CRISPR/Cas9 mutagenesis and overexpression lines analyses revealed CIPK9 homoeologs function in oil regulation of allotetraploid Brassica napus, cooperative multicopy interactions, and a superior haplotype on chromosome A10. Rapeseed (Brassica napus, B. napus), a globally significant allopolyploid oilseed crop, fulfills substantial annual vegetable oil demand. Evolutionary adaptation in this species is underpinned by gene duplication and homoeolog retention, enhancing plasticity under dynamic environmental stresses. This study focuses on BnaCIPK9, a regulator of seed oil content. Phylogenomic and structural analyses demonstrate that BnaCIPK9 homoeologs underwent duplication followed by consistent evolutionary retention within the Brassica lineage, exhibiting remarkable sequence and structural conservation. Expression profiling revealed tissue-partitioned functional specialization among homoeologs, with BnaA10.CIPK9 and BnaC05.CIPK9 showing seed-preferential expression. CRISPR/Cas9 knockout in B. napus and heterologous overexpression in Arabidopsis demonstrate these homoeologs act as dosage-dependent regulators of oil accumulation, dependent on their distinct expression patterns. They further exhibit expression-driven functional diversification in abiotic stress responses during seedling development. Population genomics reveal differential evolutionary trajectories among duplicates, with intensified selection on chromosome A10 driving adaptive divergence. Crucially, haplotype–trait association identifies hap.qCIPK9.A10.0 as a major haplotype linked to elevated oil content. This work elucidates how homoeolog subfunctionalization fine-tunes critical agronomic traits, oil biosynthesis, and stress resilience, in polyploid crops, establishing haplotype-assisted breeding as imperative for developing crop cultivars. Favorable haplotypes, exemplified by hap.qCIPK9.A10.0, offer precise targets for high-oil crop breeding improvement.

Drought poses a critical threat to global agriculture, food security, and livestock sustainability. In Brassica napus L. (B. napus), a major oilseed crop, yield losses under water deficit underscore the urgent need for breeding strategies that improve water-use efficiency. Here, this study demonstrates that CIPK9 loss-of-function lines of B. napus displayed enhanced drought tolerance compared with the wild-type (WT). Yeast two-hybrid, split-luciferase complementation (LCI), and bimolecular fluorescence complementation (BiFC) assays showed that BnaCIPK9 physically interacts with PP2C39 both in vivo and in vitro. Transcript analysis and enzymatic assays further revealed that CIPK9 functioned in an abscisic acid (ABA)-dependent pathway regulating ABA biosynthesis and enhanced antioxidant capacity by promoting reactive oxygen species (ROS) scavenging. In Arabidopsis, both pp2c39 and cipk9 mutants exhibited stronger drought tolerance than WT plants. Notably, cipk9 mutants showed greater detoxification capacity, resulting in reduced ROS accumulation, higher stomatal conductance, and increased growth, whereas pp2c39 mutants triggered hyperactive stress signaling, leading to elevated ROS levels, lower stomatal conductance, and growth inhibition. These findings highlight a dual drought-response strategy that balances stress defense with cellular homeostasis to sustain growth. Specifically, PP2C39 mediates ABA-induced stress signaling, while the PP2C39-CIPK9 module mitigates its cytotoxic consequences, and their interaction links two distinct pathways to maintain equilibrium between defense and growth. This work provides mechanistic insights for breeding, suggesting that exploiting functional redundancy can reduce excessive self-regulation to improve stress resilience while avoiding modifications that overactivate stress responses and compromise plant development.

A total of 947 saline-alkaline tolerance-related molecular markers and a 5K cGPS genotyping chipwere developed, providing practical tools for marker-assisted selection and molecular design breeding of saline-alkaline-tolerant rapeseed. Rapeseed (Brassica napus L.) has relatively strong tolerance to saline-alkaline stress and shows great potential for the sustainable utilization and improvement of saline-alkaline soils. However, the breeding of highly tolerant cultivars still mainly depends on conventional hybridization combined with phenotype-based selection, which constrains breeding efficiency. In this study, previously reported saline-alkaline tolerance-related genes from rapeseed, rice, maize, wheat, sorghum, and Arabidopsis were collected. Candidate gene-based association analysis enabled the development of molecular markers and a genotyping chip. A total of 483 significantly associated genes were identified, among which 355 genes contained favorable haplotypes. Molecular markers were successfully developed for 275 genes, including 746 KASP and 201 InDel marker pairs, and four marker pairs were randomly selected for validation. In addition, a 5K cGPS liquid-phase chip (HZSW-cGPS-BRNAP-04), was developed and showed a high call rate and excellent reproducibility in genotyping. These markers and the chip are expected to improve the breeding efficiency of saline-alkaline-tolerant rapeseed cultivars. Overall, this study provides useful tools for early-generation evaluation and marker-assisted selection (MAS), and provides a foundation for molecular design breeding of saline-alkali-tolerant rapeseed.

Mutation in centromere histone H3 (CENH3) protein could induce a paternal haploid with maternal cytoplasm in rapeseed. By paternal haploid induction, a cytoplasmic male sterile line can be created in any genetic background within one breeding cycle. Hybrid development in rapeseed relies primarily on the three-line system, which includes a cytoplasmic male sterile (CMS) line. Conventionally, these CMS lines are developed through backcrossing, a process that requires several breeding cycles to complete. More recently, the doubled haploid technique has been employed in various crops to generate homozygous lines within a single breeding cycle. In the present study, we utilized a haploid induction (HI) strategy to produce fertile homozygous lines and CMS lines via paternal haploid induction. We have created single homozygous and double heterozygous mutants of the BnaCENH3 gene in the rapeseed cultivar ganA (hau-CMS) using CRISPR/Cas9 technique. Upon hybridization of CMS-HI line with wild type can successfully induced paternal haploids with maternal sterile cytoplasm. This system offers the ability to introduce sterile cytoplasm into any genetic background within a single generation.

ABSTRACT Phosphorus fixation represents a primary constraint limiting the agronomic efficiency of phosphate fertilizers in calcareous soil. Rapeseed roots secrete amounts of organic matter, which can mobilize and decompose insoluble phosphorus in the soil. However, the activation mechanism of sparingly insoluble phosphorus in calcareous soils by rapeseed rhizosphere microorganisms remains unclear. This study aimed to screen and identify phosphate-solubilizing microorganisms from the rapeseed rhizosphere of calcareous soil, and to elucidate their key metabolic pathways for activating insoluble phosphorus. The results demonstrated that (i) fourteen dominant phosphate-solubilizing strains were isolated from rapeseed rhizosphere soil. Among these, Advenella alkanexedens was verified to significantly promote wheat growth and increase soil available phosphorus content. (ii) The culture condition optimization and functional characterization for Advenella alkanexedens revealed that its optimal growth temperature was 30°C, with an initial pH of 7. Its phosphate-solubilizing ability was regulated by Mg2+, K2+, and Ca2+ ions, and the strain exhibited considerable salt tolerance and the ability to produce siderophores. (iii) Advenella alkanexedens increased soil available phosphorus content by 11.49%–81.91% and elevated phytase activity by 36.87%–82.49%. Correlation analysis indicated that soil available phosphorus and phytase activity were significantly positively correlated with Ca2–P, Ca8–P, and Al–P fractions. (iv) Amino acids and organic acids were identified as the key metabolites influencing the phosphate-solubilizing function of Advenella alkanexedens. The KEGG pathway analysis showed these metabolites were primarily enriched in β-alanine metabolism and arginine and proline metabolism pathways. Our findings confirm that Advenella alkanexedens not only promotes crop growth but also significantly increases labile P fractions (Ca2–P, Ca8–P, Al–P) while reducing more stable forms (Ca10–P), thereby enhancing soil phosphorus use efficiency. This study holds important implications for planting rapeseed to activate insoluble phosphorus in soil, to reduce phosphate fertilizer application, and to promote sustainable utilization of soil phosphorus resources. Furthermore, it provides a theoretical foundation for developing agricultural microbial inoculants.IMPORTANCEOur results confirm that Advenella alkanexedens not only benefits crop growth but also converts insoluble phosphates (O-P, Ca10-P) into highly active inorganic phosphorus components, thereby enhancing the utilization efficiency of soil phosphorus. This study was of great significance in activating the insoluble phosphorus in the soil, reducing the input of phosphate fertilizers, achieving the sustainable utilization of phosphorus resources, and protecting the environment. Additionally, it provided a basis for developing agricultural microbial agents.

INTRODUCTION:Rapeseed (Brassica napus L.) is a major oilseed crop with considerable potential for improving saline-alkali soils, yet the molecular mechanisms underlying its salt tolerance remain unclear. OBJECTIVES:This study investigates the functional roles and regulatory mechanisms of glycine-rich protein 3 (BnaGRP3) in rapeseed under salt stress. METHODS:We employed molecular genetics, phenotypic and biochemical evaluation of transgenic rapeseed and Arabidopsis, transcriptome sequencing, protein interaction assays including immunoprecipitation-mass spectrometry (IP-MS), yeast two-hybrid (Y2H), luciferase complementation (LCA), and bimolecular fluorescence complementation (BiFC) assays, gene expression analysis by RT-qPCR, and hydrogen peroxide (H2O2) permeability assays conducted in yeast. RESULTS:BnaGRP3 was induced by salt stress and enhanced salt tolerance. Transcriptome analysis revealed that BnaGRP3 modulated expression of ion transporters under salt stress, especially NHX1 and SKOR. BnaGRP3 physically interacted with four plasma membrane intrinsic proteins (BnaPIPs). Overexpression of these BnaPIPs improved salt tolerance in Arabidopsis and increased H2O2 tolerance when expressed in yeast. In addition, these BnaPIPs formed both homomeric and heteromeric complexes, suggesting they may facilitate H2O2 permeability. CONCLUSIONS:BnaGRP3 enhances salt tolerance by maintaining Na+/K+ homeostasis and, through its interactions with BnaPIPs, may participate in the regulation of H2O2 balance·H2O2 potentially serves as a bridge linking BnaGRP3-mediated ion homeostasis and redox regulation. The previously uncharacterized BnaGRP3-BnaPIP module broadens the mechanistic framework of GRP-mediated salt stress responses, thereby expanding our understanding of salt tolerance mechanisms in Brassica napus.

Following rapid economic and social development over the past few decades, developing multipurpose plant species with environmental conservation benefits has become a major challenge. This review explores the multifunctional utilization and industrial significance of rapeseed, along with its environmental applications, to provide insights into future improvements. Additionally, it highlights the multifunctional uses and improvements in China. Rapeseed is primarily cultivated for edible oil production, biodiesel, industrial chemicals, and animal feed. Recent advancements in breeding programs, molecular techniques, and modern agronomic strategies have significantly enhanced rapeseed productivity and multifunctional applications. In China, new rapeseed lines with high oil content and superior composition quality have been developed, along with forage rapeseed cropping systems that utilize vegetative parts for animal feed. Beyond its agricultural and industrial roles, rapeseed provides numerous environmental benefits, such as serving as a cover crop, suppressing weeds, improving soil fertility as green manure, and aiding in the phytoremediation of heavy-metal-contaminated soils. Additionally, rapeseed biomass can be processed into biochar, contributing to carbon sequestration and climate change mitigation. Its capacity to reduce carbon dioxide emissions further establishes its role as a sustainable crop. At the ecological and economic levels, rapeseed fields offer aesthetic and tourism value, attracting visitors during early spring in Southern China and mid-summer in Northern China. Furthermore, rapeseed serves as an essential nectar and pollen source for honey production, medicinal extracts, and anticancer compounds. Innovations in genetic modifications and precision agriculture techniques also open new avenues for enhancing rapeseed resilience to environmental stress, improving oil yield, and expanding its applications in pharmaceuticals and biodegradable materials. This review emphasizes the multi-functionality of rapeseed as a promising crop for sustainable development. It confirms that rapeseed cultivation can enhance agricultural productivity, support environmental conservation, and reduce ecological risks, particularly in newly reclaimed lands under the pressures of global climate change.

The rapeseed material ‘DH46’ had an extremely low-SNS phenotype due to multiple megaspore mother cells in ovules. A novel SNS-related locus was mapped to a 169-kb interval on chromosome C09. Seed number per silique (SNS) is a yield-related trait in rapeseed (Brassica napus). Although numerous quantitative trait loci associated with SNS have been identified in diverse rapeseed populations, the primary loci and genetic basis underlying SNS variation remain poorly understood. In this study, an extremely low-SNS material named ‘DH46’ was employed to investigate the genetic locus associated with SNS. Cytological studies revealed that the reduced SNS phenotype is attributable to the presence of multiple megaspore mother cells within the ovules. To dissect the genetic control of this trait, a BC3F4 population developed from the cross of ‘DH46’ and the cultivar ‘ZS11’ was analyzed, and a major locus BnSNSC09 acting as a semi-dominant factor associated with SNS was identified. Fine mapping in the BC3F6 population narrowed the causal region to a 169-kb interval on chromosome C09. Candidate gene analysis revealed that BnaC09G0288500ZS, which exhibits variants in promoter and coding sequences, was the most promising candidate gene for BnSNSC09. These findings establish a robust foundation for cytological investigations and genetic analyses of the low-SNS mutant ‘DH46,’ with the ultimate goal of preventing ovule abortion and enhancing SNS to develop higher-yielding rapeseed varieties.

Heterosis holds great potential for improving yield, quality, and environmental adaptability in crop breeding, which suggests that hybrids can exhibit better performance in adapting to extreme environments. However, the epigenetic mechanisms of salt-tolerant heterosis in allopolyploid crop Brassica napus (AACC, 2n = 38), particularly chromatin accessibility, remain largely unexplored. We investigated the dynamics of chromatin accessibility and transcriptional reprogramming during a time course of salt exposure in Brassica napus hybridization. We observed the importance of epigenetic and transcriptional regulation in plant resilience. The chromatin accessibility and transcriptome rapidly changed within a short time frame of salt exposure. Hybrid possessed more accessible chromatin and more active transcriptome than that of parents driven by epigenetic aggregation and genetic complementation. Broader and more flexible genomic resources enabled hybrid preferentially unitized advantageous alleles for salt stress adaptation. Meanwhile, these salt stress-responsive genes in hybrid exerted various heterotic effects, with non-additive genetic effects, including full-dominance, partial-dominance, and overdominance effects, playing a crucial role in salt stress adaptation. Our results expanded the heterosis hypothesis from an epigenetic perspective and emphasized how the combined effects of genetic and epigenetic factors enable hybrid to better withstand salt stress.

In order to identify saline–alkali-tolerant rapeseed varieties suitable for cultivation on moderately saline–alkali soils and to expand the use of such lands, six rapeseed varieties were selected as experimental materials. Field experiments were conducted to evaluate agronomic traits, photosynthesis, stress physiology, yield, and quality throughout the entire growth period. Statistical methods, including correlation analysis, principal component analysis, membership function analysis, and cluster analysis, were employed to evaluate and select saline–alkali-tolerant varieties. The results indicated that H62 and 20C14 yielded the highest seed production, reaching 2287.99 kg·hm−2 and 2277.15 kg·hm−2, respectively. During the mid-to-late growth stages, the majority of agronomic traits, photosynthetic parameters, and stress physiology indicators for 20C14 were significantly superior to those of the other varieties. The results of the principal component analysis showed that the total root length at maturity stage, root–shoot ratio at flowering stage, and proline content at maturity stage were the most important indicators for screening saline–alkali-tolerant rapeseed varieties. A comprehensive analysis of these indicators revealed the following descending order of saline–alkali tolerance among the varieties: 20C14 > 20C17 > 20C4 > H62 > H158 > 17C2. Cluster analysis was performed to classify the rapeseed into strong saline–alkali-tolerant type (20C14 and 20C17), moderate saline–alkali-tolerant type (20C4, H62, and H158), and weak saline–alkali-tolerant type (17C2). Consequently, 20C14 and 20C17 are recommended as suitable rapeseed varieties for cultivation on soda saline–alkali soils.

Allopolyploids have successfully overcome 'genome shock', yet how their subgenomes adapt to coexistence remains largely unclear. Here, we constructed high-resolution epigenomic maps for the diploids Brassica rapa (ArAr) and Brassica oleracea (CoCo), and examined epigenomic variation in the allotetraploid Brassica napus (AnAnCnCn) relative to its putative progenitors. We discovered that coordinated genomic and epigenomic reprogramming in B. napus drove convergence of sequence and epigenomic features between An and Cn, significantly reducing expression divergence in homoeologs. Convergent homoeologs were functionally enriched in pathways related to genome stability and abiotic stress responses. Notably, Cn in B. napus exhibited greater sequence conservation and epigenetic homeostasis. Furthermore, transcription factor binding sites (TFBSs) affected by genomic variation in An showed convergent regulatory changes toward Cn, indicating that allopolyploids mitigate subgenomic conflicts through multilayered regulatory coordination. In conclusion, coordinated genomic and epigenomic convergence provides critical insights into the stability and adaptive evolution of allopolyploids.

Exploring the molecular mechanism underlying plant architecture and breeding new varieties suitable for mechanized harvesting are primary objectives for rapeseed breeders in China. However, few genes controlling plant architecture have been cloned in Brassica napus. In this study, SX3, a scattered-bud B. napus line with a dwarf and compact plant architecture, was characterized. To identify the genes underlying bud arrangement, plant height and branch angle, segregating populations were constructed by crossing SX3 with two clustered-bud lines with a tall and loose plant architecture. Genetic analysis revealed that the scattered-bud trait (SBT) was controlled by a single dominant gene, BnaSBT. BnaSBT is likely a pleiotropic gene that simultaneously controls plant height and branch angle. Using BSA-seq analysis, BnaSBT was mapped to a 4.15 Mb region on ChrA10. Owing to the lack of recombinants within this region, it was infeasible to finely map BnaSBT. RNA-seq analysis of BC2 plants with contrasting inflorescence and plant architectures revealed that the upregulation of genes involved in amino acid and lipid metabolism and genes encoding MADS-box transcription factors is related to the the phenotype of SX3. These findings together with comparative sequencing indicated that BnaA10.SEP1, BnaA10.AGL15, BnaA10.GLN1-4 and BnaA10.AGP15 are candidate genes for BnaSBT. Markers closely linked to the scattered-bud trait were developed for selecting dwarf and compact plants. These findings provide molecular markers and germplasms for breeding new varieties with ideal plant types and lay a theoretical foundation for cloning key genes and elucidating the genetic basis of inflorescence and plant architectures in B. napus.

The potherb mustard Xuecai (XC) cultivar is a cruciferous vegetable that is popular either fresh or pickled.Due to the deep notches in the edges of leaves in mustard XC,this plant can be said to have multipinnately lobed leaves.The net photosynthesis of lobed leaves is significantly greater than that of simple leaves.However,the molecular mechanism of leaf shape variation has not been determined.Here,we used HiFi and Hi-C data to assemble the XC genome.The genome was 961.72 Mb in size,with a contig N50 value of 6.565 Mb.The XC genome was compared with four previously sequenced mustard genomes,and the genomic collinearity regions,SNPs,and indels were identified.Five BjRCO genes were found on chromosome (Chr.) A10 in potherb mustard XC when the BjRCO gene locus was compared against other sequenced B.juncea genomes.Segmental duplication was found to contribute to the BjRCO gene copy number.The transcript expression of BjRCO genes was greater in multipinnately lobed leaves than in sawtooth-like leaves.Together,these findings indicate that both the greater copy number and the expression level of BjRCO genes regulate leaf shape from simple to complex in B.juncea.Gene editing of the BjRCO gene from XC changed the leaf shape from multipinnately lobed to simple.The high-quality XC genome sequence not only provides new insight into B.juncea leaf-type genomics but also helps in deciphering leaf shape variation.Our study provides insights into the variation and evolution of important traits in Brassica plants through a comparative analysis of the sequenced genomes.

The Brassica polima cytoplasmic male sterility (pol CMS) line causes complete and stable sterility and is most extensively used in breeding. The regulatory pathway, however, is not clear. In this work, we studied molecular interaction among several key genes involved in pol CMS. Firstly, we found that the multicellular organelle RNA-editing factor protein (Bna.MORF1) interacted with the pol CMS-restorer protein RFP using the yeast two-hybrid system. Secondly, knock down of Bna.MORF1 using CRISPR/Cas9 editing resulted in sterile transgenic lines. The function of the pol CMS sterility gene orf224 was further confirmed by ectopic expression of the gene in both Arabidopsis and Brassica. Furthermore, using CRISPR/Cas9 we determined that an anther-specific proline-rich protein (APG) was also involved in sterility. We propose a working model for pol CMS in Brassica napus that may expedite the utilization of this popular CMS line in Brassica breeding.

Soil salinization is a threat to global agriculture. This study used whole-genome bisulfite sequencing and transcriptomics to explore epigenetic regulation in salt-tolerant Brassica napus (cv. Huayouza 62) under NaCl (salt), Na2CO3 (alkali), and combined salt-alkali stresses. All stresses induced genome-wide DNA hypermethylation (combined > alkali > salt). The Cn subgenome had significant methylation changes (most at CHH, then at CHG), with more differentially methylated regions in transposable elements than protein-coding genes. Hypermethylation, driven by DNA methyltransferases (e.g., DRM2), inhibited growth by repressing photosynthetic genes (RBCS-1A, RBCS-1B). B. napus adapted via targeted demethylation activated stress resistance (ROS scavenging under salt, redox buffering under alkali, and protein homeostasis under combined stress). 5-Azacytidine validation confirmed that methylation balances photosynthesis and stress response, clarifying the epigenetic network and providing strategies for crop stress resistance improvement.

Leaf trichome formation is a very important agronomic trait as it confers resistance to biotic and abiotic stresses, but the causal genes involved in this process in Brassica juncea remain largely unexplored. In this study, we first characterized the haplotypes of BjB02.GL1 among different inbred lines with leaf trichomes or glabrous leaves. A comparative analysis of the number and density of leaf trichomes between the two mustard inbred lines was then performed. BSA analysis of leaves with trichomes and glabrous pools from the F2 segregating population mapped the candidate genes on Chr.A06 and Chr.B02. Two candidate genes, BjA06.GL1 and BjB02.GL1, were subsequently cloned. After sequence alignment of the BjGL1 genes, both single-nucleotide polymorphisms (SNPs) and indel were identified in the BjA06.GL1 and BjB02.GL1 genes. And quantitative real-time polymerase chain reaction (qRT-PCR) analysis further confirmed that both the BjA06.GL1 and BjB02.GL1 genes were more highly expressed in leaves with trichomes than in glabrous leaves. As the leaf size increased, the leaf trichome density decreased. Gene editing of both BjA06.GL1 and BjB02.GL1 changed the leaf trichome to a glabrous leaf phenotype in mustard. In addition, plants with leaf trichomes presented greater resistance to aphids. Taken together, our results revealed that both BjA06.GL1 and BjB02.GL1 positively regulate leaf trichome formation and help increase aphid resistance in mustard. This study provides valuable resources and helps to elucidate the molecular mechanism of leaf trichome formation in B. juncea.

The successful interaction between pollen and stigma is a critical process for plant sexual reproduction, involving a series of intricate molecular and physiological events. After self-compatible pollination, a significant reduction in reactive oxygen species (ROS) production has been observed in stigmas, which is essential for pollen grain rehydration and subsequent pollen tube growth. Several scavenging enzymes tightly regulate ROS homeostasis. However, the potential role of these ROS-scavenging enzymes in the pollen-stigma interaction in Brassica napus remains unclear. Here, we showed that the activity of ascorbate peroxidase (APX), an enzyme that plays a crucial role in the detoxification of hydrogen peroxide (H2O2), was modulated depending on the compatibility of pollination in B. napus. We then identified stigma-expressed APX1s and generated pentuple mutants of APX1s using CRISPR/Cas9 technology. After compatible pollination, the BnaAPX1 pentuple mutants accumulated higher levels of H2O2 in the stigma, while the overexpression of BnaA09.APX1 resulted in lower levels of H2O2. Furthermore, the knockout of BnaAPX1 delayed the compatible response-mediated pollen rehydration and germination, which was consistent with the effects of a specific APX inhibitor, ρ-Aminophenol, on compatible pollination. In contrast, the overexpression of BnaA09.APX1 accelerated pollen rehydration and germination after both compatible and incompatible pollinations. However, delaying and promoting pollen rehydration and germination did not affect the seed set after compatible and incompatible pollination in APX1 pentuple mutants and overexpression lines, respectively. Our results demonstrate the fundamental role of BnaAPX1 in pollen rehydration and germination by regulating ROS homeostasis during the pollen-stigma interaction in B. napus.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is crucial for profiling histone modifications and transcription factor binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits and flowers is challenging due to their sturdy cell walls and complex constituents. Here we present advanced ChIP (aChIP), an optimized method that efficiently isolates chromatin from plant tissues while simultaneously removing cell walls and cellular constituents. aChIP precisely profiles histone modifications in all 14 tested EIPOs and identifies transcription factor and chromatin-modifying enzyme binding sites. In addition, aChIP enhances ChIP efficiency, revealing numerous novel modified sites compared with previous methods in vegetative tissues. aChIP reveals the histone modification landscape for rapeseed dry seeds, highlighting the intricate roles of chromatin dynamics during seed dormancy and germination. Altogether, aChIP is a powerful, efficient and sensitive approach for comprehensive chromatin profiling in virtually all plant tissues, especially in EIPOs. This study presents an advanced ChIP-seq method, provides a valuable epigenomics resource for 14 economically important plant organs and reveals histone modification landscape dynamics and functions during rapeseed seed dormancy and germination.