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Epigenetic Regulation and Molecular Mechanisms in Brassica Crop Improvement
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Epigenetic Regulation and Molecular Mechanisms in Brassica Crop Improvement

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 6793

Special Issue Editor

Dr. Ryo Fujimoto

E-Mail Website
Guest Editor
Graduate School of Agricultural Science, Kobe University, Kobe 6578501, Japan
Interests: epigenetics; hybrid vigor; heterosis; vernalization; Brassica
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The genus Brassica includes a range of economically significant crops, such as vegetables (e.g., cabbage, cauliflower, broccoli, turnip, Chinese cabbage, and kale), oilseeds (canola, rapeseed), and condiments (mustard). Recent advancements in sequencing technologies have enabled researchers to identify genetic loci and causative genes associated with agronomically important traits in Brassica crops, offering new opportunities for molecular breeding and crop improvement.

In addition to genetic studies, epigenetics has emerged as a critical area of research in plant biology. Epigenetic mechanisms, such as DNA methylation, histone modifications, chromatin remodeling, and non-coding RNAs, play essential roles in regulating gene expression without altering the underlying DNA sequence. In Brassica crops, these epigenetic changes have significant implications for key agricultural traits, including growth regulation and phenotypic diversity. Moreover, epigenetic modifications are involved in crucial processes such as flowering time and biotic and abiotic resilience, which directly influence crop productivity and quality.

This Special Issue focuses on the latest developments in epigenetic research in Brassica crops, with an emphasis on their application in crop improvement. We invite submissions that explore the molecular mechanisms underlying biotic and abiotic stress tolerance, heterosis, flowering, and breeding in Brassica crops. We also encourage submissions that integrate epigenomics with other omics data, such as transcriptomics, proteomics, phenomics, and metabolomics, to provide a comprehensive understanding of the complex molecular networks driving crop improvement.

Dr. Ryo Fujimoto
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • abiotic stress
  • allopolyploidy
  • biotic stress
  • DNA methylation
  • defense response
  • disease resistance
  • epi-allele
  • epigenetics
  • epigenome
  • flowering time
  • heterosis
  • histone modification
  • non-coding RNA
  • reproductive development
  • self-incompatibility
  • small RNA
  • transposon
  • transcriptomics
  • vernalization

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Published Papers (4 papers)

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Research

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16 pages, 2058 KB  
Article
Overexpression of BnaMATE43b Improves Resistance to Aluminum Toxicity and Identification of Its Upstream Transcription Factors in Rapeseed (Brassica napus L.)
by Xiaojun Xiao, Huiwen Zhou, Paolan Yu, Wei Zheng, Depeng Han, Lei Yang, Zhexuan Jiang, Yewei Cheng, Yazhen Li, Tianbao Huang, Wen Xiong, Xiaoping Huang, Ming Chen, Xiaosan Liu, Meiwei Zhang, Yingjin Huang and Qinghong Zhou
Plants 2026, 15(2), 338; https://doi.org/10.3390/plants15020338 - 22 Jan 2026
Viewed by 381
Abstract
The multidrug and toxic compound extrusion (MATE) protein plays a crucial role in mediating plant responses to aluminum (Al) toxicity. The key candidate gene BnaMATE43b related to Al toxicity stress in rapeseed was identified using GWAS and transcriptome analysis. In this study, the [...] Read more.
The multidrug and toxic compound extrusion (MATE) protein plays a crucial role in mediating plant responses to aluminum (Al) toxicity. The key candidate gene BnaMATE43b related to Al toxicity stress in rapeseed was identified using GWAS and transcriptome analysis. In this study, the BnaMATE43b gene was cloned and functionally characterized in rapeseed. Compared with wild-type rapeseed (WT), the BnaMATE43b overexpression lines (OE) demonstrated stronger aluminum tolerance, specifically manifested in higher relative elongation of taproots (RETs) and relative total root length (RTRL); under Al toxicity stress, the enzyme activities (SOD and POD) and root activity were significantly increased in the OE lines, whereas the MDA content and relative electrical conductivity were reduced in rapeseed root. Further transcriptome analysis of OE-3 showed that the differentially expressed genes (DEGs) were mainly enriched in zeatin biosynthesis (map00908), glucosinolate biosynthesis (map00966), phenylpropanoid biosynthesis (map00940), and ascorbate and aldarate metabolism (map00053). In addition, the yeast cDNA library of rapeseed was constructed, and twenty-two candidate upstream transcription factors (UTFs) of BnaMATE43b were screened; furthermore, four candidate UTFs were obtained through one-on-one interaction validation and luciferase assays, comprising three bHLH transcription factors (BnaA02g28220D, BnaA06g07840D, and BnaA08g24520D) and one ERF transcription factor (BnaA05g23130D). Collectively, these results suggest that BnaMATE43b could improve Al tolerance in rapeseed by mediating antioxidant enzyme activities and the related metabolic pathway, while the obtained UTFs lay the foundation for further analysis of the gene regulatory network under Al toxicity stress. Full article
(This article belongs to the Special Issue Epigenetic Regulation and Molecular Mechanisms in Brassica Crop Improvement)
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18 pages, 4911 KB  
Article
bra-miR9569 Targets the BrAHA6 Gene to Negatively Regulate H+-ATPases, Affecting Pollen Fertility in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)
by Siyu Xiong, Xiaochun Wei, Wenjing Zhang, Yanyan Zhao, Shuangjuan Yang, Henan Su, Baoming Tian, Fang Wei, Xiaowei Zhang and Yuxiang Yuan
Plants 2025, 14(16), 2604; https://doi.org/10.3390/plants14162604 - 21 Aug 2025
Viewed by 1059
Abstract
Ogura cytoplasmic male sterility (CMS) in Chinese cabbage (Brassica rapa) is characterized by complete pollen abortion, wherein stamens fail to produce viable pollen while pistils retain normal fertility. This maternally inherited trait is valuable for hybrid breeding. This study employed integrated [...] Read more.
Ogura cytoplasmic male sterility (CMS) in Chinese cabbage (Brassica rapa) is characterized by complete pollen abortion, wherein stamens fail to produce viable pollen while pistils retain normal fertility. This maternally inherited trait is valuable for hybrid breeding. This study employed integrated analysis of miRNA, transcriptome, and degradome sequencing data aligned to the Chinese cabbage reference genome to elucidate the molecular function of bra-miR9569 in Ogura CMS pollen fertility and explore its associated pathways. Subsequently, a bra-miR9569 overexpression vector was constructed and transformed into Arabidopsis thaliana. Phenotypic characterization of transgenic Arabidopsis lines, combined with anther viability assessment and quantification of ATP content and reactive oxygen species (ROS) levels in Chinese cabbage, was performed to analyze the effects of bra-miR9569. Our findings demonstrate that mutation of the mitochondrial gene orf138 in Ogura CMS lines leads to upregulation of bra-miR9569. This microRNA negatively regulates the expression of the ATP-related gene AHA6, resulting in reduced H+-ATPase activity. The consequent energy deficiency triggers cellular content degradation, ultimately causing failure of pollen wall formation and pollen abortion. Full article
(This article belongs to the Special Issue Epigenetic Regulation and Molecular Mechanisms in Brassica Crop Improvement)
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Review

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48 pages, 6600 KB  
Review
Genetic and Epigenetic Mechanisms Underpinning Biotic Stress Resilience of Brassica Vegetables
by Mst. Arjina Akter, Mei Iwamura, Shrawan Singh, Md Asad-Ud Doullah, Ryo Fujimoto, Henrik U. Stotz and Hasan Mehraj
Plants 2025, 14(24), 3765; https://doi.org/10.3390/plants14243765 - 10 Dec 2025
Cited by 1 | Viewed by 1993
Abstract
Breeding for disease-resistant varieties is a sustainable solution to reduce substantial production losses caused by pathogenic infestations in Brassica vegetables, bypassing environmentally risky disease management practices. Host-resistant genetic mechanisms aid breeders to identify resistance loci and linked markers for the clubroot, Fusarium yellows, [...] Read more.
Breeding for disease-resistant varieties is a sustainable solution to reduce substantial production losses caused by pathogenic infestations in Brassica vegetables, bypassing environmentally risky disease management practices. Host-resistant genetic mechanisms aid breeders to identify resistance loci and linked markers for the clubroot, Fusarium yellows, downy mildew, black rot, stem rot, soft rot, white rust, and turnip mosaic virus diseases in Brassica vegetables. Introgression of the resistance (R) genes by marker-assisted selection (MAS) breeding strategies allow the development of disease-resilient varieties. Brassica rapa clubroot-resistant genes (CRa, CRc, CRd, CRk, and Crr5) have been introgressed into Chinese cabbage, while CR genes (CRa, CRb, CRc, Crr1, Crr2, and Crr3) from B. rapa were also introgressed into B. oleracea. Beyond MAS, R genes can be precisely engineered by CRISPR-based technologies into precise and durable resistant varieties. The involvement of DNA methylation and histone modifications epigenetically regulate resistance mechanisms, often via ethylene/salicylic acid/jasmonic acid signaling pathways. DNA methylation mediates systemic acquired resistance by the differential expression of genes such as JAZ1, PR3, and NDR1. Future progress will depend on identifying epiQTLs and epi-markers linked to R genes. Epigenetic insights with genetic knowledge will facilitate breeding of biotic stress-resilient Brassica vegetables. This review synthesizes current molecular understanding of biotic stressors and provides future directions for disease resistance breeding of Brassica vegetable plants. Full article
(This article belongs to the Special Issue Epigenetic Regulation and Molecular Mechanisms in Brassica Crop Improvement)
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19 pages, 788 KB  
Review
Advances in Genetic Diversity of Germplasm Resources, Origin and Evolution of Turnip Rape (Brassica rapa L.)
by Xiaoming Lu, Tianyu Zhang, Yuanqiang Ma, Chunyang Han, Wenxin Yang, Yuanyuan Pu, Li Ma, Junyan Wu, Gang Yang, Wangtian Wang, Tingting Fan, Lijun Liu and Wancang Sun
Plants 2025, 14(15), 2311; https://doi.org/10.3390/plants14152311 - 26 Jul 2025
Cited by 1 | Viewed by 2652
Abstract
During a prolonged domestication and environmental selection, Brassica rapa has formed diverse morphological types during a cultivation process of up to 8000 years, such as root-type turnips (Brassica rapa var. rapa), leaf-type Chinese cabbage (Brassica rapa var. pekinensis), oil-type [...] Read more.
During a prolonged domestication and environmental selection, Brassica rapa has formed diverse morphological types during a cultivation process of up to 8000 years, such as root-type turnips (Brassica rapa var. rapa), leaf-type Chinese cabbage (Brassica rapa var. pekinensis), oil-type rapeseed (Brassica rapa L.), and other rich types. China is one of the origins of Brassica rapa L., which is spread all over the east, west, south, and north of China. Studying its origin and evolution holds significant importance for unraveling the cultivation history of Chinese oilseed crops, intraspecific evolutionary relationships, and the utilization value of genetic resources. This article summarizes the cultivation history, evolution, classification research progress, and germplasm resource diversity of Brassica rapa var. oleifera in China. Combining karyotype analysis, genomic information, and wild relatives of Brassica rapa var. oleifera discovered on the Qinghai–Tibet Plateau, it is proposed that Brassica rapa var. oleifera has the characteristic of polycentric origin, and Gansu Province in China is one of the earliest regions for its cultivation. Brassica rapa var. oleifera, originating from the Mediterranean region, was diffused to the East Asian continent through two independent transmission paths (one via the Turkish Plateau and the other via Central Asia and Siberia). Analyzing the genetic diversity characteristics and evolutionary trajectories of these two transmission paths lays a foundation for clarifying the origin and evolutionary process of Brassica rapa var. oleifera and accelerating the breeding of Brassica rapa var. oleifera in China. Despite existing research on the origin of Brassica rapa L., the domestication process of this species remains unresolved. Future studies will employ whole-genome resequencing to address this fundamental question. Full article
(This article belongs to the Special Issue Epigenetic Regulation and Molecular Mechanisms in Brassica Crop Improvement)
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