Top: The similarities of 156 environmental adaptability and agronomically important genes in A. fatua to their homologs in A. sativa. Bottom: The functional classification of the 156 environmental adaptability and agronomically important genes. f An example of regions at 4D chromosome that are highly divergent between A. fatua and A. sativa. The heatmap of genotypes of two main haplotype in this region. Syntenic relationship of the expanded GST region in the A. fatua (W1004) compared to that in cultivated oats (Sanfensan, Sang and OT3098). The blue boxes indicate the GST genes. Red are private GST genes in A. fatua (W1004). Source data are provided as a Source Data file.

This candidate gene set provides important foundation for unveiling the genetic mechanism of the broad adaptation to diverse environments in A. fatua. To facilitate their utilization, we conducted detailed analysis of these genes, incorporating information on SNP variations, resulting amino acid changes, allele frequencies across species, functional annotations of their rice homologous, and tissue-specific expression patterns (Supplementary Data 5 and 6). For example, 2Cg0008813, the ortholog of OsTPS28, encodes a terpene synthase that confers blast and blight resistance in rice39. In oat, this gene is highly expressed in stems and harbors nine non-synonymous SNPs distinguishing A. fatua from A. sativa (Supplementary Fig. 10b; Supplementary Data 5 and 6). Similarly, 5Dg0059047, an ortholog of HIS1 that confers resistance to benzobicyclon and other β-triketone herbicides in rice40, exhibits strong floral expression and contains three non-synonymous SNPs defining divergent haplotypes between A. fatua and A. sativa (Supplementary Fig. 10b; Supplementary Data 5 and 6).

We observed significant phenotypic divergence between A. fatua and A. sativa, including stronger seed-shattering and longer awns in A. fatua (Fig. 1a; Supplementary Fig. 1b). Among our candidate genes, 3Cg0189326-a homolog of rice qSH1 that regulates seed shattering41-exhibited two major haplotypes. Haplotype1 was present in 97% of A. fatua accessions, where haplotype2 dominated cultivated oats (94%). Variant analysis revealed that two non-synonymous SNPs and a 21-bp deletion in the first exon of 3Cg0189326, prevalent in most A. fatua accessions (Supplementary Fig. 10c). Long awns are crucial for seed dispersal and propagation. We identified 2Cg0006814, encoded a cytokinin-activating enzyme to LONG AND BARBED AWN1 (LABA1), which was known to control awn elongation in rice42. Haplotype analysis revealed a non-synonymous mutation defining two haplotypes: haplotype1 was present in 93% of the A. fatua accessions, contrasting to only 12% of accessions in the A. sativa (Supplementary Fig. 10d). Furthermore, haplotype1 contained a 5-bp deletion in the upstream regulatory region, disrupting a predicted NAC transcription factor binding site. These mutations represent candidate functional variants underlying the observed interspecific variation in awn length. (Supplementary Fig. 10d). Nevertheless, the functional relevance of these candidate genes remains to be experimentally validated in oat.

The distal region of chromosome 4D, exhibiting GST gene expansions in A. fatua, emerged as a strongly differentiated region between A. fatua and A. sativa across all six detected methods (Fig. 4a, f). This locus harbored two distinct haplotypes segregating between A. fatua and A. sativa, and the density of SVs and divergent SNPs was high in this region. The high F**ST values between the two species associated with the markedly low nucleotide diversity (π) in the A. fatua population in this interval probably indicated that this genomic region was positively selected in A. fatua (Fig. 4f). This result further supports that the GST gene cluster in the locus have contributed to environmental adaptation in A. fatua.

Overall, we provided a comprehensive catalog of selective sweeps in A. fatua, which could be useful resources for future identifying important genes associated with A. fatua’s environmental adaptability.

Multi-omics analysis of herbicide response mechanisms in A. fatua

A. fatua is reported to exhibit remarkable herbicide resistance38, and our herbicide screening experiments confirm that A. fatua exhibits a significantly higher survival rate following herbicide treatment compared to A. sativa (Supplementary Data 7). However, the genetic mechanisms underlying this trait remain unknown. To investigate this, we conducted RNA-seq analysis of leaf and root tissues at three time points (6 h, 24 h, and 7 d) following fenoxaprop-P-ethyl (85 g/hm2) treatment (Fig. 5a). Principal component analysis confirmed data reproducibility (Supplementary Fig. 11a; Supplementary Data 8). We identified 23,833 differentially expressed genes (DEGs) across treatments (Supplementary Fig. 11b–d; Supplementary Table 16), with 2685 and 559 showing consistent differential expression in leaf and root, respectively (Fig. 5b; Supplementary Fig. 11d). DEGs numbers increased with duration (Fig. 5b; Supplementary Table 17). Functional enrichment revealed defense-related response, including amino acid catabolism, auxin response, glutathione metabolis