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Rapeseed ( Brassica napus ) is the second most important oilseed crop in the world but the genetic diversity underlying its massive phenotypic variations remains largely unexplored. Here, we report the sequencing, de novo assembly and annotation of eight B. napus accessions. Using pan-genome comparative analysis, millions of small variations and 77.2–149.6 megabase presence and absence variations (PAVs) were identified. More than 9.4% of the genes contained large-effect mutations or structural variations. PAV-based genome-wide association study (PAV-GWAS) directly identified causal structural variations for silique length, seed weight and flowering time in a nested association mapping population with ZS11 (reference line) as the donor, which were not detected by single-nucleotide polymorphisms-based GWAS (SNP-GWAS), demonstrating that PAV-GWAS was complementary to SNP-GWAS in identifying associations to traits. Further analysis showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotype differentiation. This study provides resources to support a better understanding of the genome architecture and acceleration of the genetic improvement of B. napus . The assembly of eight high-quality rapeseed genomes allows identification of presence and absence variations (PAVs) and small variations. PAV-based genome-wide association analysis uncovered causal variations for agronomic traits and ecotype differentiation.

Flowering time is strongly related to the environment, while the genotype-by-environment interaction study for flowering time is lacking in Brassica napus . Here, a total of 11,700,689 single nucleotide polymorphisms in 490 B. napus accessions were used to associate with the flowering time and related climatic index in eight environments using a compressed variance-component mixed model, 3VmrMLM. As a result, 19 stable main-effect quantitative trait nucleotides (QTNs) and 32 QTN-by-environment interactions (QEIs) for flowering time were detected. Four windows of daily average temperature and precipitation were found to be climatic factors highly correlated with flowering time. Ten main-effect QTNs were found to be associated with these flowering-time-related climatic indexes. Using differentially expressed gene (DEG) analysis in semi-winter and spring oilseed rapes, 5,850 and 5,511 DEGs were found to be significantly expressed before and after vernalization. Twelve and 14 DEGs, including 7 and 9 known homologs in Arabidopsis , were found to be candidate genes for stable QTNs and QEIs for flowering time, respectively. Five DEGs were found to be candidate genes for main-effect QTNs for flowering-time-related climatic index. These candidate genes, such as BnaFLC s, BnaFT s, BnaA02.VIN3 , and BnaC09.PRR7 , were further validated by the haplotype, selective sweep, and co-expression networks analysis. The candidate genes identified in this study will be helpful to breed B. napus varieties adapted to particular environments with optimized flowering time.

Inflorescence architecture is determined by inflorescence length, branch angles and the density of siliques, which affects planting density, lodging resistance and mechanical operation in rapeseed. However, the molecular mechanisms controlling inflorescence architecture are poorly understood, restricting the progress of breeding varieties with ideal plant architecture in oilseed rape. In this study, we have identified and characterized a rapeseed inflorescence development mutant, reduced inflorescence length (ril), which exhibits determinate and shortened inflorescences, reduced plant height, compact branches, and increased silique density. Through BSA-seq and map-based cloning, we find that RIL encodes a cyclic nucleotide-gated channel 20 (BnaA01.CNGC20). A substitution of proline at the 304th position to leucine (P304L) was identified in the conserved transmembrane domain of BnaA01.CNGC20. This P304L substitution neither affects the subcellular localization and self-assembly of BnaA01.CNGC20, nor disrupts the interactions with BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 (BAK1), which interacts with CNGC20 and phosphorylates it to regulate Ca2+ channel stability. However, the P304L substitution increases channel activity and Ca2+ influx, which in turn induces immune responses such as cell death, H2O2 accumulation, upregulation of pathogenesis-related genes, and pattern-triggered immunity. The enhanced immunity improves the resistance to Leptosphaeria biglobosa and Sclerotinia sclerotiorum. Transcriptome analysis further revealed that CNGC20 plays dual roles in regulating plant growth and immunity via the brassinosteroid and auxin signaling pathways. The findings in this study provide deeper insights into the intricate relationship between cytosolic Ca2+ level and plant development and immunity, as well as the trade-off between immunity and the performance of yield-related traits in the heterozygous plants (+/ril), which may serve as a guide for balancing yield and disease resistance in oilseed rape breeding.

Key messageA dominant dwarfing gene,ds-4, encodes an Aux/IAA protein that negatively regulates plant stature through an auxin signaling pathway.Dwarfism is an important agronomic trait affecting yield in many crop species. The molecular mechanisms underlying dwarfism in oilseed rape (Brassica napus) are poorly understood, restricting the progress of breeding dwarf varieties in this species. Here, we identified and characterized a new dwarf locus, DS-4, in B. napus. Next-generation sequencing-assisted genetic mapping and candidate gene analysis found that DS-4 encodes a nucleus-targeted auxin/indole-3-acetic acid (Aux/IAA) protein. A substitution (P87L) was found in the highly conserved degron motif of the Aux/IAA7 protein in the ds-4 mutant. This mutation co-segregated with the phenotype of individuals in the BC1F2 population. The P87L substitution was confirmed as the cause of the extreme dwarf phenotype by ectopic expression of the mutant allele BnaC05.iaa7 (equivalent to ds-4) in Arabidopsis. The P87L substitution blocked the interaction of BnaC05.iaa7 with TRANSPORT INHIBITOR RESPONSE 1 in the presence of auxin. The BnaC05.IAA7 gene is highly expressed in the cotyledons, hypocotyls, stems and leaves, but weakly in the roots and seeds of B. napus. Our findings provide new insights into the molecular mechanisms underlying dominant (gain-of-function) dwarfism in B. napus. Our identification of a distinct gene locus controlling plant height may help to improve lodging resistance in oilseed rape.

Key messageA single nucleotide (G) deletion in the third exon of BraA02.PES2-2 (Bra032957) leads to the conversion of flower color from yellow to white in B. rapa, and knockout mutants of its orthologous genes in B. napus showed white or pale yellow flowers.Brassica rapa (2n = 20, AA) is grown worldwide as an important crop for edible oil and vegetables. The bright yellow flower color and long-lasting flowering period give it aesthetic qualities appealing to countryside tourists. However, the mechanism controlling the accumulation of yellow pigments in B. rapa has not yet been completely revealed. In this study, we characterized the mechanism of white flower formation using a white-flowered natural B. rapa mutant W01. Compared to the petals of yellow-flowered P3246, the petals of W01 have significantly reduced content of yellowish carotenoids. Furthermore, the chromoplasts in white petals of W01 are abnormal with irregularly structured plastoglobules. Genetic analysis indicated that the white flower was controlled by a single recessive gene. By combining BSA-seq with fine mapping, we identified the target gene BraA02.PES2-2 (Bra032957) homologous to AtPES2, which has a single nucleotide (G) deletion in the third exon. Seven homologous PES2 genes including BnaA02.PES2-2 (BnaA02g28340D) and BnaC02.PES2-2 (BnaC02g36410D) were identified in B. napus (2n = 38, AACC), an allotetraploid derived from B. rapa and B. oleracea (2n = 18, CC). Knockout mutants of either one or two of BnaA02.PES2-2 and BnaC02.PES2-2 in the yellow-flowered B. napus cv. Westar by the CRISPR/Cas9 system showed pale-yellow or white flowers. The knock-out mutants of BnaA02.PES2-2 and BnaC02.PES2-2 had fewer esterified carotenoids. These results demonstrated that BraA02.PES2-2 in B. rapa, and BnaA02.PES2-2 and BnaC02.PES2-2 in B. napus play important roles in carotenoids esterification in chromoplasts that contributes to the accumulation of carotenoids in flower petals.

With the development of deep learning, medical image processing has been widely used to assist clinical research. This paper focuses on the denoising problem of low-dose computed tomography using deep learning. Although low-dose computed tomography reduces radiation exposure to patients, it also introduces more noise, which may interfere with visual interpretation by physicians and affect diagnostic results. To address this problem, inspired by Cycle-GAN for unsupervised learning, this paper proposes an end-to-end unsupervised low-dose computed tomography denoising framework. The proposed framework combines a U-Net structure for multi-scale feature extraction, an attention mechanism for feature fusion, and a residual network for feature transformation. It also introduces perceptual loss to improve the network for the characteristics of medical images. In addition, we construct a real low-dose computed tomography dataset and design a large number of comparative experiments to validate the proposed method, using both image-based evaluation metrics and medical evaluation criteria. Compared with classical methods, the main advantage of this paper is that it addresses the limitation that real clinical data cannot be directly used for supervised learning, while still achieving excellent performance. The experimental results are also professionally evaluated by imaging physicians and meet clinical needs.

Industrial recommendation systems typically involve multiple scenarios, yet existing cross-domain (CDR) and multi-scenario (MSR) methods often require prohibitive resources and strict input alignment, limiting their extensibility. We propose MTFM (Meituan Foundation Model for Recommendation), a transformer-based framework that addresses these challenges. Instead of pre-aligning inputs, MTFM transforms cross-domain data into heterogeneous tokens, capturing multi-scenario knowledge in an alignment-free manner. To enhance efficiency, we first introduce a multi-scenario user-level sample aggregation that significantly enhances training throughput by reducing the total number of instances. We further integrate Grouped-Query Attention and a customized Hybrid Target Attention to minimize memory usage and computational complexity. Furthermore, we implement various system-level optimizations, such as kernel fusion and the elimination of CPU-GPU blocking, to further enhance both training and inference throughput. Offline and online experiments validate the effectiveness of MTFM, demonstrating that significant performance gains are achieved by scaling both model capacity and multi-scenario training data.

Epigenomic modifications are instrumental for transcriptional regulation, but comprehensive reference epigenomes remain unexplored in rice. Here, we develop an enhanced chromatin immunoprecipitation (eChIP) approach for plants, and generate genome-wide profiling of five histone modifications and RNA polymerase II occupancy with it. By integrating chromatin accessibility, DNA methylation, and transcriptome datasets, we construct comprehensive epigenome landscapes across various tissues in 20 representative rice varieties. Approximately 81.8% of rice genomes are annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provides insight into transcriptional regulation. We identify extensive enhancer-like promoters with potential enhancer function on transcriptional regulation through chromatin interactions. Active and repressive histone modifications and the predicted enhancers vary largely across tissues, whereas inactive chromatin states are relatively stable. Together, these datasets constitute a valuable resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation. Comprehensive epigenomic maps of various rice varieties are still unavailable. Here, the authors report the development of eChIP as a fast and low-input upgrade of regular plant ChIP-seq protocol for epigenome analysis of 20 rice varieties and annotate over 80% of the genome with different epigenome properties for transcriptional regulation.

The segmentation of symbolic music phrases is crucial for music information retrieval and structural analysis. However, existing BiLSTM-CRF methods mainly rely on local semantics, making it difficult to capture long-range dependencies, leading to inaccurate phrase boundary recognition across measures or themes. Traditional Transformer models use static embeddings, limiting their adaptability to different musical styles, structures, and melodic evolutions. Moreover, multi-head self-attention struggles with local context modeling, causing the loss of short-term information (e.g., pitch variation, melodic integrity, and rhythm stability), which may result in over-segmentation or merging errors. To address these issues, we propose a segmentation method integrating local context enhancement and global structure awareness. This method overcomes traditional models’ limitations in long-range dependency modeling, improves phrase boundary recognition, and adapts to diverse musical styles and melodies. Specifically, dynamic note embeddings enhance contextual awareness across segments, while an improved attention mechanism strengthens both global semantics and local context modeling. Combining these strategies ensures reasonable phrase boundaries and prevents unnecessary segmentation or merging. The experimental results show that our method outperforms the state-of-the-art methods for symbolic music phrase segmentation, with phrase boundaries better aligned to musical structures.

Background: Prior pulmonary tuberculosis (PTB) might be associated with the development of chronic obstructive pulmonary disease (COPD). However, the impact of prior PTB on the risk of incident COPD has not been studied in a large prospective cohort study of the European population. Objectives: This study aimed to investigate the association of prior PTB with the risk of COPD. Design: Prospective cohort study. Methods: A multivariable Cox proportional model was used to estimate the hazard ratio (HR) and 95% confidence interval (95% CI) for the association of prior PTB with COPD. Subgroup analyses were further conducted among individuals stratified by age, sex, body mass index, smoking status, drinking status, physical activity, and polygenic risk score (PRS). Results: The study involved a total of 216,130 participants, with a median follow-up period of 12.6 years and 2788 incident cases of COPD. Individuals with a prior history of PTB at baseline had an 87% higher risk of developing incident COPD compared to those without such history [adjusted hazard ratio (aHR) = 1.87; 95% confidence interval (CI): 1.26–2.77; p = 0.002]. Subgroup analysis revealed that individuals having prior PTB history presented a higher risk of incident COPD among individuals who were aged from 50 to 59 years with aHR of 2.47 (1.02–5.95, p = 0.044), older than 59 years with aHR of 1.81 (1.16–2.81, p = 0.008), male with aHR of 2.37 (1.47–3.83, p < 0.001), obesity with aHR of 3.35 (2.16–5.82, p < 0.001), previous smoking with aHR of 2.27 (1.39–3.72, p < 0.001), current drinking with aHR of 1.98 (1.47–3.83, p < 0.001), low physical activity with aHR of 2.62 (1.30–5.26, p = 0.007), and low PRS with aHR of 3.24 (1.61–6.53, p < 0.001), as well as high PRS with aHR of 2.43 (1.15–5.14, p = 0.019). Conclusion: A history of PTB is an important independent risk factor for COPD. Clinical staff should be aware of this risk factor in patients with prior PTB, particularly in countries or regions with high burdens of PTB. Plain language summary Associations of prior pulmonary tuberculosis with the incident COPD Prior pulmonary tuberculosis (PTB) indicates that an individual has a history of PTB. The impact of prior PTB on the risk of incident chronic obstructive pulmonary disease (COPD) has not been studied in a large prospective cohort study of European population. Here, we investigated the association between prior PTB and risk of COPD in 216,130 participants from the UK biobank (a large biomedical database). After a median follow up of more than 12 years, 2,788 incident COPD cases were recorded. Individuals with prior PTB at baseline had an 87% higher risk of developing incident COPD compared to those without history of PTB. Specifically, individuals with prior PTB presented with a higher risk of incident COPD among those who were older than 50 years, male, obese, had a previous history of smoking, are currently drinking, have low physical activity, and have a low and high genetic predicted lung function. This study suggested prior PTB as an important and independent risk factor for COPD. Clinical staff should be aware of this risk factor in patients with prior PTB, particularly in countries or regions with high burdens of PTB.