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Background The study of plant phenotype by deep learning has received increased interest in recent years, which impressive progress has been made in the fields of plant breeding. Deep learning extremely relies on a large amount of training data to extract and recognize target features in the field of plant phenotype classification and recognition tasks. However, for some flower cultivars identification tasks with a huge number of cultivars, it is difficult for traditional deep learning methods to achieve better recognition results with limited sample data. Thus, a method based on metric learning for flower cultivars identification is proposed to solve this problem. Results We added center loss to the classification network to make inter-class samples disperse and intra-class samples compact, the script of ResNet18, ResNet50, and DenseNet121 were used for feature extraction. To evaluate the effectiveness of the proposed method, a public dataset Oxford 102 Flowers dataset and two novel datasets constructed by us are chosen. For the method of joint supervision of center loss and L2-softmax loss, the test accuracy rate is 91.88%, 97.34%, and 99.82% across three datasets, respectively. Feature distribution observed by T-distributed stochastic neighbor embedding (T-SNE) verifies the effectiveness of the method presented above. Conclusions An efficient metric learning method has been described for flower cultivars identification task, which not only provides high recognition rates but also makes the feature extracted from the recognition network interpretable. This study demonstrated that the proposed method provides new ideas for the application of a small amount of data in the field of identification, and has important reference significance for the flower cultivars identification research.

DNA methylation is an important epigenetic modification, that is involved in the regulation of gene expression and cell differentiation, and plays an important regulatory role in flower development in higher plants. There are two types of florets on the capitulum in the genus Chrysanthemum, the flower symmetry factor CYCLOIDEA (CYC) 2-like genes may be important candidate genes for determining the identity of the two types of florets. In this study, the diploid plant Chrysanthemum lavandulifolium was used as the research material, and qRT-PCR and bisulfite sequencing polymerase chain reaction (BSP) were used to identify the expression and DNA methylation pattern of CYC2-like genes in the two types of florets. Gene expression analysis showed that the six ClCYC2-like genes were significantly different in the two types of florets, and the expression levels of ClCYC2c, ClCYC2d, ClCYC2e and ClCYC2f in the ray florets were significantly higher than those in the disc florets. For the DNA methylation analysis of the three genes ClCYC2c, ClCYC2d, and ClCYC2e, it was found that the DNA methylation levels of these three genes were negative correlated with their expression levels, and the ways in which the three genes were regulated by the DNA methylation were different. It is speculated that the different DNA methylation of ClCYC2-like genes in the two types of florets may affect the differentiation and development of the two types of florets. This study provides new clues about epigenetics for the analysis of capitulum formation in Asteraceae.

Virus-induced gene silencing (VIGS) is a genetic tool used to assess gene function. Tobacco rattle virus (TRV) is a VIGS vector commonly used to induce endogenous gene silencing in plants. However, there is no VIGS system established for Centaurea spp. We evaluated the effectiveness of a TRV-based VIGS system using phytoene desaturase (PDS) as a reporter gene in Centaurea cyanus. Three methods including pressure-, vacuum- and apical meristem-infiltration were tested to infect C. cyanus seedlings. Photobleached leaves were only obtained using apical meristem-infiltration after a 14 d treatment. The CcPDS transcripts in photobleached leaves were significantly reduced compared with that in green leaves treated with empty TRV. Four C. cyanus cultivars were tested to detect their VIGS responses, and ‘Dwarf Tom Pouce Blue’ was the most sensitive. The agro-infiltration condition was optimized by screening for the optimal seedling stage as well as the optimum Agrobacterium density for efficient silencing. Seedlings with four true leaves and infiltration with an Agrobacterium density of OD600 0.5 were optimal conditions to obtain more photobleached leaves and more intense photobleached phenotype. The results demonstrated the feasibility of TRV-based VIGS for functional analysis of genes in C. cyanus.

Chrysanthemum lavandulifolium (Fischer ex Trautv.) Makino is a diploid plant belonging to the Asteraceae family, with typical capitula composed of female ray florets and bisexual disc florets. The differentiation and development of these two types of florets have long been important research focuses; however, the potential epigenetic mechanisms governing these processes have not been elucidated. In the present study, methylation-sensitive amplification polymorphism method was used to trace the dynamic changes of DNA methylation during capitulum development in C. lavandulifolium. DNA methylation patterns and levels were detected in the whole capitula during seven developmental stages, and the obtained results revealed that DNA demethylation was dominant during this process. In addition, DNA methylation patterns and levels showed significant differences between ray and disc florets. Moreover, the expression patterns of candidate genes potentially involved in the development processes of two types of florets were analyzed by real-time quantitative reverse transcription polymerase chain reaction, and correlation analysis indicated that the expression levels of ClPI, ClAG2, ClSEP1, ClCYC2c, ClCYC2d, and ClCYC2e were highly correlated with DNA methylation levels. These results indicate that DNA methylation may be involved in the differentiation and development of ray and disc florets. This study provides epigenetic insights into the capitulum development in C. lavandulifolium.

Anthocyanins in cornflower (Centaurea cyanus) is catalysed by a set of biosynthesis genes, however, the potential mechanism of transcriptional regulation remains unclear. In the present study, we traced the dynamic changes of petal colour development from white to violet and finally to blue on the same petal in cornflower. Pigment analysis showed that anthocyanin accumulation dramatically increased with petal colour development. Subsequently, nine libraries from above three colour regions were constructed for RNA-seq and 105,506 unigenes were obtained by de novo assembling. The differentially expressed genes among three colour regions were significantly enriched in the phenylpropanoid biosynthesis and flavonoid biosynthesis pathways, leading to the excavation and analysis of 46 biosynthesis genes involved in this process. Furthermore, four R2R3-CcMYBs clustered into subgroup 4 or subgroup 6 and one CcbHLH1 clustered into IIIf subgroup were screened out by phylogenetic analysis with Arabidopsis homologues. The promoters of flavanone 3-hydroxylase (CcF3H) and dihydroflavonol 4-reductase (CcDFR) were further isolated to investigate upstream regulation mechanism. CcMYB6-1 significantly upregulated the activity of above two promoters and stimulated anthocyanin accumulation by dual luciferase assay and transient expression in tobacco leaves, and its activity was obviously enhanced when co-infiltrated with CcbHLH1. Moreover, both yeast two-hybrid and bimolecular fluorescence complementation assays indicated the protein-protein interaction between these two activators. Based on these obtained results, it reveals that CcMYB6-1 and CcbHLH1 are two novel transcription factors synergistically involved in regulating anthocyanin biosynthesis. This study provides insights into the regulatory mechanism of anthocyanin accumulation in cornflower.

Virus-induced gene silencing (VIGS) is a technology for rapid gene functional analysis that depends on the degradation of viral RNA and is part of the natural defense mechanism in plants. Senecio cruentus is an important Compositae ornamental species that is plentiful and available in a variety of colors and has a typical blue variety that is rare in Compositae. These advantages make it a good material for studying the anthocyanin biosynthesis and blue flower formation mechanism. With the development of gene sequencing technology, the functions of many candidate genes that may be involved in anthocyanin biosynthesis in S. cruentus need to be identified. However, a stable and rapid genetic transformation system of S. cruentus is still lacking. Here, we screened two cultivars, ‘Venezia’ and ‘Jseter’, selected ScPDS and ScANS as test genes, and investigated the effect of developmental periods, bacterial cell concentrations and infection methods on gene silencing efficiency. The results showed that the silencing efficiency of S. cruentus leaves was low (13%), and it was less affected by the parameters. However, the transcription factor gene ScbHLH17 was still silenced by VIGS, which resulted in the loss of anthocyanin accumulation in leaves, and the expression levels of anthocyanin biosynthesis pathway (ABP) structural genes, including ScCHI, ScDFR3 and ScANS, were decreased significantly. The result proved that ScbHLH17 was an important transcription factor that regulated flower color formation in S. cruentus. In addition, ScANS-silencing phenotypes were observed in S. cruentus capitulum by vacuum-infiltrating S1 stage buds for 10 min after scape injection. In general, the present study provided an important technical support for the study of anthocyanin metabolism pathways in S. cruentus.

The variation of flower color of chrysanthemum (Chrysanthemum×morifolium) is extremely rich, and carotenoids, which are mainly stored in the plastid, are important pigments that determine the color of chrysanthemum. However, the genetic regulation of the carotenoid metabolism pathway in this species still remains unclear. In this study, a pink chrysanthemum cultivar, 'Jianliuxiang Pink', and its three bud sport mutants (including white, yellow and red color mutants, 'Jianliuxiang White', 'Jianliuxiang Yellow' and 'Jianliuxiang Red', respectively) were used as experimental materials to analyze the dynamic changes of carotenoid components and plastid ultrastructure at different developmental stages of ray florets. We found that the carotenoid components and plastid ultrastructure of the four color cultivars in the early developmental stage of the chrysanthemum capitulum (S1) were almost identical, and the carotenoids mainly included violaxanthin, lutein and β-carotene, which exist in proplastids and immature chloroplasts. With the development of capitulum, the chloroplasts in 'Jianliuxiang White' and 'Jianliuxiang Pink' were degraded, and the protoplasts did not transform but rather formed vesicles that accumulated trace amounts of carotenoids. The proplastids and chloroplasts in 'Jianliuxiang Yellow' and 'Jianliuxiang Red' were all transformed into chromoplasts and consist of lutein as well as lutein's isomer and derivatives. Using comparative transcriptomics combined with gene expression analysis, we found that CmPg-1, CmPAP10, and CmPAP13, which were involved in chromoplast transformation, CmLCYE, which was involved in carotenoid biosynthesis, and CmCCD4a-2, which was involved in carotenoid degradation, were differentially expressed between four cultivars, and these key genes therefore should affect the accumulation of carotenoids in chrysanthemum. In addition, six transcription factors, CmMYB305, CmMYB29, CmRAD3, CmbZIP61, CmAGL24, CmNAC1, were screened using weighted gene co-expression correlation network analysis (WGCNA) combined with correlative analysis to determine whether they play an important role in carotenoid accumulation by regulating structural genes related to the carotenoid metabolism pathway and plastid development. This study analyzed dynamic changes of carotenoid components and plastid ultrastructure of the four bud mutation cultivars of chrysanthemum and identified structural genes and transcription factors that may be involved in carotenoid accumulation. The above results laid a solid foundation for further analysis of the regulatory mechanism of the carotenoid biosynthesis pathway in chrysanthemum.

Carotenoids are the most important pigments determining the color of C. × morifolium; however, it is still unknown whether the changes of plastid ultrastructure affect carotenoids accumulation. In this study, we compared the change of carotenoid composition, content, and the plastid ultrastructures in the different developmental stages of capitulum among fourteen C. × morifolium cultivars from seven color groups. We found that the carotenoids and plastids detected at the early stage of capitulum development were similar in all cultivars, including violaxanthin, lutein, and β-carotene, which were present in proplastids and immature chloroplasts. Immature chloroplasts were degraded completely, forming loosely broken plastids during the development of the capitulum in white and pink cultivars. Meanwhile, a number of lipid vesicles appeared at proplastids, which resulted in only trace amounts of carotenoid accumulation in these cultivars. For yellow, orange, red, and brown cultivars, a great number of chromoplasts were found, which contained diverse ultrastructures, such as plastoglobules, tubules, and lipid droplets; these chromoplasts were derived from proplastids or chloroplasts. Compared with the early stage of capitulum development, these cultivars accumulated large amounts of carotenoids, primarily including lutein, lutein derivatives, and their isomers. In green cultivars, proplastids and immature chloroplasts were completely transformed into mature chloroplasts. These chloroplasts mainly contained violaxanthin, lutein, β-carotene, and two new components, (9Z)-lutein and (9'Z)-lutein, compared with carotenoid components presented in proplastids and immature chloroplasts. This research will be helpful for understanding the mechanisms of carotenoid metabolism of C. × morifolium. Furthermore, we found that two different chromoplast transformation patterns could be present in the same tissue cell, which contributed to the research on plastid differentiation and development in higher plants.

The understanding of capitulum morphogenesis is critical for modification of chrysanthemum flower type. Previous studies showed candidate genes which involved in the inflorescence architecture, such as PIN-FORMED 1 (PIN1), AUXIN RESPONSE FACTOR 5 (ARF5) and LEAFY (LFY), acted dominant role during early flower development. However, it is not known whether those candidate genes play parts in the capitulum morphogenesis. In the present study, floral morphogenesis and the corresponding external morphological changes in Chrysanthemum lavandulifolium were observed using scanning electron microscope and light microscope technology. Capitulum morphogenesis showed that ray florets primordia initiated later than the outermost disc florets primordia at the middle stage of florets primordia differentiation (stage 6), breaking the acropetal initiation of organ primordia on capitulum. Organogenesis of disc and ray florets showed that the early generation of florets corollas primordia was the key differentiation stages, in which disc and ray florets fused with actinomorphic and zygomorphic corollas, respectively. Furthermore, the expression patterns of inflorescence architecture related genes were detected at key stages of capitulum morphogenesis as well as the different organs on capitulum using quantitative real time PCR (qRT-PCR). The transcripts of ClARF5 specially increased at stage 5 and stage 6, as well as in ray florets corollas. The results indicated that ClARF5 might be responsible for the orientation and initiation of disc and ray florets during early capitulum morphogenesis. Studies on the capitulum morphogenesis of C. lavandulifolium not only bring molecular insights into capitulum morphogenesis, but also lay foundation for the flower type-oriented modification in cultivated chrysanthemums.

The head-like inflorescence in C. × morifolium was considered as a pseudianthia that bears numerous types of floral organs. ABCE-class and CYC2-like genes have been proven to play a key role in the identity of floral organs. To further understand their roles in capitulum development, expression pattern and protein interactions of ABCE-class and CYC2-like genes were detected using quantitative PCR and yeast-two hybrid. A-class genes, DenFUL and ClAP2, particularly accumulated in ray floret corollas and formed heterodimers with CYC2-like proteins. CYC2-like genes are particularly expressed in ray floret corollas, and these proteins form homodimers and heterodimers. The present study indicated that A-class genes in chrysanthemums interacted with CYC2-like genes and might be involved in the identity of reproductive organs and ray florets, especially the differentiation of disc and ray floret corollas. Moreover, the floral organ identity model in Chrysanthemums was proposed based on insights from the gene expression and protein interactions of ABCE-class and CYC2-like genes.

Flower type is an important quality trait of ornamental plants. Mastering genetic variation in flower types is of practical significance for breeding improved flower types. Chrysanthemum (non-anemone type) flowers consist of several elements; both ray floret shape and the relative number of ray florets (RNRF) on the capitulum are very important factors. However, until recently, few reports have standardized chrysanthemum flower type evaluations, hindering the development of genetic studies of chrysanthemum flower types. In this study, as an important index of ray floret shape, the corolla tube merged degree (CTMD) was defined as the corolla tube length/ray floret length (CTL/RFL). In addition, the number of ray florets/number of florets (NRF/NF) was used to describe the RNRF on the capitulum. Major gene and polygene mixed inheritance analyses were conducted based on 2 F1 populations from 2 pairs of parents that strongly differed in the CTMD and RNRF. ANOVA revealed that all traits strongly significantly differed among the different hybrids, and correlation analysis revealed that the CTMD and RNRF might have evolved independently. Additionally, according to the Q-mode cluster analysis results, we divided the RNRF into 4 levels: single, semi-double I, semi-double II and double. Genetic analysis revealed that both the CTMD and RNRF could be described by a B-2 genetic model via two additive-dominance major genes. In addition, the heritability of the major genes for these traits was greater than 50%, indicating that the CTMD and RNRF were controlled mainly by genetic factors. These results will provide a new theoretical basis for further improvement and breeding of chrysanthemum flower types.

Plants sense photoperiod signals to confirm the optimal flowering time. Previous studies have shown that Cryptochrome2 (CRY2) functions to promote floral transition in the long-day plant (LDP) Arabidopsis; however, the function and molecular mechanism by which CRY2 regulates floral transition in short-day plants (SDPs) is still unclear. In this study, we identified a CRY2 homologous gene, ClCRY2, from Chrysanthemum lavandulifolium, a typical SDP. The morphological changes in the C. lavandulifolium shoot apex and ClFTs expression analysis under SD conditions showed that adult C. lavandulifolium completed the developmental transition from vegetative growth to reproductive growth after eight SDs. Meanwhile, ClCRY2 mRNA exhibited an increasing trend from 0 to 8 d of SD treatment. ClCRY2 overexpression in wild-type (WT) Arabidopsis and C. lavandulifolium resulted in early flowering. The transcript levels of the CONSTANS-like (COL) genes ClCOL1, ClCOL4, and ClCOL5, and FLOWERING LOCUS T (FT) homologous gene ClFT1 were upregulated in ClCRY2 overexpression (ClCRY2-OE) C. lavandulifolium under SD conditions. The transcript levels of some circadian clock-related genes, including PSEUDO-REPONSE REGULATOR 5 (PRR5), ZEITLUPE (ZTL), FLAVIN-BINDING KELCH REPEAT F-BOX 1 (FKF1), and GIGANTEA (GI-1 and GI-2), were upregulated in ClCRY2-OE C. lavandulifolium, while the expression levels of other circadian clock-related genes, such as EARLY FLOWERING 3 (ELF3), ELF4, LATE ELONGATED HYPOCOTYL (LHY), PRR73, and REVEILLE8 (RVE8), were downregulated in ClCRY2-OE C. lavandulifolium under SD conditions. Taken together, the results suggest that ClCRY2 promotes floral transition by fine-tuning the expression of circadian clock-related gene, ClCOLs and ClFT1 in C. lavandulifolium under SD conditions., Genetics: Harnessing flower power in chrysanthemums Researchers have identified the genes that control the timing of flowering in chrysanthemums. For most plants, day-length indicates that it is time to flower. Greenhouse growers can produce out-of-season flowers by manipulating day length, but the process is expensive. Breeding varieties that respond more quickly could reduce costs, but requires a better understanding of the underlying genetics, especially in the subset of plants triggered by short days. Si-lan Dai and co-workers at Beijing Forestry University in China investigated which genes trigger flowering in Chrysanthemum lavandulifolium, a typical short-day plant. They found that flowering of chrysanthemum is controlled by a gene previously identified in long-day plants, and that amplifying the gene produced plants that flowered much sooner than ordinary plants. These findings may help in breeding varieties that are easily induced to bloom.

Background The ray floret shapes referred to as petal types on the chrysanthemum (Chrysanthemum × morifolium Ramat.) capitulum is extremely abundant, which is one of the most important ornamental traits of chrysanthemum. However, the regulatory mechanisms of different ray floret shapes are still unknown. C. vestitum is a major origin species of cultivated chrysanthemum and has flat, spoon, and tubular type of ray florets which are the three basic petal types of chrysanthemum. Therefore, it is an ideal model material for studying ray floret morphogenesis in chrysanthemum. Here, using morphological, gene expression and transcriptomic analyses of different ray floret types of C. vestitum, we explored the developmental processes and underlying regulatory networks of ray florets. Results The formation of the flat type was due to stagnation of its dorsal petal primordium, while the petal primordium of the tubular type had an intact ring shape. Morphological differences between the two ray floret types occurred during the initial stage with vigorous cell division. Analysis of genes related to flower development showed that CYCLOIDEA genes, including CYC2b, CYC2d, CYC2e, and CYC2f, were differentially expressed in different ray floret types, while the transcriptional levels of others, such as MADS-box genes, were not significantly different. Hormone-related genes, including SMALL AUXIN UPREGULATED RNA (SAUR), GRETCHEN HAGEN3 (GH3), GIBBERELLIN 2-BETA-DIOXYGENASE 1 (GA2OX1) and APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF), were identified from 1532 differentially expressed genes (DEGs) in pairwise comparisons among the flat, spoon, and tubular types, with significantly higher expression in the tubular type than that in the flat type and potential involvement in the morphogenesis of different ray floret types. Conclusions Our findings, together with the gene interactional relationships reported for Arabidopsis thaliana, suggest that hormone-related genes are highly expressed in the tubular type, promoting petal cell division and leading to the formation of a complete ring of the petal primordium. These results provide novel insights into the morphological variation of ray floret of chrysanthemum.

Flower type is an important and extremely complicated trait of chrysanthemum. The corolla tube merged degree (CTMD) and the relative number of ray florets (RNRF) are the two key factors affecting chrysanthemum flower type. However, few reports have clarified the inheritance of these two complex traits, which limits directed breeding for flower-type improvement. In this study, 305 F1hybrids were obtained from two parents with obvious differences in CTMD and RNRF performance. Using specific-locus amplified fragment sequencing (SLAF-seq) technology, we constructed a high-density genetic linkage map with an average map distance of 0.76 cM. Three major QTLs controlling CTMD and four major QTLs underlying RNRF were repeatedly detected in the 2 years. Moreover, the synteny between the genetic map and other Compositae species was investigated, and weak collinearity was observed. In QTL regions with a high degree of genomic collinearity, eight annotated genes were probed in theHelianthus annuusL. andLactuca sativaL. var. ramosa Hort. genomes. Furthermore, 20 and 11 unigenes were identified via BLAST searches between the SNP markers of the QTL regions and theC. vestitumandC. lavandulifoliumtranscriptomes, respectively. These results lay a foundation for molecular marker-assisted breeding and candidate gene exploration in chrysanthemum without a reference assembly.

Leaf shape is an important quality trait of agronomic crops, and to control the law of genetic variation of leaf shape is of practical significance for improving the early identification and selection of agronomic crops. Variations in the leaf morphology of chrysanthemum cultivars are abundant, and previous studies have quantitatively defined and classified the leaf morphology of chrysanthemum, however, the genetic architecture of chrysanthemum leaves has not been elucidated to date. In this study, two pairs of F1 hybrid populations were constructed by using small-flower chrysanthemum varieties with differences in leaf traits, and the genetic variation rules of these important quantitative traits were further discussed based on the major gene and polygene mixed inheritance analyses. The results showed that the leaves in blade shape (LBS), leaf length/width is controlled by two pairs of additive-dominant major genes (B-1), the widest part length/leaf length is controlled by two completely dominant genes (B-5), in leaf lobe shape (LLS), the lobe length/vein length is controlled by one pair of additive dominant major genes (A-1), and the lobe length/lobe width is controlled by two pairs of additive dominant major genes (B-2). The heritability of major genes was greater than 30%. For the leaf petiole shape (LPS), the petiole length is controlled by a pair of additive-dominant major genes (A-1). The results showed that the leaf traits were mainly controlled by genetic factors. In addition, based on the high-density genetic map of one F1 hybrid population, it was found that 51 quantitative trait loci (QTL) were used to control the leaf traits, including two QTLs that controlled the LBS. There were 18 QTLs that controlled LLS. Moreover, the primary QTLs that controlled leaf width and lobe length were obtained. The results of this study may establish a theoretical foundation for the in-depth exploration of leaf-shape-related genes in chrysanthemum and may provide a reference for future research investigating leaf-shape genetics in other agronomic crops.

The large-flowered Chinese chrysanthemum is one of the most morphologically complex ornamental plants, and its identification and classification requires a well-defined and reproducible system. The diversity of the capitulum is determined mainly by multiple shapes of ray florets. However, the existing classification systems for ray floret types are incomplete and unsystematic. In this study, 299 ray florets from 151 large-flowered chrysanthemum varieties in China, as well as 12 related traits of ray florets, were selected for quantitative classification. First, as one of the most important indices of ray floret shape, the corolla tube merged degree (CTMD) was defined as the corolla tube length/ray floret length (CTL/RFL). Combined with a probability grading method and linear regression analysis, the CTMD was divided into three groups, flat, spoon, and tubular, of which the CTL/RFL ranged from 0 to 0.20, 0.20 to 0.60, and 0.60 to 1.00, respectively. Second, Q-mode cluster analysis indicated that each group could be further categorized into three types (straight, curved, and atypical), based on other important variables in the ray floret. Finally, the ray floret was classified into nine types, including flat-straight, flat-curve, flat-atypical, spoon-straight, spoon-curve, spoon-atypical, tubular-straight, tubular-curve, and tubular-atypical. This ray floret classification system will be valuable in the classification of capitulum shape and has significance for the identification, breeding, and international standardization of chrysanthemum cultivars.

The generation of chrysanthemum (Chrysanthemum &times, morifolium) flower color is mainly attributed to the accumulation of anthocyanins. Light is one of the key environmental factors that affect the anthocyanin biosynthesis, but the deep molecular mechanism remains elusive. In our previous study, a series of light-induced structural and regulatory genes involved in the anthocyanin biosynthetic pathway in the chrysanthemum were identified using RNA sequencing. In the present study, differentially expressed proteins that are in response to light with the capitulum development of the chrysanthemum &lsquo, Purple Reagan&rsquo, were further identified using isobaric tags for relative and absolute quantification (iTRAQ) technique, and correlation between the proteomic and the transcriptomic libraries was analyzed. In general, 5106 raw proteins were assembled based on six proteomic libraries (three capitulum developmental stages &times, two light treatments). As many as 160 proteins were differentially expressed between the light and the dark libraries with 45 upregulated and 115 downregulated proteins in response to shading. Comparative analysis between the pathway enrichment and the gene expression patterns indicated that most of the proteins involved in the anthocyanin biosynthetic pathway were downregulated after shading, which was consistent with the expression patterns of corresponding encoding genes, while five light-harvesting chlorophyll a/b-binding proteins were initially downregulated after shading, and their expressions were enhanced with the capitulum development thereafter. As revealed by correlation analysis between the proteomic and the transcriptomic libraries, GDSL esterase APG might also play an important role in light signal transduction. Finally, a putative mechanism of light-induced anthocyanin biosynthesis in the chrysanthemum was proposed. This study will help us to clearly identify light-induced proteins associated with flower color in the chrysanthemum and to enrich the complex mechanism of anthocyanin biosynthesis for use in cultivar breeding.

Background Cultivar recognition is a basic work in flower production, research, and commercial application. Chinese large-flowered chrysanthemum (Chrysanthemum × morifolium Ramat.) is miraculous because of its high ornamental value and rich cultural deposits. However, the complicated capitulum structure, various floret types and numerous cultivars hinder chrysanthemum cultivar recognition. Here, we explore how deep learning method can be applied to chrysanthemum cultivar recognition. Results We propose deep learning models with two networks VGG16 and ResNet50 to recognize large-flowered chrysanthemum. Dataset A comprising 14,000 images for 103 cultivars, and dataset B comprising 197 images from different years were collected. Dataset A was used to train the networks and determine the calibration accuracy (Top-5 rate of above 98%), and dataset B was used to evaluate the model generalization performance (Top-5 rate of above 78%). Moreover, gradient-weighted class activation mapping (Grad-CAM) visualization and feature clustering analysis were used to explore how the deep learning model recognizes chrysanthemum cultivars. Conclusion Deep learning method applied to cultivar recognition is a breakthrough in horticultural science with the advantages of strong recognition performance and high recognition speed. Inflorescence edge areas, disc floret areas, inflorescence colour and inflorescence shape may well be the key factors in model decision-making process, which are also critical in human decision-making.

The generation of chrysanthemum (Chrysanthemum &times, morifolium) flower color is mainly attributed to the accumulation of anthocyanins. In the anthocyanin biosynthetic pathway in chrysanthemum, although all of the structural genes have been cloned, the regulatory function of R2R3-MYB transcription factor (TF) genes, which play a crucial role in determining anthocyanin accumulation in many ornamental crops, still remains unclear. In our previous study, four light-induced R2R3-MYB TF genes in chrysanthemum were identified using transcriptomic sequencing. In the present study, we further investigated the regulatory functions of these genes via phylogenetic and alignment analyses of amino acid sequences, which were subsequently verified by phenotypic, pigmental, and structural gene expression analyses in transgenic tobacco lines. As revealed by phylogenetic and alignment analyses, CmMYB4 and CmMYB5 were phenylpropanoid and flavonoid repressor R2R3-MYB genes, respectively, while CmMYB6 was an activator of anthocyanin biosynthesis, and CmMYB7 was involved in regulating flavonol biosynthesis. Compared with wild-type plants, the relative anthocyanin contents in the 35S:CmMYB4 and 35S:CmMYB5 tobacco lines significantly decreased (p &lt, 0.05), while for 35S:CmMYB6 and 35S:CmMYB7, the opposite result was obtained. Both in the 35S:CmMYB4 and 35S:CmMYB5 lines, the relative expression of several anthocyanin biosynthetic genes in tobacco was significantly downregulated (p &lt, 0.05), on the contrary, several genes were upregulated in the 35S:CmMYB6 and 35S:CmMYB7 lines. These results indicate that CmMYB4 and CmMYB5 negatively regulate anthocyanin biosynthesis in chrysanthemum, while CmMYB6 and CmMYB7 play a positive role, which will aid in understanding the complex mechanism regulating floral pigmentation in chrysanthemum and the functional divergence of the R2R3-MYB gene family in higher plants.

Conventional crossbreeding remains an effective technique for chrysanthemum (Chrysanthemum ×morifolium Ramat.) breeding. However, there are always many problems when breeding chrysanthemum because of its complex genetic background, such as difficulty matching parents, selecting superior hybrid progenies, quantitatively describing certain target traits, and evaluating breeding results. A recent mathematical analysis method is an effective method for evaluating plant breeding progress. In this study, we used 505 multiflora chrysanthemum germplasm resources as test materials; we divided the flowering time into five groups using a grading analysis method, including extremely early group (genotypes that flowered when daylength was longer than 13.5 hours), early group (genotypes that flowered when daylength was 13.5–12.0 hours), medium group (genotypes that flowered when daylength was 12.0–11.0 hours), late group (genotypes that flowered when daylength was 11.0–10.0 hours), and extremely late group (genotypes that flowered when daylength was shorter than 10.0 hours). Moreover, the breeding objective was to breed early-flowering genotypes. Using 15 phenotypic characters as evaluation factors, 37 excellent genotypes, including four early-flowering genotypes, were screened out from the aforementioned resources according to an analytic hierarchy process (AHP) and weighting of the gray relational grade. We selected one early-flowering genotype and eight medium-flowering genotypes from these 37 genotypes and matched six hybridized combinations based on the genetic distance between genotypes calculated by the Q cluster analysis method. We used a comprehensive evaluation method combining AHP and the gray relational analysis (GRA) method for the evaluation of 367 progenies. Moreover, we screened out 52 superior hybrids, including 36 early-flowering hybrids. The results of this study demonstrate that the mathematical analysis method is an immensely effective method to breed new cultivars of early-flowering multiflora chrysanthemum. This study also provides an effective method to define and improve the flowering time of other cultivated plants.

Flower color, which varies widely in potted multiflora chrysanthemum, is an extremely important character for classification. A quantitative definition of the flower color of potted multiflora chrysanthemums and the establishment of a standard color classification system may help us to evaluate the germplasm resources effectively. In this study, 273 potted multiflora chrysanthemum advanced lines were selected as materials. First, color classification results were compared between two methods: one is a combination of CIELAB and Munsell color systems, and the other one applying Q clustering analysis based on the CIELAB color system. We then divided the 273 lines into six color groups. The composition and content of anthocyanins and carotenoids in the different color advanced lines were identified by HPLC-MS. Two derivatives of cyanidin, cyanidin-3-O-(6″-O-malonyl-glucoside) and cyanidin-3-O-(3″,6″-O-dimalonyl-β-glucopyanoside), were identified in the pink, purple, orange-brown, and red lines. The carotenoids, primarily consisting of violanthin, z-violanthin, 9′z-lutein 5,6-epoxide, lutein, α-carotene, β-carotene, and 9z-β-carotene, were identified in all chrysanthemum advanced lines. Additionally, a*, represents the green-red component with green in the negative direction and red in the positive direction, was strongly positively correlated with cyanidin-3-O-(6″-O-malonyl-glucoside) (r = 0.884, P

Chrysanthemum (Chrysanthemum × morifolium) is an important horticultural crop with great ornamental and economic value. Most chrysanthemum cultivars are self-incompatible, which limits the creation of pure chrysanthemum lines which are the material basis for breeding and theoretical research. Here, artificial self-pollination and natural cross-pollination were used to analyze the self-compatibility (SC) and cross-compatibility (CC) of 85 chrysanthemums cultivated by our research group. By conducting a phenotypic study, observing of pollen germination in vitro and in vivo and gene expression analyses, we explored the reasons for the self-compatibility of chrysanthemum and identified self-compatible mutants. It was found that there were wide variations in self-compatibility among different chrysanthemum cultivars and the SC index ranged from 0 to 5.64, which could classify the chrysanthemum cultivars into three types: self-compatibility (SC index ≥ 1), self-incompatibility (SI, 1 > SC index > 0) and high self-incompatibility (SC index = 0). Seven chrysanthemum cultivars with self-pollinated progenies (‘Hongguan’, K183−8, A22, B12, D87, D76 and S8) were selected, and the pollen germination rates in vitro and in vivo were not significantly related to SC. The pollen tube of ‘Hongguan’ could pass through its own stigma and grow toward the embryo sac along the style, and there was no obvious inbreeding depression in self-pollinated progenies of ‘Hongguan’. In addition, we found that one S-locus receptor kinase (SRK), two S-locus cysteine-rich protein (SCR), two exocyst complex component EXo70A1 (Exo70A1) and one thioredoxin h-like 1 (THL1) were important for regulating self-compatibility of C. × morifolium. Our results not only laid a material foundation for creating pure lines through continuous self-pollination and analyzing the regulation mechanism underlying SC variation but also provided the possibility for theoretical research on the important ornamental traits of chrysanthemums in the future.

Cryptochrome (CRY), a vital photoreceptor which mediates light signals, controls photomorphogenesis in higher plants. However, the function of CRY in mediating light to regulate growth and development of ornamental plants is still unclear. In this study, we identified two CRY1 homologous genes, ClCRY1a and ClCRY1b, from Chrysanthemum lavandulifolium, a diploid wild chrysanthemum species. Expression analysis demonstrated that these two ClCRY1 genes showed the highest expression levels in seedlings leaves that were transferred to short day (SD) conditions for eight days. ClCRY1a was expressed at a higher level in the dark phase of SD, while ClCRY1b was expressed more highly in SD than that in long day (LD) conditions. Overexpression of either ClCRY1a or ClCRY1b in wild-type (WT) Arabidopsis resulted in early flowering under both LD and SD. The expression levels of GIGANTEA (GI) and FLOWERING LOCUS T (FT) were significantly up-regulated in ClCRY1a overexpressors under both LD and SD. Moreover, the transcript levels of GI, CONSTANS (CO) and FT were markedly increased in ClCRY1b overexpressors under LD; nevertheless, only the expression levels of CO and FT were up-regulated under SD. Taken together, the above results indicated that these two ClCRY1 genes could regulate flowering time via different pathways in C. lavandulifolium under LD and SD conditions. Our results provided evidence for the role of ClCRY1s in controlling photomorphogenesis and laid a foundation for further study on the molecular mechanism of ClCRYs mediating light signals to control floral transition.

Cymbidium longibracteatum is a common cultivated species in the genus Cymbidium due to its elegant appearance, rich flower colors and strong fragrance, but its classification is quite controversial. In this study, the complete chloroplast genome of C. longibracteatum was obtained by Illumina sequencing. The chloroplast genome of C. longibracteatum is 150,070 bp in length with an overall GC content of 37.12%, which contains a large single-copy (LSC;84,949 bp) region, a small single-copy (SSC;13,745bp) region, and a pair of inverted repeats (IRs; 25,688 bp) regions. The genome contains 130 genes, namely 84 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The maximum-likelihood phylogenetic tree has proved that C. longibracteatum should exist as an independent species in the genus Cymbidium, and it is most closely related to C. tortisepalum. This study provides valuable sequence resources for further study of C. longibracteatum.

Centaurea cyanus is a popular garden plant native to Europe. Although their petals show abundant colour variations, the flavonoid profiling and the potential molecular mechanisms remain unclear. In the present study, we collected six cornflower cultivars with white, pink, red, blue, mauve and black petals. Ultra-performance liquid chromatography coupled with photodiode array and tandem mass spectrometry (UPLC-MS/MS) was used to investigate the comparative profiling of flavonoids both qualitatively and quantitatively. Ten anthocyanins, six flavones and two flavonols were separated and putatively identified. Except for white petals without any anthocyanins, both pink and red flowers contained pelargonidin derivatives, whereas blue, mauve and black petals accumulated cyanidins. The expression patterns of genes involved in the flavonoid biosynthesis were performed by real-time quantitative reverse transcription-PCR. The anthocyanin biosynthetic pathway in white petals was inhibited starting from flavanone 3-hydroxylase, resulting in the absence of anthocyanin accumulation. The open reading frame of flavonoid 3'-hydroxylase in pink and red petals was truncated; this led to loss of a haem binding site, a conserved motif in the cytochrome P450 family, and loss of conversion from dihydrokaempferol to dihydroquercetin. The significantly higher expression of structural genes corresponding to the hyper-accumulation of flavonoids in black petals may play an important role in black coloration. Remarkably, the mauve and blue petals accumulated the same cyanidin derivative but contained apigenin with different modifications on the 4' position, which may cause the coloration differences. The results obtained in this study will provide insights into the mechanisms of vivid colour diversities in cornflower.

Background Roses are important plants for human beings with pivotal economical and biological traits like continuous flowering, flower architecture, color and scent. Due to frequent hybridization and high genome heterozygosity, classification of roses and their relatives remains a big challenge. Results Here, to identify potential markers for phylogenetic reconstruction and to reveal the patterns of natural selection in roses, we generated sets of high quality and comprehensive reference transcriptomes for Rosa chinensis ‘Old Blush’ (OB) and R. wichuriana ‘Basye’s Thornless’ (BT), two species exhibiting contrasted traits of high economical importance. The assembled reference transcriptomes showed transcripts N50 above 2000 bp. Two roses shared about 10,073 transcripts (N50 = 2282 bp), in which a set of 5959 transcripts was conserved within genera of Rosa. Further comparison with species in Rosaceae identified 4447 transcripts being common (Rosaceae-common) in Rosa, Malus, Prunus, Rubus, and Fragaria, while a pool of 164 transcripts being specific for roses (Rosa-specific). Among the Rosaceae-common transcripts, 409 transcripts showed a signature of positive selection and a clustered expression in different tissues. Interestingly, nine of these rapidly evolving genes were related to DNA damage repair and responses to environmental stimulus, a potential associated with genome confliction post hybridization. Coincident with this fast evolution pattern in rose genes, 24 F-box and four TMV resistant proteins were significantly enriched in the Rosa-specific genes. Conclusions We expect that these Rosaceae-common and Rosa-specific transcripts should facilitate the phylogenetic analysis of Rosaceae plants as well as investigations of Rosa-specific biology. The data reported here could provide fundamental genomic tools and knowledge critical for understanding the biology and domestication of roses and for roses breeding. Electronic supplementary material The online version of this article (10.1186/s12870-018-1585-x) contains supplementary material, which is available to authorized users.

Light is one of the key environmental factors that affect anthocyanin biosynthesis. However, the underlying molecular mechanism remains unclear, and many problems regarding phenotypic change and corresponding gene regulation have not been solved. In the present study, comparative analyses of light-induced anthocyanin accumulation and gene expression between the ray florets and leaves were performed in Chrysanthemum × morifolium 'Purple Reagan'. After contrasting the variations in the flower color phenotype and relative pigment content, as well as expression patterns of structural and regulator genes responsible for anthocyanin biosynthesis and photoreceptor between different plant organs under light and dark conditions, we concluded that (1) both the capitulum and foliage are key organs responding to light for chrysanthemum coloration; (2) compared with flavones, shading makes a greater decrease on the anthocyanins accumulation; (3) most of the structural and regulatory genes in the light-induced anthocyanin pathway specifically express in the ray florets; and (4) CmCHS, CmF3H, CmF3'H, CmANS, CmDFR, Cm3GT, CmMYB5-1, CmMYB6, CmMYB7-1, CmbHLH24, CmCOP1 and CmHY5 are key genes for light-induced anthocyanin biosynthesis in chrysanthemum ray florets, while on the transcriptional level, the expressions of CmPHYA, CmPHYB, CmCRY1a, CmCRY1b and CmCRY2 are insignificantly changed. Moreover, the inferred comprehensive effect of multiple signals on the accumulation of anthocyanins and transmission channel of light signal that exist between the leaves and ray florets were further discussed. These results further our understanding of the relationship between the gene expression and light-induced anthocyanin biosynthesis, and lay foundations for the promotion of the molecular breeding of novel flower colors in chrysanthemums.

This paper reports the first study on plant CBF transcription factors (TF) in salt and drought stress responses in Chrysanthemum lavandulifolium. A CBF homolog gene, named as ClCBF1, from C. lavandulifolium was isolated using rapid amplification of cDNA ends (RACE). The deduced peptide is comprised of 210 amino acids (AA) containing an AP2 structural domain characteristic of the AP2 gene family. Quantitative real-time PCR revealed that ClCBF1 gene exhibit differential expression patterns across root, leaf and stem tissues, and it was strongly induced under salt and drought treatments of C. lavandulifolium. Overexpression of ClCBF1 in C. morifolium ‘White Snow’ resulted in stronger tolerance to salt and drought stresses. The ClCBF1 expression level, enzymatic activities of superoxide dismutase and peroxidase, and contents of proline and soluble proteins were enhanced in these transgenic lines, they were repressed in the antisense transgenic lines under the same stress conditions. Results indicate that ClCBF1 represents a promising candidate gene in improving abiotic stress tolerance among ornamental plants.

The cyanidin (Cy), pelargonidin (Pg), and delphinidin (Dp) pathways are the three major branching anthocyanin biosynthesis pathways that regulate flavonoid metabolic flux and are responsible for red, orange, and blue flower colors, respectively. Different species have evolved to develop multiple regulation mechanisms that form the branched pathways. In the current study, five Senecio cruentus cultivars with different colors were investigated. We found that the white and yellow cultivars do not accumulate anthocyanin and that the blue, pink, and carmine cultivars mainly accumulate Dp, Pg, and Cy in differing densities. Subsequent transcriptome analysis determined that there were 43 unigenes encoding anthocyanin biosynthesis genes in the blue cultivar. We also combined chemical and transcriptomic analyses to investigate the major metabolic pathways that are related to the observed differences in flower pigmentation in the series of S. cruentus. The results showed that mutations of the ScbHLH17 and ScCHI1/2 coding regions abolish anthocyanin formation in the white and the yellow cultivars; the competition of the ScF3'H1, ScF3'5'H, and ScDFR1/2 genes for naringenin determines the differences in branching metabolic flux of the Cy, Dp, and Pg pathways. Our findings provide new insights into the regulation of anthocyanin branching and also supplement gene resources (including ScF3'5 'H, ScF3'H, and ScDFRs) for flower color modification of ornamentals.

Quantitative real-time PCR (qPCR) is a popular and powerful tool used to understand the molecular mechanisms of flower development. However, the accuracy of this approach depends on the stability of reference genes. The capitulum of chrysanthemums is very special, which is consisting of ray florets and disc florets. There are obvious differences between the two types of florets in symmetry, gender, histological structure, and function. Furthermore, the ray florets have various shapes. The objective of present study was to identify the stable reference genes in Chrysanthemum morifolium and Chrysanthemum lavandulifolium during the process of flower development. In this study, nine candidate reference genes were selected and evaluated for their expression stability acrosssamples during the process of flower development, and their stability was validated by four different algorithms (Bestkeeper, NormFinder, GeNorm, and Ref-finder). SAND (SAND family protein) was found to be the most stably expressed gene in all samples or different tissues during the process of C. lavandulifolium development. Both SAND and PGK (phosphoglycerate kinase) performed most stable in Chinese large-flowered chrysanthemum cultivars, and PGK was the best in potted chrysanthemums. There were differences in best reference genes among varieties as the genetic background of them were complex. These studies provide guidance for selecting reference genes for analyzing the expression pattern of floral development genes in chrysanthemums.