Comprehensive transcriptomic analysis provides new insights into the mechanism of ray floret morphogenesis in chrysanthemum

Morphological Characteristics and Expression Patterns of CmCYC2c of Different Flower Shapes in Chrysanthemum morifolium

The chrysanthemum is widely used as a cut flower, potted flower, and garden flower worldwide and has high ornamental, edible, and medicinal value. The flower heads, composed of ray florets and disc florets, are the most diverse in terms of morphology among ornamental plants. Here, we compared and analyzed the developmental processes of different capitulum types as well as ray florets and disc florets. Morphological differentiation of the two florets occurred on the dorsal domain of the petals at stage Ⅳ of flower development, and differences in stamen development occurred at stage Ⅴ. The dorsal domain of the ray florets and the early stage of flower development were also an essential site and period, respectively, for the differences among capitulum types. In situ hybridization revealed that CmCYC2c, whose homologs are involved in the specification of floret identity in Asteraceae, was expressed in both the dorsal and ventral domains of the ray petals in the tubular-type chrysanthemum, whereas, it was differentially transcribed in the ray petals of flat- and spoon-type chrysanthemum cultivars and had lower or no expression in the dorsal domain and higher expression in the ventral domain at stage Ⅳ. Our study indicates that the expression pattern of CmCYC2c on the dorsal domain of the ray floret at stage Ⅳ contributes to the formation of diverse flower head types in chrysanthemums.

Genome-wide identification of the TCP gene family in Chrysanthemum lavandulifolium and its homologs expression patterns during flower development in different Chrysanthemum species

TCP proteins, part of the transcription factors specific to plants, are recognized for their involvement in various aspects of plant growth and development. Nevertheless, a thorough investigation of TCPs in Chrysanthemum lavandulifolium, a prominent ancestral species of cultivated chrysanthemum and an excellent model material for investigating ray floret (RF) and disc floret (DF) development in Chrysanthemum, remains unexplored yet. Herein, a comprehensive study was performed to analyze the genome-wide distribution of TCPs in C. lavandulifolium. In total, 39 TCPs in C. lavandulifolium were identified, showing uneven distribution on 8 chromosomes. Phylogenetic and gene structural analyses revealed that ClTCPs were grouped into classes I and II. The class II genes were subdivided into two subclades, the CIN and CYC/TB1 subclades, with members of each clade having similar conserved motifs and gene structures. Four CIN subclade genes (ClTCP24, ClTCP25, ClTCP26, and ClTCP27) contained the potential miR319 target sites. Promoter analysis revealed that ClTCPs had numerous cis-regulatory elements associated with phytohormone responses, stress responses, and plant growth/development. The expression patterns of ClTCPs during capitulum development and in two different florets were determined using RNA-seq and qRT-PCR. The expression levels of TCPs varied in six development stages of capitula; 25 out of the 36 TCPs genes were specifically expressed in flowers. Additionally, we identified six key ClCYC2 genes, which belong to the class II TCP subclade, with markedly upregulated expression in RFs compared with DFs, and these genes exhibited similar expression patterns in the two florets of Chrysanthemum species. It is speculated that they may be responsible for RFs and DFs development. Subcellular localization and transactivation activity analyses of six candidate genes demonstrated that all of them were localized in the nucleus, while three exhibited self-activation activities. This research provided a better understanding of TCPs in C. lavandulifolium and laid a foundation for unraveling the mechanism by which important TCPs involved in the capitulum development.

The mechanisms of optimal nitrogen conditions to accelerate flowering of Chrysanthemum vestitum under short day based on transcriptome analysis

Nitrogen (N) plays an important role in the development of plants, with N application having been shown to accelerate flowering of cultivated plants. However, the mechanism of optimal N conditions to accelerate flowering of short-day plants is still unclear. In this study, it was found that Chrysanthemum vestitum is a typical short-day plant like most chrysanthemum varieties, and its flowering must go through a short-day induction stage. Further observations on the growth of C. vestitum showed that the N range of external application for growth was limited to between 0.25 and 2.50 mM. The results showed that, under optimal N (ON, 1.25 mM) conditions, the plants increased rapidly and flowering time was advanced; under high N (HN, 2.50 mM) or limited N (LN, 0.25 mM) conditions, the growth of plants were inhibited and flowering time was delayed. On the basis of transcriptome data, analysis of differentially expressed genes (DEGs) revealed that the floral-related genes B-box19 (BBX19), Cryptochromes (CRYs), CONSTANS-like (COLs), nitrate transporter protein (NRT), and NIN-like protein (NLP) could respond to N availability. Most of the genes in the photoperiod pathway were upregulated by ON conditions, and their expression was inhibited under HN and LN conditions. Our findings indicated that N could affect flowering by regulating the transcription levels of genes that are involved mainly in the photoperiod pathway. These candidate genes provide important clues for the subsequent analysis of the mechanism of N-induced flowering of short-day plants, and provide a possibility to improve the flowering of chrysanthemum by molecular breeding.

HD-ZIP Transcription Factors and Brassinosteroid Signaling Play a Role in Capitulum Patterning in Chrysanthemum

Chrysanthemum is a genus in the Asteraceae family containing numerous cut flower varieties with high ornamental value. It owes its beauty to the composite flower head, which resembles a compact inflorescence. This structure is also known as a capitulum, in which many ray and disc florets are densely packed. The ray florets are localized at the rim, are male sterile, and have large colorful petals. The centrally localized disc florets develop only a small petal tube but produce fertile stamens and a functional pistil. Nowadays, varieties with more ray florets are bred because of their high ornamental value, but, unfortunately, this is at the expense of their seed setting. In this study, we confirmed that the disc:ray floret ratio is highly correlated to seed set efficiency, and therefore, we further investigated the mechanisms that underlie the regulation of the disc:ray floret ratio. To this end, a comprehensive transcriptomics analysis was performed in two acquired mutants with a higher disc:ray floret ratio. Among the differentially regulated genes, various potential brassinosteroid (BR) signaling genes and HD-ZIP class IV homeodomain transcription factors stood out. Detailed follow-up functional studies confirmed that reduced BR levels and downregulation of HD-ZIP IV gene Chrysanthemum morifolium PROTODERMAL FACTOR 2 (CmPDF2) result in an increased disc:ray floret ratio, thereby providing ways to improve seed set in decorative chrysanthemum varieties in the future.

Floral Development Stage-Specific Transcriptomic Analysis Reveals the Formation Mechanism of Different Shapes of Ray Florets in Chrysanthemum

The formation mechanism of different ray floret shapes of chrysanthemum (Chrysanthemum × morifolium) remains elusive due to its complex genetic background. C. vestitum, with the basic ray floret shapes of the flat, spoon, and tubular types, is considered a model material for studying ray floret morphogenesis. In this study, the flat and tubular type lines of C. vestitum at specific stages were used to investigate the key genes that regulate morphological differences in ray florets. We found that the expression levels of genes related to auxin synthesis, transport, and response were generally higher in the tubular type than in the flat type. CvARF3 was highly expressed in the flat type, while CvARF5 and CvARF6 were highly expressed in the tubular type. Additionally, the transcription levels of Class B and E genes closely related to petal development, including CvPI, CvAP3, Cvdefh21, CvSEP3, and CvCDM77, were expressed at higher levels in the tubular type than the flat type. Based on the results, it is proposed that auxin plays a key role in the development of ray florets, and auxin-related genes, especially CvARFs, may be key genes to control the morphological difference of ray florets. Simultaneously, MADS-box genes are involved in the co-regulation of ray floret morphogenesis. The results provide novel insights into the molecular mechanism of different petal type formation and lay a theoretical foundation for the directional breeding of petal type in chrysanthemums.

Advances in Research on the Regulation of Floral Development by CYC-like Genes

CYCLOIDEA (CYC)-like genes belong to the TCP transcription factor family and play important roles associated with flower development. The CYC-like genes in the CYC1, CYC2, and CYC3 clades resulted from gene duplication events. The CYC2 clade includes the largest number of members that are crucial regulators of floral symmetry. To date, studies on CYC-like genes have mainly focused on plants with actinomorphic and zygomorphic flowers, including Fabaceae, Asteraceae, Scrophulariaceae, and Gesneriaceae species and the effects of CYC-like gene duplication events and diverse spatiotemporal expression patterns on flower development. The CYC-like genes generally affect petal morphological characteristics and stamen development, as well as stem and leaf growth, flower differentiation and development, and branching in most angiosperms. As the relevant research scope has expanded, studies have increasingly focused on the molecular mechanisms regulating CYC-like genes with different functions related to flower development and the phylogenetic relationships among these genes. We summarize the status of research on the CYC-like genes in angiosperms, such as the limited research conducted on CYC1 and CYC3 clade members, the necessity to functionally characterize the CYC-like genes in more plant groups, the need for investigation of the regulatory elements upstream of CYC-like genes, and exploration of the phylogenetic relationships and expression of CYC-like genes with new techniques and methods. This review provides theoretical guidance and ideas for future research on CYC-like genes.

Comparative analysis of the chrysanthemum transcriptome with DNA methylation inhibitors treatment and silencing MET1 lines

BACKGROUND

As one of the ten most famous flowers in China, the chrysanthemum has rich germplasm with a variety of flowering induction pathways, most of which are photoperiod-induced. After treatment with DNA methylation inhibitors, it was found that DNA methylation plays an important role in flowering regulation, but the mechanism of action remains unclear. Therefore, in this study, curcumin, 5-azaC, their mixed treatment, and MET1_-RNAi lines were used for transcriptome sequencing to find out how different treatments affected gene expression in chrysanthemums at different stages of flowering.

RESULTS

Genomic DNA methylation levels were measured using HPLC technology. The methylation level of the whole genome in the vegetative growth stage was higher than that in the flowering stage. The methylation level of DNA in the vegetative growth stage was the lowest in the curcumin and mixed treatment, and the methylation level of DNA in the transgenic line, mixed treatment, and curcumin treatment was the lowest in the flowering stage. The flowering rate of mixed treatment and curcumin treatment was the lowest. Analysis of differentially expressed genes in transcriptomes showed that 5-azaC treatment had the most differentially expressed genes, followed by curcumin and transgenic lines, and mixed treatment had the fewest. In addition, 5-azaC treatment resulted in the differential expression of multiple DNA methylation transferases, which led to the differential expression of many genes. Analysis of differentially expressed genes in different treatments revealed that different treatments had gene specificity. However, the down-regulated GO pathway in all 4 treatments was involved in the negative regulation of the reproductive process, and post-embryonic development, and regulation of flower development. Several genes associated with DNA methylation and flowering regulation showed differential expression in response to various treatments.

CONCLUSIONS

Both DNA methylase reagent treatment and targeted silencing of the MET1 gene can cause differential expression of the genes. The operation of the exogenous application is simple, but the affected genes are exceedingly diverse and untargeted. Therefore, it is possible to construct populations with DNA methylation phenotypic diversity and to screen genes for DNA methylation regulation.

Transcriptomic analysis reveals the formation mechanism of anemone-type flower in chrysanthemum

BACKGROUND

The ray and disc florets on the chrysanthemum capitulum are morphologically diverse and have remarkably abundant variant types, resulting in a rich variety of flower types. An anemone shape with pigmented and elongated disk florets is an important trait in flower shape breeding of chrysanthemums. The regulatory mechanism of their anemone-type disc floret formation was not clear, thus limiting the directional breeding of chrysanthemum flower types. In this study, we used morphological observation, transcriptomic analysis, and gene expression to investigate the morphogenetic processes and regulatory mechanisms of anemone-type chrysanthemum.

RESULT

Scanning electron microscopy (SEM) observation showed that morphological differences between non-anemone-type disc florets and anemone-type disc florets occurred mainly during the petal elongation period. The anemone-type disc florets elongated rapidly in the later stages of development. Longitudinal paraffin section analysis revealed that the anemone-type disc florets were formed by a great number of cells in the middle layer of the petals with vigorous division. We investigated the differentially expressed genes (DEGs) using ray and disc florets of two chrysanthemum cultivars, 082 and 068, for RNA-Seq and their expression patterns of non-anemone-type and anemone-type disc florets. The result suggested that the CYCLOIDEA2 (CYC2s), MADS-box genes, and phytohormone signal-related genes appeared significantly different in both types of disc florets and might have important effects on the formation of anemone-type disc florets. In addition, it is noteworthy that the auxin and jasmonate signaling pathways might play a vital role in developing anemone-type disc florets.

CONCLUSIONS

Based on our findings, we propose a regulatory network for forming non-anemone-type and anemone-type disc florets. The results of this study lead the way to further clarify the mechanism of the anemone-type chrysanthemum formation and lay the foundation for the directive breeding of chrysanthemum petal types.

Comparison of chrysanthemum flowers grown under hydroponic and soil-based systems: yield and transcriptome analysis

BACKGROUND

Flowers of Chrysanthemum × morifolium Ramat. are used as tea in traditional Chinese cuisine. However, with increasing population and urbanization, water and land availability have become limiting for chrysanthemum tea production. Hydroponic culture enables effective, rapid nutrient exchange, while requiring no soil and less water than soil cultivation. Hydroponic culture can reduce pesticide residues in food and improve the quantity or size of fruits, flowers, and leaves, and the levels of active compounds important for nutrition and health. To date, studies to improve the yield and active compounds of chrysanthemum have focused on soil culture. Moreover, the molecular effects of hydroponic and soil culture on chrysanthemum tea development remain understudied.

RESULTS

Here, we studied the effects of soil and hydroponic culture on yield and total flavonoid and chlorogenic acid contents in chrysanthemum flowers (C. morifolium 'wuyuanhuang'). Yield and the total flavonoids and chlorogenic acid contents of chrysanthemum flowers were higher in the hydroponic culture system than in the soil system. Transcriptome profiling using RNA-seq revealed 3858 differentially expressed genes (DEGs) between chrysanthemum flowers grown in soil and hydroponic conditions. Gene Ontology (GO) enrichment annotation revealed that these differentially transcribed genes are mainly involved in "cytoplasmic part", "biosynthetic process", "organic substance biosynthetic process", "cell wall organization or biogenesis" and other processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed enrichment in "metabolic pathways", "biosynthesis of secondary metabolites", "ribosome", "carbon metabolism", "plant hormone signal transduction" and other metabolic processes. In functional annotations, pathways related to yield and formation of the main active compounds included phytohormone signaling, secondary metabolism, and cell wall metabolism. Enrichment analysis of transcription factors also showed that under the hydroponic system, bHLH, MYB, NAC, and ERF protein families were involved in metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction.

CONCLUSIONS

Hydroponic culture is a simple and effective way to cultivate chrysanthemum for tea production. A transcriptome analysis of chrysanthemum flowers grown in soil and hydroponic conditions. The large number of DEGs identified confirmed the difference of the regulatory machinery under two culture system.

Sepal Identity of the Pappus and Floral Organ Development in the Common Dandelion (Taraxacum officinale; Asteraceae)

The dry one-seeded fruits (cypselae) of the Asteraceae are often crowned with a pappus, an appendage of hairs or scales that assists in dispersal. It is generally assumed, but little investigated, that the pappus represents the outer floral whorl where the sepals are usually located. We analysed pappus–sepal homology in dandelions using micromorphological and floral gene expression analyses. We show that the pappus initiates from a ring primordium at the base of the corolla, heterochronic to the petals. Pappus parts form from this ring, with those in the alternipetalaous position usually being ahead in growth, referring to sepal identity. Tof-APETALLA1 expression increased during floret development and was highest in mature pappus. Tof-PISTILLATA expression was high and confined to the floral tissues containing the petals and stamens, consistent with expectations for sepals. Apart from the pappus, the dispersal structure of dandelion consists of the upper part of the fruit, the beak, which originates from the inner floral whorl. Thus, our results support the homology of the pappus with the sepals, but show that it is highly derived. Together with our floral stage definitions and verified qPCR reference genes, they provide a basis for evolution and development studies in dandelions and possibly other Asteraceae.

Isolation and Functional Analysis of Genes Involved in Polyacylated Anthocyanin Biosynthesis in Blue Senecio cruentus

Polyacylated anthocyanins with multiple glycosyl and aromatic acyl groups tend to make flowers display bright and stable blue colours. However, there are few studies on the isolation and functional characterization of genes involved in the polyacylated anthocyanin biosynthesis mechanism, which limits the molecular breeding of truly blue flowers. Senecio cruentus is an important potted ornamental plant, and its blue flowers contain 3',7-polyacylated delphinidin-type anthocyanins that are not reported in any other plants, suggesting that it harbours abundant gene resources for the molecular breeding of blue flowers. In this study, using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis of blue, carmine and white colours of cineraria cultivars "Venezia" (named VeB, VeC, and VeW, respectively), we found that 3',7-polyacylated anthocyanin, cinerarin, was the main pigment component that determined the blue colour of ray florets of cineraria. Based on the transcriptome sequencing and differential gene expression (DEG) analysis combined with RT- and qRT-PCR, we found two genes encoding uridine diphosphate glycosyltransferase, named ScUGT1 and ScUGT4; two genes encoding acyl-glucoside-dependent glucosyltransferases which belong to glycoside hydrolase family 1 (GH1), named ScAGGT11 and ScAGGT12; one gene encoding serine carboxypeptidase-like acyltransferase ScSCPL2; and two MYB transcriptional factor genes ScMYB2 and ScMYB4, that were specifically highly expressed in the ray florets of VeB, which indicated that these genes may be involved in cinerarin biosynthesis. The function of ScSCPL2 was analysed by virus-induced gene silencing (VIGS) in cineraria leaves combined with HPLC-MS/MS. ScSCPL2 mainly participated in the 3' and 7-position acylation of cinerarin. These results will provide new insight into the molecular basis of the polyacylated anthocyanin biosynthesis mechanism in higher plants and are of great significance for blue flower molecular breeding of ornamental plants.

Ray flower initiation in the Helianthus radula inflorescence is influenced by a functional allele of the HrCYC2c gene

The radiate pseudanthium, with actinomorphic disk flowers surrounded by showy marginal zygomorphic ray flowers, is the most common inflorescence in the Helianthus genus. In Helianthus radula, ray flower primordia are normally absent at the dorsal domain of the inner phyllaries (discoid heads) while the occurrence of radiate inflorescences is uncommon. In Helianthus spp., flower symmetry and inflorescence architecture are mainly controlled by CYCLOIDEA (CYC)-like genes but the putative role of these genes in the development of discoid inflorescences has not been investigate. Three CYC genes of H. radula with a role in ray flower identity (HrCYC2c, HrCYC2d, and HrCYC2e) were isolated. The phylogenetic analysis placed these genes within the CYC2 subclade. We identified two different alleles for the HrCYC2c gene. A mutant allele, designed HrCYC2c-m, shows a thymine to adenine transversion, which generates a TGA stop codon after a translation of 14 amino acids. We established homozygous dominant (HrCYC2c/HrCYC2c) and recessive (HrCYC2c-m/HrCYC2c-m) plants for this nonsense mutation. Inflorescences of both HrCYC2c/HrCYC2c and HrCYC2c/HrCYC2c-m plants initiated ray flowers, despite at low frequency. By contrast, plants homozygous for the mutant allele (HrCYC2c-m/HrCYC2c-m) failed at all to develop ray flowers. The results support, for the first time, a role of the HrCYC2c gene on the initiation of ray flower primordia. However, also in the two dominant phenotypes, discoid heads are the prevalent architecture suggesting that this gene is required but not sufficient to initiate ray flowers in pseudanthia. Other unknown major genes are most likely required in the shift from discoid to radiate inflorescence.