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Agriculture
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Genetics, Breeding and Transcriptomic Analysis of Chrysanthemum
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Genetics, Breeding and Transcriptomic Analysis of Chrysanthemum

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Crop Genetics, Genomics and Breeding".

Deadline for manuscript submissions: 20 September 2025 | Viewed by 1076

Special Issue Editors

Dr. Lijie Zhou

E-Mail Website
Guest Editor
College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
Interests: flower color; flavonoids; carotenoids; light; temperature
Prof. Dr. Aiping Song

E-Mail Website
Guest Editor
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
Interests: ornamental plants; bioinformatics; biotechnology; gene editing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As one of the four major cut flowers in the world, the chrysanthemum holds a pivotal position in both fundamental research on flowering plants and global flower production. The upcoming issue of Agriculture aims to explore the most significant topics related to the genetics, breeding and transcriptomic analysis of chrysanthemum, including the aspects of flower color, flower development, flowering time, flower scents, disease resistance and chrysanthemum–environment interactions. Therefore, I cordially invite you to submit your relevant research papers to the incoming Special Issue of our journal. Your valuable research findings will undoubtedly enrich our understanding and practical approaches to the global production of chrysanthemums, contributing new insights to the knowledge system in this field.

Dr. Lijie Zhou
Prof. Dr. Aiping Song
Guest Editors

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 100 words) can be sent to the Editorial Office for announcement on this website.

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. Agriculture 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 2600 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

  • flower color
  • development
  • flowering time
  • scents
  • disease resistance
  • environment interactions

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Published Papers (2 papers)

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Research

26 pages, 15883 KiB  
Article
Anthocyanin Degradation Drives Heat-Induced Petal Fading in Chrysanthemum morifolium at Full Bloom: A Multi-Omics Analysis
by Ge Zhao, Yanan Li, Jialin Peng, Xiuge Li, Wenhao Xia, Yuhe Tian, Yukun Li and Lijie Zhou
Agriculture 2025, 15(9), 950; https://doi.org/10.3390/agriculture15090950 (registering DOI) - 27 Apr 2025
Viewed by 61
Abstract
Chrysanthemum morifolium, a major cut flower worldwide, undergoes petal fading under heat stress due to reduced anthocyanin accumulation, significantly compromising its ornamental value. While previous studies have focused on heat-induced inhibition of anthocyanin biosynthesis, the mechanisms governing anthocyanin degradation remain unclear. In [...] Read more.
Chrysanthemum morifolium, a major cut flower worldwide, undergoes petal fading under heat stress due to reduced anthocyanin accumulation, significantly compromising its ornamental value. While previous studies have focused on heat-induced inhibition of anthocyanin biosynthesis, the mechanisms governing anthocyanin degradation remain unclear. In this study, ‘Nannong Fencui’ chrysanthemums at full bloom—when anthocyanin accumulation peaks—were exposed to 35 °C, while a control group was maintained at 22 °C, to assess heat stress effects on anthocyanin metabolism, including both biosynthesis and degradation. Transcriptomic analysis identified nine core structural genes and three key transcription factors involved in anthocyanin biosynthesis, along with twelve core genes linked to enzymatic anthocyanin degradation. Notably, the FPKM values of structural genes for anthocyanin biosynthesis were extremely low in both groups, indicating that anthocyanin biosynthesis was largely inactive at full bloom. Untargeted metabolomic analysis identified the 30 most significantly enriched metabolic pathways. Compared to the control, heat treatment led to a significant increase in 93 metabolites (FC > 1.5, p < 0.05, VIP > 1) and a significant decrease in 160 metabolites (FC < 1/1.5, p < 0.05, VIP > 1). Cyanidin glucoside, the primary anthocyanin in chrysanthemum petals, significantly decreased under heat treatment, while its potential degradation product, protocatechuic acid, was undetectable. Meanwhile, 5-carboxyvanillic acid levels significantly increased in heat-treated groups, suggesting that protocatechuic acid may have been converted into 5-carboxyvanillic acid via an O-methylation pathway. These findings provide new insights into the metabolic regulation of anthocyanins in chrysanthemums under heat stress and offer potential strategies for maintaining flower color quality during summer production, highlighting key candidate genes (CmPRXs and CmOMT1) for future functional validation and breeding efforts aimed at improving heat tolerance and color stability. Full article
(This article belongs to the Special Issue Genetics, Breeding and Transcriptomic Analysis of Chrysanthemum)
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16 pages, 3162 KiB  
Article
Metabolomics Combined with Transcriptomics Reveals the Formation Mechanism of Different Colored Flowers of Cosmos bipinnata Cav.
by Yuxi Wang, Xiaodong Yang, Qi Zhou, Xiaohua Meng, Jialin Peng and Yueheng Hu
Agriculture 2025, 15(3), 255; https://doi.org/10.3390/agriculture15030255 - 24 Jan 2025
Viewed by 598
Abstract
In nature, plants have rich and vivid colors. Flower color can confer economic and ornamental value to ornamental plants, and is one of the target traits for current directed breeding. Therefore, it is essential to understand the molecular regulatory mechanisms behind flower color [...] Read more.
In nature, plants have rich and vivid colors. Flower color can confer economic and ornamental value to ornamental plants, and is one of the target traits for current directed breeding. Therefore, it is essential to understand the molecular regulatory mechanisms behind flower color formation in ornamental plants. However, in Cosmos bipinnata Cav., one of the most important ornamental plants, the metabolic pathways and molecular regulatory mechanisms underlying the formation of different flower colors are not yet clear, which greatly restricts the molecular breeding of flower color varieties. We selected three varieties of Cosmos bipinnata Cav. with white, pink, and red flowers as research materials, and identified significantly different metabolites among them through ultra performance liquid chromatography mass spectrometry (UPLC-MS/MS) analysis and principal component analysis (PCA). Then, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and transcriptome sequencing analysis in different colors flowers were used to reveal that the differential metabolites were enriched in flavonoid metabolic pathways and related structural genes were differentially expressed. Furthermore, we identified differentially expressed members of the MYB and bHLH transcription factor families, which play key roles in regulating the anthocyanin biosynthesis. By constructing a phylogenetic tree and performing a joint analysis of transcriptome and metabolome data, we further elucidated the molecular regulatory network underlying the formation of flower colors in Cosmos bipinnata Cav. This study not only provides a theoretical basis and gene resources for color-oriented breeding and the creation of new color varieties, but also offers new insights into the molecular mechanisms of flower color formation in plants. Full article
(This article belongs to the Special Issue Genetics, Breeding and Transcriptomic Analysis of Chrysanthemum)
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