A HORT1 Retrotransposon Insertion in the PeMYB11 Promoter Causes Harlequin/Black Flowers in Phalaenopsis Orchids

The road less taken: Dihydroflavonol 4-reductase inactivation and delphinidin anthocyanin loss underpins a natural intraspecific flower colour variation

Visual cues are of critical importance for the attraction of animal pollinators, however, little is known about the molecular mechanisms underpinning intraspecific floral colour variation. Here, we combined comparative spectral analysis, targeted metabolite profiling, multi-tissue transcriptomics, differential gene expression, sequence analysis and functional analysis to investigate a bee-pollinated orchid species, Glossodia major with common purple- and infrequent white-flowered morphs. We found uncommon and previously unreported delphinidin-based anthocyanins responsible for the conspicuous and pollinator-perceivable colour of the purple morph and three genetic changes underpinning the loss of colour in the white morph - (1) a loss-of-function (LOF; frameshift) mutation affecting dihydroflavonol 4-reductase (DFR1) coding sequence due to a unique 4-bp insertion, (2) specific downregulation of functional DFR1 expression and (3) the unexpected discovery of chimeric Gypsy transposable element (TE)-gene (DFR) transcripts with potential consequences to the genomic stability and post-transcriptional or epigenetic regulation of DFR. This is one of few known cases where regulatory changes and LOF mutation in an anthocyanin structural gene, rather than transcription factors, are important. Furthermore, if TEs prove to be a frequent source of mutation, the interplay between environmental stress-induced TE evolution and pollinator-mediated selection for adaptive colour variation may be an overlooked mechanism maintaining floral colour polymorphism in nature.

Breeding of ornamental orchids with focus on Phalaenopsis: current approaches, tools, and challenges for this century

Ornamental orchid breeding programs have been conducted to develop commercially valuable cultivars with improved characteristics of commercial interest, such as size, flower color, pattern, shape, and resistance to pathogens. Conventional breeding, including sexual hybridization followed by selection of desirable characteristics in plants, has so far been the main method for ornamental breeding, but other techniques, including mutation induction by polyploidization and gamma irradiation, and biotechnological techniques, such as genetic transformation, have also been studied and used in ornamental breeding programs. Orchids are one of the most commercially important families in floriculture industry, having very particular reproductive biology characteristics and being a well-studied group of ornamentals in terms of genetic improvement. The present review focuses on the conventional and biotechnological techniques and approaches specially employed in breeding Phalaenopsis orchids, the genus with highest worldwide importance as an ornamental orchid, highlighting the main limitations and strengths of the approaches. Furthermore, new opportunities and future prospects for ornamental breeding in the CRISPR/Cas9 genome editing era are also discussed. We conclude that conventional hybridization remains the most used method to obtain new cultivars in orchids. However, the emergence of the first biotechnology-derived cultivars, as well as the new biotechnological tools available, such as CRISPR-Cas9, rekindled the full potential of biotechnology approaches and their importance for improve ornamental orchid breeding programs.

Molecular mechanism of different flower color formation of Cymbidium ensifolium

Cymbidium ensifolium is one of the national orchids in China, which has high ornamental value with changeable flower colors. To understand the formation mechanism of different flower colors of C. ensifolium, this research conducted transcriptome and metabolome analyses on four different colored sepals of C. ensifolium. Metabolome analysis detected 204 flavonoid metabolites, including 17 polyphenols, 27 anthocyanins, 75 flavones, 34 flavonols, 25 flavonoids, 18 flavanones, and 8 isoflavones. Among them, purple-red and red sepals contain a lot of anthocyanins, including cyanidin, pelargonin, and paeoniflorin, while yellow-green and white sepals have less anthocyanins detected, and their metabolites are mainly flavonols, flavanones and flavonoids. Transcriptome sequencing analysis showed that the expression levels of the anthocyanin biosynthetic enzyme genes in red and purple-red sepals were significantly higher than those in white and yellow-green sepals of C. ensifolium. The experimental results showed that CeF3'H2, CeDFR, CeANS, CeF3H and CeUFGT1 may be the key genes involved in anthocyanin production in C. ensifolium sepals, and CeMYB104 has been proved to play an important role in the flower color formation of C. ensifolium. The results of transformation showed that the CeMYB104 is involved in the synthesis of anthocyanins and can form a purple-red color in the white perianth of Phalaenopsis. These findings provide a theoretical reference to understand the formation mechanism of flower color in C. ensifolium.

Research Progress on Anthocyanin-Mediated Regulation of 'Black' Phenotypes of Plant Organs

The color pattern is one of the most important characteristics of plants. Black stands out among the vibrant colors due to its rare and distinctive nature. While some plant organs appear black, they are, in fact, dark purple. Anthocyanins are the key compounds responsible for the diverse hues in plant organs. Cyanidin plays an important role in the deposition of black pigments in various plant organs, such as flower, leaf, and fruit. A number of structural genes and transcription factors are involved in the metabolism of anthocyanins in black organs. It has been shown that the high expression of R2R3-MYB transcription factors, such as PeMYB7, PeMYB11, and CsMYB90, regulates black pigmentation in plants. This review provides a comprehensive overview of the anthocyanin pathways that are involved in the regulation of black pigments in plant organs, including flower, leaf, and fruit. It is a great starting point for further investigation into the molecular regulation mechanism of plant color and the development of novel cultivars with black plant organs.

High light triggers flavonoid and polysaccharide synthesis through DoHY5-dependent signaling in Dendrobium officinale

Dendrobium officinale is edible and has medicinal and ornamental functions. Polysaccharides and flavonoids, including anthocyanins, are important components of D. officinale that largely determine the nutritional quality and consumer appeal. There is a need to study the molecular mechanisms regulating anthocyanin and polysaccharide biosynthesis to enhance D. officinale quality and its market value. Here, we report that high light (HL) induced the accumulation of polysaccharides, particularly mannose, as well as anthocyanin accumulation, resulting in red stems. Metabolome and transcriptome analyses revealed that most of the flavonoids showed large changes in abundance, and flavonoid and polysaccharide biosynthesis was significantly activated under HL treatment. Interestingly, DoHY5 expression was also highly induced. Biochemical analyses demonstrated that DoHY5 directly binds to the promoters of DoF3H1 (involved in anthocyanin biosynthesis), DoGMPP2, and DoPMT28 (involved in polysaccharide biosynthesis) to activate their expression, thereby promoting anthocyanin and polysaccharide accumulation in D. officinale stems. DoHY5 silencing decreased flavonoid- and polysaccharide-related gene expression and reduced anthocyanin and polysaccharide accumulation, whereas DoHY5 overexpression had the opposite effects. Notably, naturally occurring red-stemmed D. officinale plants similarly have high levels of anthocyanin and polysaccharide accumulation and biosynthesis gene expression. Our results reveal a previously undiscovered role of DoHY5 in co-regulating anthocyanin and polysaccharide biosynthesis under HL conditions, improving our understanding of the mechanisms regulating stem color and determining nutritional quality in D. officinale. Collectively, our results propose a robust and simple strategy for significantly increasing anthocyanin and polysaccharide levels and subsequently improving the nutritional quality of D. officinale.

Fine mapping of genes controlling pigment accumulation in oilseed rape (Brassica napus L.)

Purple/red appearance is one of the common phenotypic variations in leaves, stems, and siliques of oilseed rape (Brassica napus L.) but very rare in flowers. In this study, the causal genes for the purple/red traits in stems and flowers in two accessions of oilseed rape (DH_PR and DH_GC001, respectively) derived from the wide hybridization were fine mapped, and candidate genes were determined by methods combined with bulked segregant analysis (BSA) and RNA-seq analysis. Both traits of purple stem and red flowers were mapped to the locus as AtPAP2 homologous genes (BnaPAP2.C6a and BnaPAP2.A7b, respectively) belonging to the R2R3-MYB family. Sequence comparisons of full-length allelic genes revealed several InDels and SNPs in intron 1 as well as exons, and completely different promoter region of BnaPAP2.C6a and a 211 bp insertion was identified in the promoter region of BnaPAP2.A7b of DH_GC001. Our results not only contribute to a better understanding of anthocyanin inheritance in B. napus, but also provide a useful toolbox for future breeding of cultivars with purple/red traits through the combination of different functional alleles and homologs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01365-5.

Transcriptomic analysis reveals biosynthesis genes and transcription factors related to leaf anthocyanin biosynthesis in Aglaonema commutatum

BACKGROUND

Aglaonema commutatum 'Red Valentine', as a foliage ornamental plant, is widely used for interior and exterior decoration because of its easy cultivation and management. However, reduced proportion of red foliage during large-scale production of A. commutatum seedlings is a frequent occurrence, which has considerable implications on the plant's ornamental and market value. However, the molecular mechanisms underlying this phenomenon remain unclear.

RESULTS

To explore the molecular basis of the variation in leaf color of A. commutatum Red Valentine, we performed transcriptome sequencing with the Illumina platform using two different varieties of A. commutatum, namely Red Valentine and a green mutant, at three different stages of leaf development. We annotated 63,621 unigenes and 14,186 differentially expressed genes by pairwise comparison. Furthermore, we identified 26 anthocyanin biosynthesis structural genes. The transcript per million (TPM) values were significantly higher for Red Valentine than for the green mutant in all three developmental stages, consistent with the high anthocyanin content of Red Valentine leaves. We detected positive transcription factors that may be involved in the regulation of anthocyanin biosynthesis using BLAST and through correlation analysis. Downregulation of these transcription factors may downregulate the expression of anthocyanin genes. We obtained full-length cDNA of the anthocyanin biosynthesis and regulatory genes and constructed phylogenetic trees to ensure accuracy of the analysis.

CONCLUSIONS

Our study provides insights into the molecular mechanisms underlying leaf variation in A. commutatum Red Valentine and may be used to facilitate the breeding of ornamental cultivars with high anthocyanin levels.

DhMYB2 and DhbHLH1 regulates anthocyanin accumulation via activation of late biosynthesis genes in Phalaenopsis-type Dendrobium

Phalaenopsis-type Dendrobium is a popular orchid with good ornamental and market value. Despite their popularity, molecular regulation of anthocyanin biosynthesis during flower development remains poorly understood. In this study, we systematically investigated the regulatory roles of the transcription factors DhMYB2 and DhbHLH1 in anthocyanins biosynthesis. Gene expression analyses indicated that both DhMYB2 and DhbHLH1 are specifically expressed in flowers and have similar expression patterns, showing high expression in purple floral tissues with anthocyanin accumulation. Transcriptomic analyses showed 29 differentially expressed genes corresponding to eight enzymes in anthocyanin biosynthesis pathway have similar expression patterns to DhMYB2 and DhbHLH1, with higher expression in the purple lips than the yellow petals and sepals of Dendrobium 'Suriya Gold'. Further gene expression analyses and Pearson correlation matrix analyses of Dendrobium hybrid progenies revealed expression profiles of DhMYB2 and DhbHLH1 were positively correlated with the structural genes DhF3'H1, DhF3'5'H2, DhDFR, DhANS, and DhGT4. Yeast one-hybrid and dual-luciferase reporter assays revealed DhMYB2 and DhbHLH1 can bind to promoter regions of DhF3'H1, DhF3'5'H2, DhDFR, DhANS and DhGT4, suggesting a role as transcriptional activators. These results provide new evidence of the molecular mechanisms of DhMYB2 and DhbHLH1 in anthocyanin biosynthesis in Phalaenopsis-type Dendrobium.

PeMYB4L interacts with PeMYC4 to regulate anthocyanin biosynthesis in Phalaenopsis orchid

Phalaenopsis spp., one genus of Orchidaceae, have become very popular worldwide for their fascinating flowers with various colors and pigmentation patterns. Several R2R3-MYB transcription factors have been reported to function in anthocyanin accumulation in Phalaenopsis spp. However, its molecular mechanism underlying the detailed regulatory pathway remains poorly understood. In this study, we identified a novel subgroup 2 R2R3-MYB transcription factor PeMYB4L, the expression profile of which was concomitant with red color formation in Phalaenopsis spp. flowers. Virus-induced gene silencing (VIGS) and transient overexpression assay verified that PeMYB4L promotes anthocyanin accumulation in flower tissues. In addition, PeMYB4L could directly regulates the expression of Phalaenopsis spp. chalcone synthase gene (PeCHS) through MYBST1 (GGATA) binding site. It's interesting that the basic-helix-loop-helix (bHLH) protein PeMYC4 shows opposite expression pattern from PeMYB4L in anthocyanin accumulation. Furthermore, PeMYC4 was verified to form MYB-bHLH complex with PeMYB4L, and attenuated the expression of PeCHS and weakened anthocyanin production, indicating a novel regulatory model of MYB-bHLH complex. Our findings uncover the detailed regulatory pathway of MYB-bHLH, and might provide a new insight into the complicated anthocyanin pigmentation in Phalaenopsis spp.

Analysis of Flavonoid Metabolism during the Process of Petal Discoloration in Three Malus Crabapple Cultivars

Malus crabapple has high ornamental and ecological value. Here, the flavonoids in the petals of three pink Malus crabapple cultivars, Malus 'Strawberry Parfait' (GD), M. 'Pink Spire' (FY), and M. 'Hongyi' (HY), at the bud stage (flower buds are swollen, and the pistils and stamens are about to appear; L), full bloom stage (the flowers are fully open, and the stigma and anthers have recently appeared; S), and end bloom stage (the stigma and anthers are dry; M) were identified, and their abundances were determined. First, Kodak Color Control Patches were used to describe the colors of petals, and a colorimeter was used to determine the phenotypic values of flower colors. Flavonoids were determined using ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). In all three crabapple cultivars, the red and yellow hues of the petals gradually disappeared, the color of the flowers changed from bright to dull, and the petals gradually faded. The extent of fading of the red hue of the petals was highest in GD, followed by FY and HY. A total of 302 metabolites were detected in the three cultivars. The content of total flavonoids in the three cultivars significantly differed, but there were no significant differences among species. The total flavonoid content of the three crabapple varieties was highest in HY, followed by FY and GD. The content of the anthocyanins delphinidin-3-O-sophoricoside-5-O-glucoside, pelargonidin-3-O-(6″-O-malonyl)glucoside, pelargonidin-3-O-glucoside, peonidin-3-O-glucoside, and cyanidin-3-O-arabinoside decreased significantly, which resulted in the discoloration of GD petals from L to M. The flavonoids and flavonols in FY might interact with anthocyanins in metabolic pathways. The content of these five anthocyanins decreased slowly, which resulted in the weaker discoloration of FY and HY compared with GD. The content of the five anthocyanins in HY did not decrease significantly, but the content of chalcone increased significantly, which might facilitate the production of anthocyanin auxiliary pigments and result in less pronounced fading of the petals. Cyanidin-3-O-arabinoside and pelargonidin-3-O-glucoside were the key flavonoids of the three crabapple cultivars. The total content and changes in anthocyanins were the key factors affecting petal color development and fading. Nonanthocyanin polyphenols, such as flavonoids, flavonols, and chalcone, are auxiliary pigments that affect petal fading. Overall, the results of this study provide new insights into the mechanism underlying the fading of the color of Malus crabapple flowers, and these new insights could aid the breeding of cultivars with different flower colors.

Advances and prospects of orchid research and industrialization

Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology and pollination syndromes that exhibit exclusive specializations, more than any other plants on Earth. These intrinsic factors together with human influences also make it a keystone group in biodiversity conservation. The advent of sequencing technologies and transgenic techniques represents a quantum leap in orchid research, enabling molecular approaches to be employed to resolve the historically interesting puzzles in orchid basic and applied biology. To date, 16 different orchid genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae, and Orchidoideae) have been released. These genome projects have given rise to massive data that greatly empowers the studies pertaining to key innovations and evolutionary mechanisms for the breadth of orchid species. The extensive exploration of transcriptomics, comparative genomics, and recent advances in gene engineering have linked important traits of orchids with a multiplicity of gene families and their regulating networks, providing great potential for genetic enhancement and improvement. In this review, we summarize the progress and achievement in fundamental research and industrialized application of orchids with a particular focus on molecular tools, and make future prospects of orchid molecular breeding and post-genomic research, providing a comprehensive assemblage of state of the art knowledge in orchid research and industrialization.

High-density genetic map and genome-wide association studies of aesthetic traits in Phalaenopsis orchids

Phalaenopsis spp. represent the most popular orchids worldwide. Both P. equestris and P. aphrodite are the two important breeding parents with the whole genome sequence available. However, marker–trait association is rarely used for floral traits in Phalaenopsis breeding. Here, we analyzed markers associated with aesthetic traits of Phalaenopsis orchids by using genome-wide association study (GWAS) with the F1 population P. Intermedia of 117 progenies derived from the cross between P. aphrodite and P. equestris. A total of 113,517 single nucleotide polymorphisms (SNPs) were identified in P. Intermedia by using genotyping-by-sequencing with the combination of two different restriction enzyme pairs, Hinp1 I/Hae III and Apek I/Hae III. The size-related traits from flowers were negatively related to the color-related traits. The 1191 SNPs from Hinp1 I/ Hae III and 23 simple sequence repeats were used to establish a high-density genetic map of 19 homolog groups for P. equestris. In addition, 10 quantitative trait loci were highly associated with four color-related traits on chromosomes 2, 5 and 9. According to the sequence within the linkage disequilibrium regions, 35 candidate genes were identified and related to anthocyanin biosynthesis. In conclusion, we performed marker-assisted gene identification of aesthetic traits with GWAS in Phalaenopsis orchids.

Why Black Flowers? An Extreme Environment and Molecular Perspective of Black Color Accumulation in the Ornamental and Food Crops

Pollinators are attracted to vibrant flower colors. That is why flower color is the key agent to allow successful fruit set in food or ornamental crops. However, black flower color is the least attractive to pollinators, although a number of plant species produce black flowers. Cyanidin-based anthocyanins are thought to be the key agents to induce black color in the ornamental and fruit crops. R2R3-MYB transcription factors (TFs) play key roles for the tissue-specific accumulation of anthocyanin. MYB1 and MYB11 are the key TFs regulating the expression of anthocyanin biosynthesis genes for black color accumulation. Post-transcriptional silencing of flavone synthase II (FNS) gene is the technological method to stimulate the accumulation of cyanidin-based anthocyanins in black cultivars. Type 1 promoter of DvIVS takes the advantage of FNS silencing to produce large amounts of black anthocyanins. Exogenous ethylene application triggers anthocyanin accumulation in the fruit skin at ripening. Environment cues have been the pivotal regulators to allow differential accumulation of anthocyanins to regulate black color. Heat stress is one of the most important environmental stimulus that regulates concentration gradient of anthocyanins in various plant parts, thereby affecting the color pattern of flowers. Stability of black anthocyanins in the extreme environments can save the damage, especially in fruits, caused by abiotic stress. White flowers without anthocyanin face more damages from abiotic stress than dark color flowers. The intensity and pattern of flower color accumulation determine the overall fruit set, thereby controlling crop yield and human food needs. This review paper presents comprehensive knowledge of black flower regulation as affected by high temperature stress, and the molecular regulators of anthocyanin for black color in ornamental and food crops. It also discusses the black color-pollination interaction pattern affected by heat stress for food and ornamental crops.

Transcriptome atlas of Phalaenopsis equestris

The vast diversity of Orchidaceae together with sophisticated adaptations to pollinators and other unique features make this family an attractive model for evolutionary and functional studies. The sequenced genome of Phalaenopsis equestris facilitates Orchidaceae research. Here, we present an RNA-seq-based transcriptome map of P. equestris that covers 19 organs of the plant, including leaves, roots, floral organs and the shoot apical meristem. We demonstrated the high quality of the data and showed the similarity of the P. equestris transcriptome map with the gene expression atlases of other plants. The transcriptome map can be easily accessed through our database Transcriptome Variation Analysis (TraVA) for visualizing gene expression profiles. As an example of the application, we analyzed the expression of Phalaenopsis “orphan” genes–those that do not have recognizable similarity with the genes of other plants. We found that approximately half of these genes were not expressed; the ones that were expressed were predominantly expressed in reproductive structures.

Characterisation of novel endogenous geminiviral elements in macadamia

Background

The presence of geminivirus sequences in a preliminary analysis of sRNA sequences from the leaves of macadamia trees with abnormal vertical growth (AVG) syndrome was investigated.

Results

A locus of endogenous geminiviral elements (EGE) in the macadamia genome was analysed, and the sequences revealed a high level of deletions and/or partial integrations, thus rendering the EGE transcriptionally inactive. The replication defective EGE in the macadamia genome indicates its inability to be the source of new viral infections and thus cause AVG or any other disease in macadamia. The EGE sequences were detected in two edible Macadamia species that constitute commercial cultivars and the wild germplasm of edible and inedible species of Macadamia. This strongly suggests that the integration preceded speciation of the genus Macadamia. A draft genome of a locus of EGE in Macadamia was developed. The findings of this study provide evidence to suggest the endogenization of the geminiviral sequences in the macadamia genome and the ancestral relationship of EGE with Macadamia in the Proteaceae family. Random mutations accumulating in the EGE inform that the sequence is evolving.

Conclusions

The EGE in Macadamia is inactive and thus not a direct cause of any diseases or syndromes including AVG in macadamia. The insertion of the EGE in the macadamia genome preceded speciation of the genus Macadamia.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08174-0.

Identification of high-copy number long terminal repeat retrotransposons and their expansion in Phalaenopsis orchids

BACKGROUND

Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of eukaryotic genomes. The identification and characterization of TEs facilitates understanding the transpositional activity of TEs with their effects on the orchid genome structure.

RESULTS

We combined the draft whole-genome sequences of Phalaenopsis equestris with BAC end sequences, Roche 454, and Illumina/Solexa, and identified long terminal repeat (LTR) retrotransposons in these genome sequences by using LTRfinder and classified by using Gepard software. Among the 10 families Gypsy-like retrotransposons, three families Gypsy1, Gypsy2, and Gypsy3, contained the most copies among these predicted elements. In addition, six high-copy retrotransposons were identified according to their reads in the sequenced raw data. The 12-kb Orchid-rt1 contains 18,000 copies representing 220 Mbp of the P. equestris genome. Southern blot and slot blot assays showed that these four retrotransposons Gypsy1, Gypsy2, Gypsy3, and Orchid-rt1 contained high copies in the large-genome-size/large-chromosome species P. violacea and P. bellina. Both Orchid-rt1 and Gypsy1 displayed various ratios of copy number for the LTR sequences versus coding sequences among four Phalaenopsis species, including P. violacea and P. bellina and small-genome-size/small-chromosome P. equestris and P. ahprodite subsp. formosana, which suggests that Orchid-rt1 and Gypsy1 have been through various mutations and homologous recombination events. FISH results showed amplification of Orchid-rt1 in the euchromatin regions among the four Phalaenopsis species. The expression levels of Peq018599 encoding copper transporter 1 is highly upregulated with the insertion of Orchid-rt1, while it is down regulated for Peq009948 and Peq014239 encoding for a 26S proteasome non-ATP regulatory subunit 4 homolog and auxin-responsive factor AUX/IAA-related. In addition, insertion of Orchid-rt1 in these three genes are all in their intron regions.

CONCLUSION

Orchid-rt1 and Gypsy1-3 have amplified within Phalaenopsis orchids concomitant with the expanded genome sizes, and Orchid-rt1 and Gypsy1 may have gone through various mutations and homologous recombination events. Insertion of Orchid-rt1 is in the introns and affects gene expression levels.

Integrated metabolic profiling and transcriptome analysis of pigment accumulation in diverse petal tissues in the lily cultivar 'Vivian'

BACKGROUND

Petals are the colorful region of many ornamental plants. Quality traits of petal color directly affect the value of ornamental plants. Although the regulatory mechanism of flower color has been widely studied in many plants, that of lily flower color is still worth further exploration.

RESULTS

In this study, the pigmentation regulatory network in different regions of the petal of lily cultivar 'Vivian' was analyzed through tissue structure, metabolites biosynthesis, and gene expression. We found that cell morphology of the petal in un-pigmented region differed from that in pigmented region. The cell morphology tends to flatten in un-pigmented region where the color is lighter. Moreover, high level anthocyanin was found in the pigmented regions by metabonomic analysis, especially cyanidin derivatives. However, flavanones were accumulated, contrast with anthocyanin in the un-pigmented regions of lily petal. To understand the relationship of these different metabolites and lily flower color, RNA-Seq was used to analyze the differentially expressed genes-related metabolite biosynthesis. Among these genes, the expression levels of several genes-related cyanidin derivatives biosynthesis were significantly different between the pigmented and un-pigmented regions, such as LvMYB5, LvMYB7, LvF3'H, LvDFR, LvANS and Lv3GT.

CONCLUSIONS

This data will help us to further understand the regulation network of lily petal pigmentation and create different unique color species.

Alternatively Spliced BnaPAP2.A7 Isoforms Play Opposing Roles in Anthocyanin Biosynthesis of Brassica napus L

Brassica napus L. (rapeseed, oilseed rape, and canola) and varieties of its two diploid parents, B. oleracea and B. rapa, display a large amount of variation in anthocyanin pigmentation of the leaf, stem, and fruit. Here, we demonstrate that BnaPAP2.A7, an ortholog of the B. oleracea anthocyanin activator BoMYB2 that confers purple traits, positively regulates anthocyanin biosynthesis in leaves of B. napus. Sequencing of BnaPAP2.A7 and transgenic analysis suggests that activation of this gene in purple rapeseed may result from a single nucleotide and/or 2bp insertion in its promoter region. BnaPAP2.A7 gives rise to three splice variants, designated BnaPAP2.A7-744, BnaPAP2.A7-910, and BnaPAP2.A7-395 according to the length of the transcripts. While BnaPAP2.A7-744 encodes a full-length R2R3-MYB, both BnaPAP2.A7-910 and BnaPAP2.A7-395 encode truncated proteins that lack both a partial R3 repeat and the complete C terminal domain, and so in vitro are unable to interact with the Arabidopsis bHLH protein AtTT8. Although expression of either BnaPAP2.A7-910 or BnaPAP2.A7-395 in green rapeseed does not result in purple leaves, both genes do modify genome-wide gene expression, with a strong repression of anthocyanin-related genes. We have demonstrated that BnaPAP.A7 regulates anthocyanin accumulation in leaves of B. napus and propose a potential mechanism for modulation of anthocyanin biosynthesis by alternative splicing.

Isolation and identification of MYB transcription factors (MYB19Long and MYB19Short) involved in raised spot anthocyanin pigmentation in lilies (Lilium spp.)

Although anthocyanin color patterns on flowers are among the most attractive characteristics, the genetic mechanisms through which color patterns are developed are not well understood, especially for color patterns associated with altered petal structure. Lilium species and cultivars often develop raised spots, where the interior surfaces of tepals increase to develop bumps with accompanying anthocyanin accumulation. The aim of this study was to identify transcription factors regulating pigmentation of the bumps. We identified two R2R3-MYB genes, MYB19Long and MYB19Short, in Lilium leichtlinii, L. lancifolium, and Asiatic hybrid lily cultivars. Their amino acid sequences were similar; however, part of the C-terminal region was triplicated in MYB19Long. Spatial and temporal expression profiles in lilies were strongly associated with anthocyanin biosynthesis gene expression in the bumps, and some defects were found in these genes in L. lancifolium 'Pure Gold' that developed colorless bumps. Thus, both MYB19Long and MYB19Short were likely to be involved in the bump pigmentation. MYB19Long had a stronger ability to stimulate target gene expression than MYB19Short, and expression levels of MYB19Long were greater than those of MYB19Short in lily tepals; thus, the ability to biosynthesize anthocyanin pigments was greater for MYB19Long than for MYB19Short. Among the F₁ population, MYB19Short expression was found only in the tepals of F₁ plants that developed bumps, although all of the F₁ plants possessed the MYB19Short gene, indicating that MYB19 expression followed bump development. These findings helped to elucidate the genetic mechanisms underlying raised spot development.

Assessment of violet-blue color formation in Phalaenopsis orchids

BACKGROUND

Phalaenopsis represents an important cash crop worldwide. Abundant flower colors observed in Phalaenopsis orchids range from red-purple, purple, purple-violet, violet, and violet-blue. However, violet-blue orchids are less bred than are those of other colors. Anthocyanin, vacuolar pH and metal ions are three major factors influencing flower color. This study aimed to identify the factors causing the violet-blue color in Phalaenopsis flowers and to analyze whether delphinidin accumulation and blue pigmentation formation can be achieved by transient overexpression of heterologous F3'5'H in Phalaenopsis.

RESULTS

Cyanidin-based anthocyanin was highly accumulated in Phalaenopsis flowers with red-purple, purple, purple-violet, and violet to violet-blue color, but no true-blue color and no delphinidin was detected. Concomitantly, the expression of PeF3'H (Phalaenopsis equestrsis) was high, but that of PhF3'5'H (Phalaenopsis hybrid) was low or absent in various-colored Phalaenopsis flowers. Transient overexpression of DgF3'5'H (Delphinium grandiflorum) and PeMYB2 in a white Phalaenopsis cultivar resulted a 53.6% delphinidin accumulation and a novel blue color formation. In contrast, transient overexpression of both PhF3'5'H and PeMYB2 did not lead to delphinidin accumulation. Sequence analysis showed that the substrate recognition site 6 (SRS6) of PhF3'5'H was consistently different from DgF3'5'Hs at positions 5, 8 and 10. Prediction of molecular docking of the substrates showed a contrary binding direction of aromatic rings (B-ring) with the SRS6 domain of DgF3'5'H and PhF3'5'H. In addition, the pH values of violet-blue and purple Phalaenopsis flowers ranged from 5.33 to 5.54 and 4.77 to 5.04, respectively. Furthermore, the molar ratio of metal ions (including Al3+, Ca2+ and Fe3+) to anthocyanin in violet-blue color Phalaenopsis was 190-, 49-, and 51-fold higher, respectively, than those in purple-color Phalaenopsis.

CONCLUSION

Cyanidin-based anthocyanin was detected in violet-blue color Phalaenopsis and was concomitant with a high pH value and high molar ratio of Al3+, Ca2+ and Fe3+ to anthocyanin content. Enhanced expression of delphinidin is needed to produce true-blue Phalaenopsis.

mRNA and miRNA Expression Analysis Reveal the Regulation for Flower Spot Patterning in Phalaenopsis 'Panda'

Phalaenopsis cultivar ‘Panda’ is a beautiful and valuable ornamental for its big flower and unique big spots on the petals and sepals. Although anthocyanins are known as the main pigments responsible for flower colors in Phalaenopsis, and the anthocyanins biosynthetic pathway in Phalaenopsis is generally well known, the detailed knowledge of anthocynins regulation within the spot and non-spot parts in ‘Panda’ flower is limited. In this study, transcriptome and small RNA libraries analysis from spot and non-spot sepal tissues of ‘Panda’ were performed, and we found PeMYB7, PeMYB11, and miR156g, miR858 is associated with the purple spot patterning in its sepals. Transcriptome analyses showed a total 674 differentially expressed genes (DEGs), with 424 downregulated and 250 upregulated (Non-spot-VS-Spot), and 10 candidate DEGs involved in anthocyanin biosynthetic pathway. The qPCR analysis confirmed that seven candidate structure genes (PeANS, PeF3′H, PeC4H, PeF3H, PeF3H1, Pe4CL2, and PeCHI) have significantly higher expressing levels in spot tissues than non-spot tissues. A total 1552 differentially expressed miRNAs (DEMs) were detected with 676 downregulated and 876 upregulated. However, microRNA data showed no DEMs targeting on anthocyanin biosynthesis structure gene, while a total 40 DEMs target transcription factor (TF) genes, which expressed significantly different level in spot via non-spot sepal, including 2 key MYB regulator genes. These results indicated that the lack of anthocyanidins in non-spot sepal may not directly be caused by microRNA suppressing anthocyanidin synthesis genes rather than the MYB genes. Our findings will help in understanding the role of miRNA molecular mechanisms in the spot formation pattern of Phalaenopsis, and would be useful to provide a reference to similar research in other species.