The R2R3 MYB transcription factor PavMYB10.1 involves in anthocyanin biosynthesis and determines fruit skin colour in sweet cherry (Prunus avium L.)

Molecular mechanisms underlying natural deficient and ultraviolet-induced accumulation of anthocyanin in the peel of 'Jinxiu' peach

Peach varieties that differ in red coloration due to varied anthocyanin accumulation result from transcriptional regulation by PpMYB10s, a group of specific R2R3 MYBs. Here we investigated the mechanisms driving a lack of anthocyanin in yellow-skinned 'Jinxiu' peach peel, as well as accumulation induced by UV irradiance. It was found that PpMYB10.1, PpMYB10.2 and PpMYB10.3 were positive regulators of anthocyanin accumulation, but the stimulation by PpMYB10.2 was weak. Low expression of PpMYB10.1 causes natural anthocyanin deficiency in 'Jinxiu' peel. However, the promoter sequences of PpMYB10.1 were identical in 'Jinxiu' and a naturally red-coloured peach 'Hujingmilu'. Therefore, potential negative regulator(s) upstream of PpMYB10.1 were explored. A novel R2R3-MYB repressor termed PpMYB80 was identified through comparative transcriptomic analysis and then functionally confirmed via transiently overexpressing and silencing in peach fruit, as well as transformation in tobacco. PpMYB80 directly binds to the promoter of PpMYB10.1 and inhibits its expression, but does not affect PpMYB10.3. In UV-exposed 'Jinxiu' fruit, expression of PpMYB10.3 was upregulated, while PpMYB10.1 remained low and PpMYB80 enhanced, which results in accumulation of anthocyanin in peel. This study revealed a transcriptional cascade involving PpMYB activators and repressors in regulating basal and UV-induced anthocyanin accumulation in peach peel.

Biochemical and in silico characterization of glycosyltransferases from red sweet cherry (Prunus avium L.) reveals their broad specificity toward phenolic substrates

Polyphenolic compounds are a class of phytonutrients that play important roles in plants and contribute to human health when incorporated into our diet through fruit consumption. A large proportion occur as glycoconjugates but the enzymes responsible for their glycosylation are poorly characterized. Here, we report the biochemical and structural characterization of two glycosyltransferases from sweet cherry named PaUGT1 and PaUGT2. Both are promiscuous glucosyltransferases active on diverse anthocyanidins and flavonols, as well as phenolic acids in the case of PaUGT1. They also exhibit weaker galactosyltransferase activity. The expression of the gene encoding PaUGT1, the most active of the two proteins, follows anthocyanin accumulation during fruit ripening, suggesting that this enzyme is the primary glycosyltransferase involved in flavonoid glycosylation in sweet cherry. It can potentially be used to synthesize diverse glycoconjugates of flavonoids for integration into bioactive formulations, and for generating new fruit cultivars with enhanced health-promoting properties using breeding methods.

De novo transcriptome analysis identifies RpMYB1 as an activator of anthocyanin biosynthesis in Rehmannia piasezkii

Rehmannia piasezkii is a kind of medicinal plants, of the Orobanchaceae family, and well known for its large pink or purple corolla. However, no research on the molecular mechanism of flower color formation in R. piasezkii has been conducted so far. In this study, we investigated the transcriptome of root, stem, leaf and corollas of R. piasezkii using transcriptome sequencing technology and assembled 144,582 unigenes. A total of 58 anthocyanin biosynthetic genes were identified in the R. piasezkii transcriptome, fourteen of which were highly correlated with anthocyanin content, especially RpF3H2, RpDFR2, RpANS1, RpANS2 and RpUFGT. Totally, 35 MYB genes with FPKM values greater than 5 were identified in the R. piasezkii transcriptome, including an R2R3 MYB transcriptional factor RpMYB1, which belongs to subgroup 6 of the R2R3 MYB family. Agrobacterium-mediated transient expression of Nicotiana benthamiana revealed that overexpression of RpMYB1 could activate the expression of structural genes in anthocyanin synthesis pathway and promote the accumulation of anthocyanins in N. benthamiana leaves, indicating that RpMYB1 is a positive regulator of anthocyanin synthesis. Furthermore, combined transient overexpression of RpMYB1 with RpANS1, RpMYB1+RpANS1 with other structural genes all could further enhance the accumulation of anthocyanins in N. benthamiana leaves. Permanent overexpression of RpMYB1 in R. glutinosa promoted anthocyanin accumulation and expression levels of RgCHS, RgF3H, RgDFR and RgANS. Further evidence from dual-luciferase assay suggested that RpMYB1 could bind to the promoter of RpDFR2 and hence activating its expression. These findings provide insight into the molecular regulation in anthocyanin biosynthesis in R. piasezkii and provide valuable genetic resources for the genetic improvement of flower color.

R2R3-MYB transcription factor CsMYB60 controls mature fruit skin color by regulating flavonoid accumulation in cucumber

Skin color is an important trait that determines the cosmetic appearance and quality of fruits. In cucumber, the skin color ranges from white to brown in mature fruits. However, the genetic basis for this important trait remains unclear. We conducted a genome-wide association study of natural cucumber populations, along with map-based cloning techniques, on an F2 population resulting from a cross between Pepino (with yellow-brown fruit skin) and Zaoer-N (with creamy fruit skin). We identified CsMYB60 as a candidate gene responsible for skin coloration in mature cucumber fruits. In cucumber accessions with white to pale yellow skin color, a premature stop mutation (C to T) was found in the second exon region of CsMYB60, whereas light yellow cucumber accessions exhibited splicing premature termination caused by an intronic mutator-like element insertion in CsMYB60. Transgenic CsMYB60c cucumber plants displayed a yellow-brown skin color by promoting accumulation of flavonoids, especially hyperoside, a yellow-colored flavonol. CsMYB60c encodes a nuclear protein that primarily acts as a transcriptional activator through its C-terminal activation motif. RNA sequencing and DNA affinity purification sequencing assays revealed that CsMYB60c promotes skin coloration by directly binding to the YYTACCTAMYT motif in the promoter regions of flavonoid biosynthetic genes, including CsF3'H, which encodes flavonoid 3'-hydroxylase. The findings of our study not only offer insight into the function of CsMYB60 as dominantly controlling fruit coloration, but also highlight that intronic DNA mutations can have a similar phenotypic impact as exonic mutations, which may be valuable in future cucumber breeding programs.

Comparative metabolomics profiling highlights unique color variation and bitter taste formation of Chinese cherry fruits

Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don], native to China, is an economically important fruit crop with attractive colors and delicious flavors. However, the specific metabolites present in cherry fruits have remained unknown. Here, we firstly characterized 1439 metabolite components of Chinese cherry fruits, predominantly including amino acids, flavonoids, and phenolic acids. Moreover, we screened ten biomarkers of Chinese cherry accessions by ROC curve analysis. Among 250 flavonoids, 26 structurally unique anthocyanins collectively determined fruit color, with cyanidins playing a dominant role. Differences in accumulated metabolites between anthocyanin and proanthocyanidin pathways were likely responsible for the variation in fruit color, ranging from yellow to black purple. Meanwhile, we found limocitrin-7-O-glucoside, along with eight other compounds, as underlying contributors to bitter off-taste experienced in fruits. This study provides insights into the regulatory network of metabolites involved in color variation and bitterness formation and genetic improvement of Chinese cherry fruits.

Haplotype-resolved genome assembly of the diploid Rosa chinensis provides insight into the mechanisms underlying key ornamental traits

Roses are consistently ranked at the forefront in cut flower production. Increasing demands of market and changing climate conditions have resulted in the need to further improve the diversity and quality of traits. However, frequent hybridization leads to highly heterozygous nature, including the allelic variants. Therefore, the absence of comprehensive genomic information leads to them making it challenging to molecular breeding. Here, two haplotype-resolved chromosome genomes for Rosa chinensis 'Chilong Hanzhu' (2n = 14) which is high heterozygous diploid old Chinese rose are generated. An amount of genetic variation (1,605,616 SNPs, 209,575 indels) is identified. 13,971 allelic genes show differential expression patterns between two haplotypes. Importantly, these differences hold valuable insights into regulatory mechanisms of traits. RcMYB114b can influence cyanidin-3-glucoside accumulation and the allelic variation in its promoter leads to differences in promoter activity, which as a factor control petal color. Moreover, gene family expansion may contribute to the abundance of terpenes in floral scents. Additionally, RcANT1, RcDA1, RcAG1 and RcSVP1 genes are involved in regulation of petal number and size under heat stress treatment. This study provides a foundation for molecular breeding to improve important characteristics of roses.

Metabolome integrated with transcriptome reveals the mechanism of three different color formations in Taxus mairei arils

Maire yew (Taxus mairei), an evergreen conifer, has high ornamental and medicinal value. The arils of this species has three different colors. However, the variation mechanisms of arils color formation remains unclear. Here, the gene expression and metabolite concentration were profiled for red (RTM), yellow (YTM), and purple (PTM) arils in different developmental stages. A total of 266 flavonoids and 35 carotenoids were identified. The predominant pigments identified in YTM were epiafzelechin, lutein, and β-Cryptoxanthin, while malvidin-3,5-di-O-glucoside and apigenin played crucial roles in PTM. And significant differential expression was observed among the HCT, DFR, LAR, ANS, crtB, NCED, and CCoAOMT genes across different color arils. During the maturation of yellow arils, the upregulation of HCT was strongly correlated with the accumulation of epiafzelechin. The diminished expression of DFR, LAR, and ANS seemed to inhibit the production of delphinidin-3-O-rutinoside. The decrease in crtB expression and concurrent increase in NCED expression potentially regulate the heightened accumulation of lutein. Meanwhile, the accumulation of β-cryptoxanthin appeared seemed to be positively influenced by NCED. As aril turning purple, the decreased expression of CCoAOMT seemed to facilitate the synthesis of apigenin. The substantial upregulation of DFR promoted the production of malvidin-3,5-di-O-glucoside. Additionally, the overexpression of MYBs may plays the important role in regulating the formation of different colored arils. In total, 14 genes were selected for qRT-PCR validation, the results indicated the reliability of the transcriptome sequences data. Our findings could provide valuable insight into the molecular breeding, development, and application of Maire yew resources.

Comparative Metabolome and Transcriptome Analyses Reveal the Regulatory Mechanism of Purple Leafstalk Production in Taro (Colocasia esculenta L. Schott)

Taro is a plant in the Araceae family, and its leafstalk possesses significant botanical and culinary value owing to its noteworthy medicinal and nutritional attributes. Leafstalk colour is an essential attribute that significantly influences its desirability and appeal to both breeders and consumers. However, limited information is available about the underlying mechanism responsible for the taro plant's colouration. Thus, the purpose of the current study was to elucidate the information on purple leafstalks in taro through comprehensive metabolome and transcriptome analysis. In total, 187 flavonoids, including 10 anthocyanins, were identified. Among the various compounds analysed, it was observed that the concentrations of five anthocyanins (keracyanin chloride (cyanidin 3-O-rutinoside chloride), cyanidin 3-O-glucoside, tulipanin (delphinidin 3-rutinoside chloride), idaein chloride (cyanidin 3-O-galactoside), and cyanidin chloride) were found to be higher in purple taro leafstalk compared to green taro leafstalk. Furthermore, a total of 3330 differentially expressed genes (DEGs) were identified by transcriptome analysis. Subsequently, the correlation network analysis was performed to investigate the relationship between the expression levels of these differentially expressed genes and the content of anthocyanin. There were 18 DEGs encoding nine enzymes detected as the fundamental structural genes contributing to anthocyanin biosynthesis, along with seven transcription factors (3 MYB and 4 bHLH) that may be promising candidate modulators of the anthocyanin biosynthesis process in purple taro leafstalk. The findings of the current investigation not only provide a comprehensive transcriptional code, but also give information on anthocyanin metabolites as well as beneficial insights into the colour mechanism of purple taro leafstalk.

Occurrence and Characterization of Sclerotinia sclerotiorum Causing Fruit Rot on Sweet Cherry in Southern China

Sweet cherry (Prunus avium L.) is widely planted in northern China due to its high economic value, and its cultivation has gradually spread south to warm regions. However, fruit rot, observed on the young fruits, poses a considerable threat to the development of sweet cherry. To determine the causal agent, morphological observation, molecular identification, and pathogenicity tests were performed on isolates obtained from diseased fruits. As a result, Sclerotinia sclerotiorum was identified as the pathogen. Pathogenicity tests on different sweet cherry cultivars indicated that 'Summit' was highly sensitive to S. sclerotiorum, whereas 'Hongmi' showed significant resistance. Besides sweet cherry, S. sclerotiorum could also infect other vegetable crops we tested, such as cowpea, soybean, tomato, and chili. Fungicide sensitivity and efficacy assays showed that both fludioxonil and pyraclostrobin can effectively inhibit the mycelial growth of S. sclerotiorum and decrease disease incidences on the young fruits of sweet cherry. Furthermore, genome sequencing resulted in a 37.8 Mb assembly of S. sclerotiorum strain ScSs1, showing abundant SNPs, InDels, and SVs with the genome of S. sclerotiorum reference strain 1980 UF-70. The above results provide an important basis for controlling the fruit rot of sweet cherry caused by S. sclerotiorum in China.

Comparative analysis of the difference in flavonoid metabolic pathway during coloring between red-yellow and red sweet cherry (Prunus avium L.)

The color of a fruit is an important contributor to the perception of its nutritional value. It is widely acknowledged that the color of sweet cherry changes obviously during ripening. Variations in anthocyanins and flavonoids account for the heterogeneous color of sweet cherries. In this study, we showed that anthocyanins but not carotenoids determine the color of sweet cherry fruits. The difference between red-yellow and red sweet cherry may be attributed to seven anthocyanins, including Cyanidin-3-O-arabinoside, Cyanidin-3,5-O-diglucoside, Cyanidin 3-xyloside, Peonidin-3-O-glucoside, Peonidin-3-O-rutinoside, Cyanidin-3-O-galactoside, Cyanidin-3-O-glucoside (Kuromanin), Peonidin-3-O-rutinoside-5-O-glucoside, Pelargonidin-3-O-glucoside and Pelargonidin-3-O-rutinoside. The content of 85 flavonols differed between red and red-yellow sweet cherries. The transcriptional analysis identified 15 key structural genes involved in the flavonoid metabolic pathway and four R2R3-MYB transcription factors. The expression level of Pac4CL, PacPAL, PacCHS1, PacCHS2, PacCHI, PacF3H1, PacF3H2, PacF3'H, PacDFR, PacANS1, PacANS2, PacBZ1 and four R2R3-MYB were positively correlated with anthocyanin content (ps < 0.05). PacFLS1, PacFLS2 and PacFLS3 expression was negatively correlated with anthocyanin content but positively correlated with flavonols content (ps < 0.05). Overall, our findings suggests that the heterogeneous expression of structural genes in the flavonoid metabolic pathway accounts for the variation in levels of final metabolites, leading to differences between red 'Red-Light' and red-yellow 'Bright Pearl'.

Physiological and molecular responses of different rose (Rosa hybrida L.) cultivars to elevated ozone levels

The increasing ground-level ozone (O₃) pollution resulting from rapid global urbanization and industrialization has negative effects on many plants. Nonetheless, many gaps remain in our knowledge of how ornamental plants respond to O₃. Rose (Rosa hybrida L.) is a commercially important ornamental plant worldwide. In this study, we exposed four rose cultivars ("Schloss Mannheim," "Iceberg," "Lüye," and "Spectra") to either unfiltered ambient air (NF), unfiltered ambient air plus 40 ppb O₃ (NF40), or unfiltered ambient air plus 80 ppb O₃ (NF80). Only the cultivar "Schloss Mannheim" showed significant O₃-related effects, including foliar injury, reduced chlorophyll content, reduced net photosynthetic rate, reduced stomatal conductance, and reduced stomatal apertures. In "Schloss Mannheim," several transcription factor genes-HSF, WRKY, and MYB genes-were upregulated by O₃ exposure, and their expression was correlated with that of NCED1, PP2Cs, PYR/PYL, and UGTs, which are related to ABA biosynthesis and signaling. These results suggest that HSF, WRKY, and MYB transcription factors and ABA are important components of the plant response to O₃ stress, suggesting a possible strategy for cultivating O₃-tolerant rose varieties.

In-silico mining and characterization of MYB family genes in wilt-resistant hybrid guava (Psidium guajava × Psidium molle)

BACKGROUND

The MYB family is one of the most significant groups of transcription factors in plants. However, several MYBs have been linked to secondary metabolism and are important for determining the color of fruit's peel and pulp. Despite being a substantial fruit crop in tropical and subtropical areas of the world, wilt-resistant hybrid guava (Psidium guajava × Psidium molle; PGPM) has not yet been the subject of a thorough examination. This study's goal was to assess the expression of MYB in guava fruit pulp, roots, and seeds to predict its function by in silico analysis of the guava root transcriptome data.

RESULTS

In the current study, we have mined the MYBs family of MYB genes from the transcriptome of the PGPM guava root. We have mined 15 distinct MYB transcription factor genes/transcripts viz MYB3, MYB4, MYB23, MYB86, MYB90, MYB308, MYB5, MYB82, MYB114, MYB6, MYB305, MYB44, MYB51, MYB46, and MYB330. From the analyses, it was found that R2-MYB and R3-MYB domains are conserved in all known guava MYB proteins. The expression of six different MYB TFs was examined using semi-quantitative RT-PCR in "Shweta" pulp (white colour pulp), "Lalit" pulp (red color pulp), "Lalit" root, and "Lalit" seed.

CONCLUSION

There were 15 MYB family members observed in guava. They were unequally distributed across the chromosomes, most likely as a result of gene duplication. Additionally, the expression patterns of the particular MYBs showed that MYB may be involved in the control of wilt, fruit ripening, seed development, and root development. Our results allow for a more thorough functional characterization of the guava MYB family genes and open the door to additional research into one essential MYB transcription factor family of genes and its involvement in the growth and ripening of guava fruit.

ABA Biosynthesis- and Signaling-Related Gene Expression Differences between Sweet Cherry Fruits Suggest Attenuation of ABA Pathway in Bicolored Cultivars

Fruit development involves exocarp color evolution. However, signals that control this process are still elusive. Differences between dark-red and bicolored sweet cherry cultivars rely on MYB factor gene mutations. Color evolution in bicolored fruits only occurs on the face receiving sunlight, suggesting the perception or response to color-inducing signals is affected. These color differences may be related to synthesis, perception or response to abscisic acid (ABA), a phytohormone responsible for non-climacteric fruit coloring. This work aimed to determine the involvement of ABA in the coloring process of color-contrasting varieties. Several phenolic accumulation patterns differed between bicolored 'Royal Rainier' and dark-red 'Lapins'. Transcript abundance of ABA biosynthetic genes (PavPSY, PavZEP and PavNCED1) decreased dramatically from the Pink to Red stage in 'Royal Rainier' but increased in 'Lapins', which correlated with a higher ABA content in this dark-red cultivar. Transcripts coding for ABA signaling (PavPP2Cs, PavSnRKs and PavMYB44.1) were almost undetectable at the Red stage in 'Royal Rainier'. Field trials revealed that 'Royal Rainier' color development was insensitive to exogenous ABA, whereas it increased in 'Lapins'. Furthermore, ABA treatment only increased transcript levels of signaling genes in 'Lapins'. Further studies may address if the ABA pathway is attenuated in bicolor cultivars.

Development of an inducible excision system of a visual marker Ipomoea batatas Myb gene from the genome of transgenic cells

In the plant genetic transformation process, single selection by a chemical-resistant marker gene occasionally allows the proliferation of non-transgenic cells, escaping selection pressure. The additional use of a visual marker gene is effective for accurate selection. For instance, R2R3-MYB genes are used for regulating anthocyanin biosynthesis; however, constitutive Myb expression in transgenic plants is not always desirable and may cause developmental abnormalities due to excess anthocyanin accumulation. To overcome the remaining problems in the use of Myb as a visible marker, we developed T-DNA. Ipomoea batatas Myb (IbMyb) and Cre expression cassettes were inserted between two loxP sequences, and the hygromycin phosphotransferase (HPT) and green fluorescent protein (GFP) expression cassettes were located outside of the loxP-IbMyb-Cre-loxP region. In the developed system, IbMyb and Cre were excised from the genomes of transgenic cells using heat-inducible Cre-loxP recombination. Upon heat treatment in a general incubator, green shoots emerged from purple tobacco transgenic calli that were pigmented with IbMyb expression. The excision of IbMyb from the genome of green shoots was confirmed using polymerase chain reaction (PCR) and sequencing. GFP expression was observed in the roots of the obtained green transgenic plants. We report that the system developed here operated successfully in tobacco, showing the potential to provide an easier and cheaper visual selection of transgenic cells in the genetic transformation process.

PsERF1B-PsMYB10.1-PsbHLH3 module enhances anthocyanin biosynthesis in the flesh-reddening of amber-fleshed plum (cv. Friar) fruit in response to cold storage

Flesh-reddening usually occurs in the amber-fleshed plum (Prunus salicina Lindl.) fruit during cold storage but not during ambient storage direct after harvest. It is not clear how postharvest cold signal is mediated to regulate the anthocyanin biosynthesis in the forming of flesh-reddening yet. In this study, anthocyanins dramatically accumulated and ethylene produced in the 'Friar' plums during cold storage, in comparison with plums directly stored at ambient temperature. Expression of genes associated with anthocyanin biosynthesis, as well as transcription factors of PsMYB10.1, PsbHLH3, and PsERF1B were strongly stimulated to upregulated in the plums in the period of cold storage. Suppression of ethylene act with 1-methylcyclopropene greatly suppressed flesh-reddening and downregulated the expression of these genes. Transient overexpression and virus-induced gene silencing assays in plum flesh indicated that PsMYB10.1 encodes a positive regulator of anthocyanin accumulation. The transient overexpression of PsERF1B, coupled with PsMYB10.1 and PsbHLH3, could further prompt the anthocyanin biosynthesis in a tobacco leaf system. Results from yeast two-hybrid and luciferase complementation assays verified that PsERF1B directly interacted with PsMYB10.1. PsERF1B and PsMYB10.1 enhanced the activity of the promoter of PsUFGT individually, and the enhancement was prompted by the co-action of PsERF1B and PsMYB10.1. Overall, the stimulation of the PsERF1B-PsMYB10.1-PsbHLH3 module mediated cold signal in the transcriptomic supervision of the anthocyanin biosynthesis in the 'Friar' plums. The results thereby revealed the underlying mechanism of the postharvest alteration of the flesh phenotype of 'Friar' plums subjected to low temperature.

The mechanisms underpinning anthocyanin accumulation in a red-skinned bud sport in pear (Pyrus ussuriensis)

KEY MESSAGE

In our study, we demonstrated that histone acetylation promotes anthocyanin accumulation in pears by affecting the expression of key genes. Color is an important trait of horticultural plants, and the anthocyanin content directly affects the nutritional value and commercial value of colored fruits. Therefore, it is important for fruit breeding to cultivate new varieties with bright colors. 'Nanhong' (NH) pear (Pyrus ussuriensis) is a bud sport cultivar of 'Nanguo' (NG) pear. The anthocyanin content in NH pear is significantly higher than that in NG pear, but the underlying molecular mechanism remains unclear. Here, we observed that the anthocyanin biosynthesis structural gene PuUFGT (UDP-glucose: flavonoids 3-O-glucosyltransferase) and an anthocyanin transporter gene PuGSTF6 (glutathione S-transferase) had significantly higher expression levels in NH than in NG pears during the late stages of fruit development. Meanwhile, the R2R3-MYB transcription factor PuMYB110a was also highly expressed in NH pears and could positively regulate the transcription of PuUFGT and PuGSTF6. Overexpression of PuMYB110a in pear increased the fruit anthocyanin content. In addition, despite no significant differences in methylation levels being found in the promoters of PuMYB110a, PuUFGT, and PuGSTF6 when comparing the two varieties, the histone acetylation levels of PuMYB110a were significantly higher in NH pear compared with those in NG pear. Our findings suggest a mechanism for anthocyanin accumulation in NH fruit.

Metabolome and transcriptome analyses reveal the molecular mechanisms of LcMYB1 regulating anthocyanin accumulation in litchi hairy roots

Agrobacterium rhizogenes-mediated hairy root culture offer a promising approach for gene function analysis and production of plant secondary metabolites. Here, we obtained red litchi hairy roots using A. rhizogenes-mediated LcMYB1 transformation. Using high performance liquid chromatography, the main anthocyanins in the red hairy roots were determined to be cyanidin 3-rutinoside and cyanidin 3-glucoside. A total of 164 metabolites were significantly upregulated or downregulated in the red hairy roots, which were mostly involved in flavone and flavonol pathway, and flavonoid pathway. The transcriptome analysis revealed 472 differentially expressed genes (DEGs). Up-regulated genes were considerably enriched in anthocyanin, flavone and flavonol biosynthesis. Integrative metabolite profiling and transcriptome analyses showed that LcF3'H, LcUFGT1, and LcGST4 were key structural genes in anthocyanin biosynthesis. However, the expression of Cinnamyl-alcohol dehydrogenase (CAD) and Peroxidase (POD) leading to the production of lignin were significantly down-regulated, suggesting flavonoids and lignin compete with each other in the phenylpropanoid pathway. A total of 52 DEGs were identified as transcription factors. Correlation analysis showed that 8 transcription factors were positively correlated with LcUFGT1, and LcGST4, involving in anthocyanin biosynthesis. These findings clarify the molecular mechanisms of LcMYB1 regulating anthocyanin accumulation in litchi hairy roots.

Metabolomics and transcriptomics provide insights into the molecular mechanisms of anthocyanin accumulation in the seed coat of differently colored mung bean (Vigna radiata L.)

Black mung bean is rich in anthocyanin, however, the accumulation and the molecular mechanism of anthocyanin synthesis in black mung bean are unclear. In this study, anthocyanin metabolomics and transcriptomics on the seed coats of two different colors of mung bean were performed to clarify the composition of anthocyanins, and identify transcription factors involved in regulating anthocyanin biosynthesis. In the mature stage, 23 kinds of anthocyanin compounds were identified. All anthocyanin components contents were significantly higher in seed coat of black mung bean compare with green mung bean. Transcriptome analysis suggested that most of the structural genes for anthocyanin biosynthesis and some potential regulatory genes were significantly differentially expressed. WGCNA suggested VrMYB90 was an important regulatory gene in anthocyanin biosynthesis. Arabidopsis thaliana overexpressing VrMYB90 showed significant accumulation of anthocyanins. PAL, 4CL, DFR, F3'5'H, LDOX, F3'H and UFGT were up-regulated in 35S:VrMYB90 Arabidopsis thaliana. These findings provide valuable information for understanding the synthesis mechanism of anthocyanins in black mung bean seed coats.

Purple Rehmannnia : investigation of the activation of R2R3-MYB transcription factors involved in anthocyanin biosynthesis

Engineering anthocyanin biosynthesis in herbs could provide health-promoting foods for improving human health. Rehmannia glutinosa is a popular medicinal herb in Asia, and was a health food for the emperors of the Han Dynasty (59 B.C.). In this study, we revealed the differences in anthocyanin composition and content between three Rehmannia species. On the 250, 235 and 206 identified MYBs in the respective species, six could regulate anthocyanin biosynthesis by activating the ANTHOCYANIDIN SYNTHASE (ANS) gene expression. Permanent overexpression of the Rehmannia MYB genes in tobacco strongly promoted anthocyanin content and expression levels of NtANS and other genes. A red appearance of leaves and tubers/roots was observed, and the total anthocyanin content and the cyanidin-3-O-glucoside content were significantly higher in the lines overexpressing RgMYB41, RgMYB42 and RgMYB43 from R. glutinosa,as well as RcMYB1 and RcMYB3 in R. chingii and RhMYB1 from R. henryi plants. Knocking out of RcMYB3 by CRISPR/Cas9 gene editing resulted in the discoloration of the R. chingii corolla lobes, and decreased the content of anthocyanin. R. glutinosa overexpressing RcMYB3 displayed a distinct purple color in the whole plants, and the antioxidant activity of the transgenic plants was significantly enhanced compared to WT. These results indicate that Rehmannia MYBs can be used to engineer anthocyanin biosynthesis in herbs to improve their additional value, such as increased antioxidant contents. This article is protected by copyright. All rights reserved.

Identification and functional characterization of AcMYB113 in anthocyanin metabolism of Aesculus chinensis Bunge var. chinensis leaves

Anthocyanins can be induced by environmental factors such as low-temperature and play essential roles in plant color formation. In this study, leaves of Aesculus chinensis Bunge var. chinensis with different colors under natural low-temperature in autumn were collected and grouped into green leaf (GL) and red leaf (RL). To reveal the underlying mechanism of color formation in RL, a combined analysis of the metabolome and transcriptome was conducted with GL and RL. Metabolic analyses revealed that total anthocyanin content and primary anthocyanin components were increased RL relative to GL and cyanidin was the main anthocyanin compound in RL. Transcriptome analysis provided a total of 18720 differentially expressed genes (DEGs), of which 9150 DEGs were upregulated and 9570 DEGs were downregulated in RL relative to GL. KEGG analysis showed that DEGs were mainly enriched in flavonoid biosynthesis, phenylalanine metabolism, and phenylpropanoid biosynthesis. Furthermore, co-expression network analysis indicated that 56 AcMYB transcription factors were highly expressed in RL compared with GL, among which AcMYB113 (an R2R3-MYB TF) had a strong correlation with anthocyanins. Overexpression of AcMYB113 in apple resulted in dark-purple transgenic calluses. In addition, the transient expression experiment showed that AcMYB113 enhanced anthocyanin synthesis by activating pathways of anthocyanin biosynthesis in leaves of Aesculus chinensis Bunge var. chinensis. Taken together, our findings reveal new insights into the molecular mechanism of anthocyanin accumulation in RL and provide candidate genes for the breeding of anthocyanin-rich cultivars.

Genome-wide identification of WD40 transcription factors and their regulation of the MYB-bHLH-WD40 (MBW) complex related to anthocyanin synthesis in Qingke (Hordeum vulgare L. var. nudum Hook. f.)

BACKGROUND

WD40 transcription factors, a large gene family in eukaryotes, are involved in a variety of growth regulation and development pathways. WD40 plays an important role in the formation of MYB-bHLH-WD (MBW) complexes associated with anthocyanin synthesis, but studies of Qingke barley are lacking.

RESULTS

In this study, 164 barley HvWD40 genes were identified in the barley genome and were analyzed to determine their relevant bioinformatics. The 164 HvWD40 were classified into 11 clusters and 14 subfamilies based on their structural and phylogenetic protein profiles. Co-lineage analysis revealed that there were 43 pairs between barley and rice, and 56 pairs between barley and maize. Gene ontology (GO) enrichment analysis revealed that the molecular function, biological process, and cell composition were enriched. The Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that the RNA transport pathway was mainly enriched. Based on the identification and analysis of the barley WD40 family and the transcriptome sequencing (RNA-seq) results, we found that HvWD40-140 (WD40 family; Gene ID: r1G058730), HvANT1 (MYB family; Gene ID: HORVU7Hr1G034630), and HvANT2 (bHLH family; Gene ID: HORVU2Hr1G096810) were important components of the MBW complex related to anthocyanin biosynthesis in Qingke, which was verified via quantitative real-time fluorescence polymerase chain reaction (qRT-PCR), subcellular location, yeast two-hybrid (Y2H), and bimolecular fluorescent complimentary (BiFC) and dual-luciferase assay analyses.

CONCLUSIONS

In this study, we identified 164 HvWD40 genes in barley and found that HvnANT1, HvnANT2, and HvWD40-140 can form an MBW complex and regulate the transcriptional activation of the anthocyanin synthesis related structural gene HvDFR. The results of this study provide a theoretical basis for further study of the mechanism of HvWD40-140 in the MBW complex related to anthocyanin synthesis in Qingke.

LhANS-rr1, LhDFR, and LhMYB114 Regulate Anthocyanin Biosynthesis in Flower Buds of Lilium ‘Siberia’

The bulb formation of Lilium is affected by many physiological and biochemical phenomena, including flower bud differentiation, starch and sucrose accumulation, photoperiod, carbon fixation, plant hormone transduction, etc. The transcriptome analysis of flower buds of Lilium hybrid ‘Siberia’ at different maturity stages showed that floral bud formation is associated with the accumulation of anthocyanins. The results of HPLC-MS showed that cyanidin is the major anthocyanin found in Lilium ‘Siberia’. Transcriptome KEGG enrichment analysis and qRT-PCR validation showed that two genes related to flavonoid biosynthesis (LhANS-rr1 and LhDFR) were significantly up-regulated. The functional analysis of differential genes revealed that LhMYB114 was directly related to anthocyanin accumulation among 19 MYB transcription factors. Furthermore, the qRT-PCR results suggested that their expression patterns were very similar at different developmental stages of the lily bulbs. Virus-induced gene silencing (VIGS) revealed that down-regulation of LhANS-rr1, LhDFR, and LhMYB114 could directly lead to a decrease in anthocyanin accumulation, turning the purple phenotype into a white color. Moreover, this is the first report to reveal that LhMYB114 can regulate anthocyanin accumulation at the mature stage of lily bulbs. The accumulation of anthocyanins is an important sign of lily maturity. Therefore, these findings have laid a solid theoretical foundation for further discussion on lily bulb development in the future.

Integrated Transcriptome and Metabolome Analyses Provide Insights into the Coloring Mechanism of Dark-red and Yellow Fruits in Chinese Cherry [Cerasus pseudocerasus (Lindl.) G. Don]

Chinese cherry [Cerasus pseudocerasus (Lindl.) G. Don] is an important fruit tree from China that has excellent ornamental, economic, and nutritional values with various colors. The dark-red or red coloration of fruit, an attractive trait for consumers, is determined by anthocyanin pigmentation. In this study, the coloring patterns during fruit development in dark-red and yellow Chinese cherry fruits were firstly illustrated by integrated transcriptome and widely-targeted metabolome analyses. Anthocyanin accumulation in dark-red fruits was significantly higher compared with yellow fruits from the color conversion period, being positively correlated to the color ratio. Based on transcriptome analysis, eight structural genes (CpCHS, CpCHI, CpF3H, CpF3'H, CpDFR, CpANS, CpUFGT, and CpGST) were significantly upregulated in dark-red fruits from the color conversion period, especially CpANS, CpUFGT, and CpGST. On contrary, the expression level of CpLAR were considerably higher in yellow fruits than in dark-red fruits, especially at the early stage. Eight regulatory genes (CpMYB4, CpMYB10, CpMYB20, CpMYB306, bHLH1, CpNAC10, CpERF106, and CpbZIP4) were also identified as determinants of fruit color in Chinese cherry. Liquid chromatography-tandem mass spectrometry identified 33 and 3 differential expressed metabolites related to anthocyanins and procyanidins between mature dark-red and yellow fruits. Cyanidin-3-O-rutinoside was the predominant anthocyanin compound in both fruits, while it was 6.23-fold higher in dark-red than in yellow fruits. More accumulated flavanol and procyanidin contents resulted in less anthocyanin content in flavonoid pathway in yellow fruits due to the higher expression level of CpLAR. These findings can help understand the coloring mechanism of dark-red and yellow fruits in Chinese cherry, and provide genetic basis for breeding new cultivars.

High Light Intensity Triggered Abscisic Acid Biosynthesis Mediates Anthocyanin Accumulation in Young Leaves of Tea Plant (Camellia sinensis)

There is increasing interest in the production and consumption of tea (Camellia sinensis L.) processed from purple-leaved cultivar due to their high anthocyanin content and health benefits. However, how and why seasonal changes affect anthocyanin accumulation in young tea leaves still remains obscured. In this study, anthocyanin and abscisic acid (ABA) contents in young leaves of Zifuxing 1 (ZFX1), a cultivar with new shoots turning to purple in Wuyi Mountain, a key tea production region in China, were monitored over four seasons. Young leaves produced in September were highly purplish, which was accompanied with higher anthocyanin and ABA contents. Among the environmental factors, the light intensity in particular was closely correlated with anthocyanin and ABA contents. A shade experiment also indicated that anthocyanin content significantly decreased after 168 h growth under 75% shade, but ABA treatment under the shade conditions sustained anthocyanin content. To confirm the involvement of ABA in the modulation of anthocyanin accumulation, anthocyanin, carotenoids, chlorophyll, ABA, jasmonic acid (JA), and salicylic acid (SA) in the young leaves of four cultivars, including ZFX1, Zijuan (ZJ), wherein leaves are completely purple, Rougui (RG) and Fudingdabaicha (FDDB) wherein leaves are green, were analyzed, and antioxidant activities of the leaf extracts were tested. Results showed that ABA, not other tested hormones, was significantly correlated with anthocyanin accumulation in the purple-leaved cultivars. Cultivars with higher anthocyanin contents exhibited higher antioxidant activities. Subsequently, ZFX1 plants were grown under full sun and treated with ABA and fluridone (Flu), an ABA inhibitor. ABA treatment elevated anthocyanin level but decreased chlorophyll contents. The reverse was true to those treated with Flu. To pursue a better understanding of ABA involvement in anthocyanin accumulation, RNA-Seq was used to analyze transcript differences among ABA- or Flu-treated and untreated ZFX1 plants. Results indicated that the differentially expressed genes in ABA or Flu treatment were mainly ABA signal sensing and metabolism-related genes, anthocyanin accumulation-related genes, light-responsive genes, and key regulatory MYB transcription factors. Taking all the results into account, a model for anthocyanin accumulation in ZFX1 cultivar was proposed: high light intensity caused reactive oxygen stress, which triggered the biosynthesis of ABA; ABA interactions with transcription factors, such as MYB-enhanced anthocyanin biosynthesis limited chlorophyll and carotenoid accumulation; and transport of anthocyanin to vacuoles resulting in the young leaves of ZFX1 with purplish coloration. Further research is warranted to test this model.

Tobacco rattle virus-induced VcANS gene silencing in blueberry fruit

Blueberry (Vaccinium corymbosum L.), a woody perennial bush in the genus Vaccinium, is an economically important and popular fruit crop worldwide. Development the superior cultivars, which including excellent fruit traits, not only means higher yielding and economic efficiency, but also produce fruit that to meet the preferences of different consumers. Excavating fruit quality-related genes, studying their functions, and using transgenic or molecular-assisted breeding are beneficial to the development of excellent blueberry varieties. Genetic transformation is an excellent way to study the function of genes in plants, however, it is a labor-intensive and time-consuming process to genetically transform many woody plants, including blueberry. Virus-induced gene silencing (VIGS) provides an efficient approach to knock-down the expression of target genes for functional analysis. In this study, tobacco rattle virus induced genes silencing (TRV-VIGS) was established in blueberry fruits using the VcANS gene as a reporter. The silenced sector of the skin of blueberry fruits injected with pTRV2 (plasmid Tobacco Rattle Virus, TRV-RNA2)::VcANS remained green or white at 25 days after agroinfiltration. In agroinfiltrated materials, the VcANS transcript levels were much lower in fruits with phenotypic changes (delayed color change) than in those infiltrated with the pTRV2 empty vector. Silencing of VcANS also affected the expression of other genes involved in the anthocyanin synthesis pathway. The experimental results support that VcANS can be used as an effective marker gene for VIGS system. In addition, the TRV-VIGS system has been successfully established in blueberry fruits, which provided an effective verification method for functional identification of unknown genes in blueberry fruits.

Chromosome-Level Assembly of Flowering Cherry (Prunus campanulata) Provides Insight into Anthocyanin Accumulation

The flowering cherries (genus Prunus, subgenus Cerasus) are popular ornamental trees in China, Japan, Korea, and elsewhere. Prunus campanulata Maxim. is an important species of flowering cherry native to Southern China, which is also distributed in Taiwan, the Ryukyu Islands of Japan, and Vietnam. It produces bell-shaped flowers with colors ranging from bright pink to crimson during the Chinese Spring Festival from January to March each year. We selected the P. campanulata cultivar "Lianmeiren", with only 0.54% of heterozygosity, as the focus of this study, and generated a high-quality chromosome-scale genome assembly of P. campanulata by combining Pacific Biosciences (PacBio) single-molecule sequencing, 10× Genomics sequencing, and high-throughput chromosome conformation capture (Hi-C) technology. We first assembled a 300.48 Mb genome assembly with a contig N50 length of 2.02 Mb. In total, 28,319 protein-coding genes were predicted from the genome, 95.8% of which were functionally annotated. Phylogenetic analyses indicated that P. campanulata diverged from a common ancestor of cherry approximately 15.1 million years ago. Comparative genomic analyses showed that the expanded gene families were significantly involved in ribosome biogenesis, diterpenoid biosynthesis, flavonoid biosynthesis, and circadian rhythm. Furthermore, we identified 171 MYB genes from the P. campanulata genome. Based on the RNA-seq of five organs at three flowering stages, expression analyses revealed that the majority of the MYB genes exhibited tissue-specific expression patterns, and some genes were identified as being associated with anthocyanin accumulation. This reference sequence is an important resource for further studies of floral morphology and phenology, and comparative genomics of the subgenera Cerasus and Prunus.

Genome-Wide Identification of the SQUAMOSA Promoter-Binding Protein-like (SPL) Transcription Factor Family in Sweet Cherry Fruit

Plant-specific SQUAMOSA promoter-binding protein-like (SPL) transcription factors play important regulatory roles during plant growth and development, fruit ripening, inflorescence branching, and biotic and abiotic stresses. However, there have been no identification or systematic studies of the SPL gene family in the sweet cherry. In this study, 12 SPL genes were identified in the sweet cherry reference genome, which were distributed over 6 chromosomes and classified into six groups according to phylogenetic relationships with other SPL gene families. Nine PavSPLs were highly expressed at green fruit stages and dramatically decreased at the onset of fruit ripening, which implied that they were important regulators during fruit development and ripening. The expression patterns of PavSPL genes under ABA, GA, and MeJA treatments showed that the PavSPLs were involved in the process of fruit ripening. A subcellular localization experiment proved that PavSPL4 and PavSPL7 proteins were localized in the nucleus. The genome-wide identification of the SPL gene family provided new insights while establishing an important foundation for sweet cherry studies.

PhAAT1, encoding an anthocyanin acyltransferase, is transcriptionally regulated by PhAN2 in petunia

Anthocyanins widely exist in plants and they are important pigments for color of petals and fruits. They are produced through a multi-step pathway controlled by transcription factor complexes. The anthocyanin skeleton modification is the last reaction in the anthocyanin synthesis pathway, which improves the stability of anthocyanins. Acylation modification is an important modification of anthocyanins. However, the identification and function of anthocyanin acyltransferase genes and their expression regulation are rarely reported. In this study, we identified the petunia anthocyanin acyltransferase gene, PhAAT1. PhAAT1 is located in the cytoplasm and PhAAT1 silencing changed flower color and reduced the stability of anthocyanin. Metabolomics analysis showed that PhAAT1 silencing led to the reduction of p-coumaroylated and caffeoylated anthocyanins. In addition, PhAAT1 was positively regulated by the MYB transcription factor, PhAN2, which directly interacts with the promoter of PhAAT1.

Identification of Chalcone Isomerase Family Genes and Roles of CnCHI4 in Flavonoid Metabolism in Camellia nitidissima

Camellia nitidissima is a woody plant with high ornamental value, and its golden-yellow flowers are rich in a variety of bioactive substances, especially flavonoids, that are beneficial to human health. Chalcone isomerases (CHIs) are key enzymes in the flavonoid biosynthesis pathway; however, there is a scarcity of information regarding the CHI family genes of C. nitidissima. In this study, seven CHI genes of C. nitidissima were identified and divided into three subfamilies by phylogenetic analysis. The results of multiple sequence alignment revealed that, unlike CnCHI1/5/6/7, CnCHI2/3/4 are bona fide CHIs that contain all the active site and critical catalytic residues. Analysis of the expression patterns of CnCHIs and the total flavonoid content of the flowers at different developmental stages revealed that CnCHI4 might play an essential role in the flavonoid biosynthesis pathway of C. nitidissima. CnCHI4 overexpression significantly increased flavonoid production in Nicotiana tabacum and C. nitidissima. The results of the dual-luciferase reporter assay and yeast one-hybrid system revealed that CnMYB7 was the key transcription factor that governed the transcription of CnCHI4. The study provides a comprehensive understanding of the CHI family genes of C. nitidissima and performed a preliminary analysis of their functions and regulatory mechanisms.

Identification of Candidate Genes Associated with Pulp Color by Transcriptomic Analysis of 'Huaxiu' Plum (Prunus salicina Lindl.) during Fruit-Ripening

The plum (Prunus salicina Lindl.) is one of the traditional and economically important stone fruit trees in China. Anthocyanins are important pigments in plums. However, little is known about the molecular mechanisms underlying anthocyanin accumulation in plum fruits, which has hindered research on the molecular mechanism of its utilization. Our research shows that the chlorophyll content was gradually decreased and the contents of anthocyanin and flavonoid increased during the coloring process of the pulp in 'Huaxiu' plums (P. salicina). Then, the RNA-Seq technique was used to analyze the transcriptome of pulp color changes with three different stages (yellow, orange, and red) in the 'Huaxiu' plum (P. salicina). A total of 57,119 unigenes with a mean length of 953 bp were generated, and 61.6% of them were annotated to public databases. The Gene Ontology (GO) database assigned 21,438 unigenes with biological process, cellular components, and molecular function. In addition, 32,146 unigenes were clustered into 25 categories for functional classification by the COG database, and 7595 unigenes were mapped to 128 KEGG pathways by the KEGG pathway database. Of these, 1095 (YS-versus-OS), 4947 (YS-versus-RS), and 3414 (OS-versus-RS) genes were significantly expressed differentially between two coloration stages. The GO and KEGG pathway enrichment analysis revealed that 20 and 1 differentially expressed genes (DEG) are involved in flavonoid biosynthesis and anthocyanin biosynthesis, respectively. Finally, we mainly identified three structural genes as candidate genes. The transcriptome information in this study provide a basis for further studies of pulp colors in plum and contribute to our understanding of the molecular mechanisms underlying anthocyanin biosynthesis in pulp.

Investigation and Expression Analysis of R2R3-MYBs and Anthocyanin Biosynthesis-Related Genes during Seed Color Development of Common Bean (Phaseolus vulgaris)

Anthocyanins are responsible for the coloration of common bean seeds, and their accumulation is positively correlated with the expression level of anthocyanin biosynthetic genes. The MBW (MYB-bHLH-WD40) complex is thought to regulate the expression of these genes, and MYB proteins, which are a key factor in activating anthocyanin pathway genes, have been identified in several plants. This study demonstrated gene structures, chromosomal placements, gene duplications of R2R3-MYBs, miRNAs associated with R2R3-MYBs, and the interaction of these genes with other flavonoid regulatory genes. qRT-PCR was used to investigate the role of specific R2R3-MYBs and flavonoid genes in common bean seed color development. As a result of a comprehensive analysis with the help of in silico tools, we identified 160 R2R3-MYB genes in the common bean genome. We divided these genes into 16 classes on the basis of their intron-exon and motif structures. Except for three, the rest of the common bean R2R3-MYB members were distributed to all chromosomes with different densities, primarily located on chromosomes 3 and 8. We identified a total of 44 duplicated gene pairs dispersed across 11 chromosomes and evolved under purifying selection (Ka/Ks  <  1), 19 of which were derived from a whole-genome duplication. Our research uncovered 25 putative repressor PvMYB proteins that contain the EAR motif. Additionally, fifty different cis-regulatory elements regulated by light, stress, and hormone were identified. Within the genome of the common bean, we discovered a total of 36 microRNAs that target a total of 72 R2R3-MYB transcripts. The effect of 16 R2R3-MYB genes and 16 phenylpropanoid pathway genes, selected on the basis of their interaction in the protein-protein interaction map, playing role in the regulation of seed coat color development was evaluated using qRT-PCR in 5 different tissues at different developmental stages. The results revealed that these specific genes have different expression levels during different developmental periods, with higher levels in the pod filling and early pod stages than in the rest of the developmental periods. Furthermore, it was shown that PvTT8 (bHLH), PvTT2 (PvMYB42), PvMYB113, PvTTG1, and PvWD68 genes have effects on the regulation of seed coat color. The findings of this study, which is the first to use whole-genome analysis to identify and characterize the R2R3-MYB genes in common bean, may serve as a reference for future functional research in the legume.

Abscisic acid-responsive transcription factors PavDof2/6/15 mediate fruit softening in sweet cherry

Softening is a key step during fruit ripening that is modulated by the interplay between multiple phytohormones. The antagonistic action of abscisic acid (ABA) and auxin determines the rate of fruit ripening and softening. However, the transcription factors that integrate ABA and auxin signals to regulate fruit softening remain to be determined. In this study, we identified several DNA-binding with One Finger (Dof) transcription factors essential for ABA-promoted fruit softening, based on transcriptome analysis of two sweet cherry (Prunus avium L.) varieties with different fruit firmness. We show that PavDof6 directly binds to the promoters of genes encoding cell wall-modifying enzymes to activate their transcription, while PavDof2/15 directly repress their transcription. Transient overexpression of PavDof6 and PavDof2/15 in sweet cherry fruits resulted in precocious and delayed softening, respectively. In addition, we show that the auxin response factor PavARF8, the expression of whose encoding gene is repressed by ABA, activates PavDof2/15 transcription. Furthermore, PavDof2/6/15 and PavARF8 directly bind to the 9-cis-epoxycarotenoid dioxygenase 1 (PavNCED1) promoter and regulate its expression, forming a feedback mechanism for ABA-mediated fruit softening. These findings unveil the physiological framework of fruit softening and establish a direct functional link between the ABA-PavARF8-PavDofs module and cell-wall-modifying genes in mediating fruit softening.

Heterozygous frameshift mutation in FaMYB10 is responsible for the natural formation of red and white-fleshed strawberry (Fragaria x ananassa Duch)

During natural evolution and artificial selection, the fruit color of many species has been repeatedly gained or lost and is generally associated with mutations in genes encoding R2R3-MYB transcription factors, especially MYB10. In this study, we show that a heterozygous frameshift mutation (FaMYB10^AG-insert/FaMYB10^wild ) is responsible for the loss of anthocyanins in the flesh of cultivated strawberry. Comparative transcriptomic and metabolomic analyses of red- and white-fleshed strawberry indicated that the low expression level of FaUFGT (flavonol-O-glucosyltransferases) was responsible for the loss of anthocyanins and accumulation of proanthocyanidin in the white-fleshed strawberry and was the crucial gene that encodes enzymes of the anthocyanin biosynthesis pathway. Accordingly, overexpression and silencing of FaUFGT altered anthocyanin content and changed the flesh color of strawberry fruits. Furthermore, whole-genome resequencing analyses identified an AG insertion in the FaMYB10 coding region (FaMYB10^AG-insert ) of white-fleshed strawberry. Y1H and EMSA assays showed that FaMYB10^wild was able to bind to the promoter of the FaUFGT gene, while the FaMYB10^AG-insert could not. The skin and flesh color were tightly linked to the number of fully functional FaMYB10 copies in the selfing progeny of white-fleshed strawberry. Our results suggested that heterozygous frameshift mutation of FaMYB10 resulted in the loss of the ability to activate the expression of the FaUFGT gene, was responsible for the natural formation of red and white-fleshed strawberry.

The upstream regulatory mechanism of BplMYB46 and the function of upstream regulatory factors that mediate resistance to stress in Betula platyphylla

Previously, we have shown that the transcription factor BplMYB46 in Betula platyphylla can enhance tolerance to salt and osmotic stress and promote secondary cell wall deposition, and we characterized its downstream regulatory mechanism. However, its upstream regulatory mechanism remains unclear. Here, the promoter activity and upstream regulatory factors of BplMYB46 were studied. Analyses of β-glucuronidase (GUS) staining and activity indicated that BplMYB46 promoter was specific temporal and spatial expression, and its expression can be induced by salt and osmotic stress. We identified three upstream regulatory factors of BplMYB46: BpDof1, BpWRKY3, and BpbZIP3. Yeast-one hybrid assays, GUS activity, chromatin immunoprecipitation, and quantitative real-time polymerase chain reaction revealed that BpDof1, BpWRKY3, and BpbZIP3 can directly regulate the expression of BplMYB46 by specifically binding to Dof, W-box, and ABRE elements in the BplMYB46 promoter, respectively. BpDof1, BpWRKY3, and BpbZIP3 were all localized to the nucleus, and their expressions can be induced by stress. Overexpression of BpDof1, BpWRKY3, and BpbZIP3 conferred the resistance of transgenic birch plants to salt and osmotic stress. Our findings provide new insights into the upstream regulatory mechanism of BplMYB46 and reveal new upstream regulatory genes that mediate resistance to adverse environments. The genes identified in our study provide novel targets for the breeding of forest tree species.

High-resolution genome-wide association study of a large Czech collection of sweet cherry (Prunus avium L.) on fruit maturity and quality traits

In sweet cherry (Prunus avium L.), quantitative trait loci have been identified for fruit maturity, colour, firmness, and size to develop markers for marker-assisted selection. However, resolution is usually too low in those analyses to directly target candidate genes, and some associations are missed. In contrast, genome-wide association studies are performed on broad collections of accessions, and assemblies of reference sequences from Tieton and Satonishiki cultivars enable identification of single nucleotide polymorphisms after whole-genome sequencing, providing high marker density. Two hundred and thirty-five sweet cherry accessions were sequenced and phenotyped for harvest time and fruit colour, firmness, and size. Genome-wide association studies were used to identify single nucleotide polymorphisms associated with each trait, which were verified in breeding material consisting of 64 additional accessions. A total of 1 767 106 single nucleotide polymorphisms were identified. At that density, significant single nucleotide polymorphisms could be linked to co-inherited haplotype blocks (median size ~10 kb). Thus, markers were tightly associated with respective phenotypes, and individual allelic combinations of particular single nucleotide polymorphisms provided links to distinct phenotypes. In addition, yellow-fruit accessions were sequenced, and a ~ 90-kb-deletion on chromosome 3 that included five MYB10 transcription factors was associated with the phenotype. Overall, the study confirmed numerous quantitative trait loci from bi-parental populations using high-diversity accession populations, identified novel associations, and genome-wide association studies reduced the size of trait-associated loci from megabases to kilobases and to a few candidate genes per locus. Thus, a framework is provided to develop molecular markers and evaluate and characterize genes underlying important agronomic traits.

Anthocyanin Biosynthesis Induced by MYB Transcription Factors in Plants

Anthocyanins act as polyphenolic pigment that is ubiquitously found in plants. Anthocyanins play a role not only in health-promoting as an antioxidant, but also in protection against all kinds of abiotic and biotic stresses. Most recent studies have found that MYB transcription factors (MYB TFs) could positively or negatively regulate anthocyanin biosynthesis. Understanding the roles of MYB TFs is essential in elucidating how MYB TFs regulate the accumulation of anthocyanin. In the review, we summarized the signaling pathways medicated by MYB TFs during anthocyanin biosynthesis including jasmonic acid (JA) signaling pathway, cytokinins (CKs) signaling pathway, temperature-induced, light signal, 26S proteasome pathway, NAC TFs, and bHLH TFs. Moreover, structural and regulator genes induced by MYB TFs, target genes bound and activated or suppressed by MYB TFs, and crosstalk between MYB TFs and other proteins, were found to be vitally important in the regulation of anthocyanin biosynthesis. In this study, we focus on the recent knowledge concerning the regulator signaling and mechanism of MYB TFs on anthocyanin biosynthesis, covering the signaling pathway, genes expression, and target genes and protein expression.

An LTR retrotransposon in the promoter of a PsMYB10.2 gene associated with the regulation of fruit flesh color in Japanese plum

Japanese plums exhibit wide diversity of fruit coloration. The red to black hues are caused by the accumulation of anthocyanins, while their absence results in yellow, orange or green fruits. In Prunus, MYB10 genes are determinants for anthocyanin accumulation. In peach, QTLs for red plant organ traits map in an LG3 region with three MYB10 copies (PpMYB10.1, PpMYB10.2 and PpMYB10.3). In Japanese plum the gene copy number in this region differs with respect to peach: there are at least three copies of PsMYB10.1, with the expression of one of them (PsMYB10.1a) correlating with fruit skin color. The objective of this study was to determine a possible role of LG3-PsMYB10 genes in the natural variability of the flesh color trait and to develop a molecular marker for marker-assisted selection (MAS). We explored the variability within the LG3-PsMYB10 region using long-range sequences obtained in previous studies through CRISPR-Cas9 enrichment sequencing. We found that the PsMYB10.2 gene was only expressed in red flesh fruits. Its role in promoting anthocyanin biosynthesis was validated by transient overexpression in Japanese plum fruits. The analysis of long-range sequences identified an LTR retrotransposon in the promoter of the expressed PsMYB10.2 gene that explained the trait in 93.1% of the 145 individuals analyzed. We hypothesize that the LTR retrotransposon may promote the PsMYB10.2 expression and activate the anthocyanin biosynthesis pathway. We propose for the first time the PsMYB10.2 gene as candidate for the flesh color natural variation in Japanese plum and provide a molecular marker for MAS.

Transcriptomic and Metabolomic Analysis of Quality Changes during Sweet Cherry Fruit Development and Mining of Related Genes

Sweet cherries are economically important fruit trees, and their quality changes during development need to be determined. The mechanism of fruit quality changes in sweet cherries were determined by analyzing sweet cherry fruits at 12 developmental stages. The results showed that the soluble sugar, anthocyanin content, and hormones of sweet cherries all changed drastically during the color transition. Therefore, the fruits at the beginning of color conversion, at the end of color conversion, and at the ripening state were selected for the comprehensive analysis of their metabolome and transcriptome. Different sugars, such as D-glucose, sucrose, and trehalose, were identified in the metabolome. Dihydroquercetin, delphinidin-3-glucoside, cyanidin-3-rutincoside, and other flavonoid species were also identified. D-glucose and cyanidin-3-rutinoside were among the most important components of sweet cherry soluble sugars and anthocyanins, respectively. The transcriptional analysis identified key structural genes and nine transcription factors involved in the ABA, sugar, organic acid, and anthocyanin synthesis pathways, with the following specific regulatory patterns. NAC71, WRKY57, and WRKY3 regulate fruit sugar accumulation mainly by acting on INV, SPS, and SUS. MYC2 is involved in the synthesis of anthocyanin precursors by activating PAL and C4H, whereas TCP7 mainly regulates CHI and F3H. WRKY3, NAC71, and WRKY57 have important positive regulatory significance on anthocyanin accumulation, mainly by activating the expression of DFR, ANS, and 3GT.

Bagging Strategy and Identification of Coloring Mode of ‘Xinqihong’ Pear

‘Xinqihong’ is a recently selected and well-colored red pear (Pyrus bretschneideri Rehd.) cultivar that is popular in the marketplace owing to the bright red color and high quality of the fruit. The red pigmentation is strongly associated with the light signal. However, its responses to bagging treatment and to light exposure after shading are unknown. In this study, the fruit were treated with three types of fruit bags. ’Xinqihong’ fruit colored rapidly in response to light stimulation. A white fruit bag was optimal for bagging of ‘Xinqihong’ fruit. To ensure satisfactory red pigmentation, the fruit required exposure to 30 days of light after bag removal. A transcriptome analysis was conducted to screen light-signal-related genes and identify their possible functions. PbCRY1 activated the promoter of PbHY5.2 and enhanced its expression. PbHY5.2 activated the promoter activity of PbUFGT and induced anthocyanin synthesis, and also showed self-activation characteristics. Both PbCRY2 and PbPHY1 induced anthocyanin accumulation. Thus, blue-light receptors played an important role in anthocyanin synthesis. This study provides a theoretical basis for the bagging cultivation of new varieties of ‘Xinqihong’, and lays a foundation for the study of the mechanisms of red pear fruit coloring in response to light signals.

Metabolome and Transcriptome Analyses of Anthocyanin Accumulation Mechanisms Reveal Metabolite Variations and Key Candidate Genes Involved in the Pigmentation of Prunus tomentosa Thunb. Cherry Fruit

Prunus tomentosa Thunb. has excellent nutritional, economic, and ornamental values with different fruit color. The red coloration of fruit is determined by anthocyanin pigmentation, which is an attractive trait for consumers. However, the mechanisms underlying fruit color formation in the P. tomentosa cherry are not well understood. In this research, the pigmentation patterns in red-color P. tomentosa (RP) fruit and white-color P. tomentosa (WP) were evaluated. Anthocyanin content in matured RP fruit was significantly abundant compared with WP fruit. Metabolomic profiling revealed that pelargonidin 3-O-glucoside, cyanidin 3-O-rutinoside, and pelargonidin 3-O-rutinoside were the predominant anthocyanin compounds in the RP fruit, while, WP fruit had less anthocyanin compositions and lower level. Then, integrative analyses of transcriptome and metabolome identified 285 significant differentially expressed genes (DEGs) closely related to anthocyanin differentially expressed metabolites (DEMs). Among them, nine genes were involved in anthocyanin biosynthesis, transport and degradation pathway, including four biosynthesis genes (PtPAL1, PtDFR, PtANS, and PtUFGT), two transport genes (PtGST11, PtABC10), and three degradation genes (PtPOD1, PtPOD16, PtPOD73). Transcriptome data and real-time PCR showed that the transcript levels of biosynthesis and transport genes were significantly higher in RP than in WP, especially PtANS, PtUFGT, and PtGST11, suggesting they may play key roles in red-colored fruit formation. Meanwhile, the degradation-related genes PtPOD1/16/73 took on exactly opposite trend, suggesting their potential effects on anthocyanin degradation. These results provide novel insights into color patterns formation mechanisms of cherries fruit, and the candidate key genes identified in anthocyanin biosynthesis, transport and degradation may provide a valuable resource for cherry breeding research in future.

Rosa1, a Transposable Element-Like Insertion, Produces Red Petal Coloration in Rose Through Altering RcMYB114 Transcription

Rose (Rosa sp.) flowers have a rich diversity of colors resulting from the differential accumulation of anthocyanins, flavonols, and carotenoids. However, the genetic and molecular determinants of the red-petal trait in roses remains poorly understood. Here we report that a transposable element-like insertion (Rosa1) into RcMYB114, a R2R3-MYB transcription factor's promoter region causes its transcription, resulting in red petals. In red-petal varieties, RcMYB114 is expressed specifically in flower organs, but is absent from non-red varieties. Sequencing, yeast two-hybrid, transient transformation, and promoter activity assays of RcMYB114 independently confirmed the role of Rosa1 in altering RcMYB114's transcription and downstream effects on flower color. Genetic and molecular evidence confirmed that the Rosa1 transposable element-like insertion, which is a previously unknown DNA transposable element, is different from those in other plants and is a reliable molecular marker to screen red-petal roses.

RNA-Seq Analysis Identifies Transcription Factors Involved in Anthocyanin Biosynthesis of 'Red Zaosu' Pear Peel and Functional Study of PpPIF8

Red-skinned pears are favored by people for their attractive appearance and abundance of anthocyanins. However, the molecular basis of anthocyanin biosynthesis in red pears remains elusive. Here, a comprehensive transcriptome analysis was conducted to explore the potential regulatory mechanism of anthocyanin biosynthesis in 'Red Zaosu' pear (Pyrus pyrifolia × Pyrus communis). Gene co-expression analysis and transcription factor mining identified 263 transcription factors, which accounted for 6.59% of the total number of transcription factors in the pear genome in two gene modules that are highly correlated with anthocyanin biosynthesis. Clustering, gene network modeling with STRING-DB, and local motif enrichment analysis (CentriMo) analysis suggested that PpPIF8 may play a role in anthocyanin biosynthesis. Furthermore, eight PIFs were identified in the pear genome, of which only PpPIF8 was rapidly induced by light. Functional studies showed that PpPIF8 localizes in the nucleus and is preferentially expressed in the tissue of higher levels of anthocyanin. The overexpression of PpPIF8 in pear peel and pear calli promotes anthocyanin biosynthesis and upregulates the expression of anthocyanin biosynthesis genes. Yeast-one hybrid and transgenic analyses indicated that PpPIF8 binds to the PpCHS promoter to induce PpCHS expression. The positive effect of PpPIF8 on anthocyanin biosynthesis is different from previously identified negative regulators of PyPIF5 and MdPIF7 in pear and apple. Taken together, our data not only provide a comprehensive view of transcription events during the coloration of pear peel, but also resolved the regulatory role of PpPIF8 in the anthocyanin biosynthesis pathway.

A Sweet Cherry Glutathione S-Transferase Gene, PavGST1, Plays a Central Role in Fruit Skin Coloration

Sweet cherry, an economically important horticultural crop, has strong antioxidant activity. The fruits contain compounds potentially beneficial to human health—particularly anthocyanins, which are synthesized in cytosol and predominantly accumulated in vacuoles. Although anthocyanin levels differ among dark-red, blush, and yellow sweet cherry cultivars, the regulatory mechanism of anthocyanin transport and accumulation is not well understood in this species. In this study, we identified 53 glutathione S-transferase genes (PavGSTs) from sweet cherry and found that PavGST1 expression was well correlated with anthocyanin accumulation in cultivars with different fruit skin colors. TRV-mediated virus-induced silencing of PavGST1 decreased anthocyanin accumulation in sweet cherry fruits and downregulated the expressions of anthocyanin biosynthetic and regulatory genes. In addition, transient overexpression of PavGST1 promoted anthocyanin accumulation. Furthermore, yeast one-hybrid and dual-luciferase assays revealed that PavMYB10.1 and PavMYB75 directly bind to different MYB binding sites of the PavGST1 promoter (MBS-1 and MBS-3) to activate PavGST1 transcription. According to our results, PavGST1 plays a central role in sweet cherry fruit anthocyanin accumulation. Our findings provide novel insights into the coordinative regulatory mechanisms of PavGST1 and PavMYBs in anthocyanin accumulation in sweet cherry.

Low temperature inhibits anthocyanin accumulation in strawberry fruit by activating FvMAPK3-induced phosphorylation of FvMYB10 and degradation of Chalcone Synthase 1

Low temperature causes poor coloration of strawberry (Fragaria sp.) fruits, thus greatly reducing their commercial value. Strawberry fruits accumulate anthocyanins during ripening, but how low temperature modulates anthocyanin accumulation in plants remains largely unknown. We identified MITOGEN-ACTIVATED PROTEIN KINASE3 (FvMAPK3) as an important negative regulator of anthocyanin accumulation that mediates the poor coloration of strawberry fruits in response to low temperature. FvMAPK3 activity was itself induced by low temperature, leading to the repression of anthocyanin accumulation via two mechanisms. Activated FvMAPK3 acted as the downstream target of MAPK KINASE4 (FvMKK4) and SUCROSE NONFERMENTING1-RELATED KINASE2.6 (FvSnRK2.6) to phosphorylate the transcription factor FvMYB10 and reduce its transcriptional activity. In parallel, FvMAPK3 phosphorylated CHALCONE SYNTHASE1 (FvCHS1) to enhance its proteasome-mediated degradation. These results not only provide an important reference to elucidate the molecular mechanisms underlying low-temperature-mediated repression of anthocyanin accumulation in plants, but also offer valuable candidate genes for generating strawberry varieties with high tolerance to low temperature and good fruit quality.

Automatic identification and annotation of MYB gene family members in plants

BACKGROUND

MYBs are among the largest transcription factor families in plants. Consequently, members of this family are involved in a plethora of processes including development and specialized metabolism. The MYB families of many plant species were investigated in the last two decades since the first investigation looked at Arabidopsis thaliana. This body of knowledge and characterized sequences provide the basis for the identification, classification, and functional annotation of candidate sequences in new genome and transcriptome assemblies.

RESULTS

A pipeline for the automatic identification and functional annotation of MYBs in a given sequence data set was implemented in Python. MYB candidates are identified, screened for the presence of a MYB domain and other motifs, and finally placed in a phylogenetic context with well characterized sequences. In addition to technical benchmarking based on existing annotation, the transcriptome assembly of Croton tiglium and the annotated genome sequence of Castanea crenata were screened for MYBs. Results of both analyses are presented in this study to illustrate the potential of this application. The analysis of one species takes only a few minutes depending on the number of predicted sequences and the size of the MYB gene family. This pipeline, the required bait sequences, and reference sequences for a classification are freely available on github: https://github.com/bpucker/MYB_annotator .

CONCLUSIONS

This automatic annotation of the MYB gene family in novel assemblies makes genome-wide investigations consistent and paves the way for comparative studies in the future. Candidate genes for in-depth analyses are presented based on their orthology to previously characterized sequences which allows the functional annotation of the newly identified MYBs with high confidence. The identification of orthologs can also be harnessed to detect duplication and deletion events.

ECAP is a key negative regulator mediating different pathways to modulate salt stress-induced anthocyanin biosynthesis in Arabidopsis

Anthocyanins are a subgroup of plant flavonoids with antioxidant activities and are often induced by various biotic and abiotic stresses in plants, probably to efficiently scavenge free radicals and reactive oxygen species. However, the regulatory mechanisms of salt stress-induced anthocyanin biosynthesis remain unclear. Using molecular and genetic techniques we demonstrated key roles of ECAP in differential salt-responsive anthocyanin biosynthesis pathways in Arabidopsis thaliana. ECAP, JAZ6/8 and TPR2 are known to form a transcriptional repressor complex, and negatively regulate jasmonate (JA)-responsive anthocyanin accumulation. In this study, we demonstrated that under moderate salt stress, the accumulation of anthocyanins is partially dependent on JA signaling, which degrades JAZ proteins but not ECAP. More interestingly, we found that high salinity rather than moderate salinity induces the degradation of ECAP through the 26S proteasome pathway, and this process is independent of JA signaling. Further analysis revealed that ECAP interacts with MYB75 (a transcription factor activating anthocyanin biosynthetic genes) and represses its transcriptional activity in the absence of high salinity. Our results indicated that plants adopt different strategies for fine-tuning anthocyanin accumulation under different levels of salt stress, and further elucidated the complex regulation of anthocyanin biosynthesis during plant development and responses to environmental stresses.

Comprehensive Transcriptome–Metabolome Analysis and Evaluation of the Dark_Pur Gene from Brassica juncea That Controls the Differential Regulation of Anthocyanins in Brassica rapa

Chinese cabbage (Brassica rapa) is a major vegetable crop in China. The accumulation of anthocyanins improves the quality and flavor of Brassica crops and is beneficial for human health. There has been great research interest in breeding purple Chinese cabbage, for which it is necessary to study the key genes and mechanisms of anthocyanin accumulation. Through distant hybridization between purple mustard (Brassica. juncea) and green Chinese cabbage (B. rapa), purple Chinese cabbage plants were obtained. Furthermore, the Dark_Pur gene was cloned in the purple Chinese cabbage plants, which came from purple mustard and may be responsible for the purple phenotype in purple Chinese cabbage plants. Through particle bombardment of isolated microspores from Chinese cabbage to transform the Dark_Pur gene, the transformed purple Chinese cabbage plant was obtained, thus verifying the function of the Dark_Pur gene. To further study the Dark_Pur gene regulatory mechanism of anthocyanin accumulation in Chinese cabbage, the purple/green Chinese cabbage lines and purple/green mustard lines were subjected to transcriptome–metabolome analysis. Three stages (cotyledon, seedling, and large-leaf stages) of the purple/green Chinese cabbage lines and purple/green mustard lines were selected for analysis. The results indicated that the expression level of the transcription factor genes BraA09g028560.3C, BraA03g019460.3C, and BraA07g035710.3C may be induced by the Dark_Pur gene and they play an important role in purple Chinese cabbage, and BjuB010898 and BjuO006089 may be responsible for anthocyanin accumulation in mustard. Studying the structural genes of the purple Chinese cabbage showed that PAL, C4H, 4CL, CHS, CHI, F3H, F3'H, FLS, DFR, ANS, and UGT were up-regulated in three growth periods. There were 22 and 10 differentially expressed metabolites (DEMs) in seedling and large-leaf stages between purple/green Chinese cabbage, respectively, and 12 and 14 differentially expressed metabolites (DEMs) in seedling and large-leaf stages between purple/green mustard, respectively, which may indicate that the Dark_Pur gene from purple mustard greatly regulates anthocyanin accumulation in purple Chinese cabbage. This study provides a foundation for further elucidating anthocyanin regulation.