Retrotransposon promoter of Ruby1 controls both light- and cold-induced accumulation of anthocyanins in blood orange

Influence of Preharvest sorbitol and calcium-sorbitol applications on the ripening process and anthocyanin biosynthesis in blood Orange (Citrus sinensis cv. Sanguinelli)

Blood oranges are valued for their color and nutritional properties, thriving in Mediterranean climates where temperature variations enhance anthocyanin (ACN) synthesis. Climate change threatens this process. This study evaluated six foliar applications of sorbitol (2 %, 5 %) and sorbitol-Ca (2 % + 0.7 %) from early fruit development to harvest. All treatments enhanced peel and pulp redness, particularly sorbitol-Ca, as confirmed by lower hue angle and higher color index. Treated fruits had higher total soluble solids (TSS), with 11.07 % in 2 % sorbitol-treated fruits versus 9.63 % in controls. Sorbitol-Ca reduced respiration rates (15.63 vs. 21.57 mg CO₂ kg-1 h-1) and increased firmness (9.72 vs. 8.89 Nmm-1). Phenolic content, antioxidant activity, and bound calcium levels improved fruit quality. ACN content increased over 20 % and 40 % in sorbitol- and sorbitol-Ca-treated fruits, mainly due to Cyanidin derivatives. Sorbitol-based treatments offer a strategy to enhance blood orange resilience to climate change, improving functional and commercial value.

Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome

Transposon is the main component of the eukaryotic genome, and more and more plant genome data show that transposons are diverse in regulating genome structure, variation, function and evolution, with different transposition mechanisms in the genome. Hybridization and polyploidy play an important role in promoting plant speciation and evolution, and recent studies have shown that polyploidy is usually accompanied by the expansion of transposons, which affect the genome size and structure of polyploid plants. Transposons can insert into genes and intergenic regions, resulting in great differences in the overall genome structure of closely related plant species, and it can also capture gene segments in the genome to increase the copy number of genes. In addition, transposons influence the epigenetic modification state of the genome and regulate the expression of the gene, while plant phenotype, biological and abiotic stress response are also regulated by transposons. Overall, transposons play an important role in the plant genome, especially polyploid plant genome, adaptation and evolution.

Unravelling the gene regulatory network linking red leaf and red flesh traits in teinturier grape

Despite the extensive research conducted on grape anthocyanins, previous studies have predominantly focused on grape skin colour changes, with limited research on flesh colour and leaf colour. In this study, we utilised the superior line 'Zhongshan 151' strain (red flesh and red leaves) as a target and identified that the primary driving force for the transition of leaf colour from green to red was the accumulation of anthocyanins. The study identified a candidate gene, VvMYBA6, and determined that the encoded protein is located in the nucleus and possesses transcriptional activation activity. Subsequent experiments revealed that VvMYBA6 significantly promoted anthocyanin accumulation in tobacco through its overexpression. Further mechanistic investigations elucidated the interaction of VvMYBA6 with the VvMYC1 protein, which activates the expression of VvUFGT, thereby promoting anthocyanin accumulation. Furthermore, an interaction between VvMYBA1 and VvMYC1 was identified in leaves, which is consistent with the mechanism of flesh colour regulation in red-fleshed grapes and affects anthocyanin accumulation by regulating the expression of VvUFGT. The interaction between VvMYBA1 and VvMYBA6 was further verified by yeast two-hybrid (Y2H) and pull-down experiments. This finding indicates that the interaction between VvMYBA6, VvMYBA1 and VvMYC1 plays a pivotal role in the regulation of anthocyanin synthesis, which may significantly impact the development of fruit colour in teinturier grapes.

Orchestrating anthocyanin biosynthesis in fruit of fruit trees: Transcriptional, post-transcriptional, and post-translational regulation

Coloration is an important appearance quality that contributes to product value. Anthocyanins, a type of flavonoid, not only impart rich plants color, but also contribute to human health because of their antioxidant properties, such as preventing cardiovascular disease and reducing obesity. This benefit mainly stems from various fruits. Accordingly, based on the consumption demand of beauty and nutrition, the creation of fruit tree products rich in anthocyanin is becoming an important breeding goal. The synthesis of anthocyanin has been investigated in various fruits, which is modulated by a variety of endogenous and exogenous factors, including transcription factors (TFs), plant hormones, and environmental factors (such as light, low temperature, drought). However, the detailed mechanisms in fruits of fruit trees have not been thoroughly elucidated. This review comprehensively examines the regulation of anthocyanin biosynthesis at the transcriptional, post-transcriptional, and post-translational levels, which is important for the application of molecular design strategies to cultivate high-quality fruits. At the transcriptional level, TFs were summarized to directly regulate anthocyanin biosynthesis genes, target non-anthocyanin biosynthesis pathway genes, interact with other proteins to mediate anthocyanin synthesis, and regulate anthocyanin synthesis by environmental factors and plant hormones. At the post-transcriptional level, non-coding RNAs (ncRNAs) were elucidated to mediate anthocyanin synthesis. At the post-translational level, a variety of post-translational modifications, including phosphorylation, ubiquitination, sumoylation, and persulfidation, have been elucidated to exhibit crucial functions in anthocyanin biosynthesis.

TmCOP1-TmHY5 module-mediated blue light signal promotes chicoric acid biosynthesis in Taraxacum mongolicum

Chicoric acid, a phenolic compound derived from plants, exhibits a range of pharmacological activities. Light significantly influences the chicoric acid biosynthesis in Taraxacum mongolicum; however, the transcriptional regulatory network governing this process remains unclear. A combined analysis of the metabolome and transcriptome revealed that blue light markedly enhances chicoric acid accumulation compared to red light. The blue light-sensitive transcription factor ELONGATED HYPOCOTYL5 (HY5) is closely associated with multiple core proteins, transcription factors and chicoric acid synthase genes involved in light signalling. Both in vivo and in vitro experiments demonstrated that TmHY5 directly regulates several chicoric acid biosynthetic genes, including TmPAL3, Tm4CL1 and TmHQT2. Additionally, TmHY5 promotes the accumulation of luteolin and anthocyanins by increasing the expression of TmCHS2 and TmANS2. The E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) forms a protein complex with TmHY5, significantly inhibiting chicoric acid biosynthesis. Blue light inhibits TmCOP1-TmHY5 complex protein formation while enhancing the expression levels of TmCOP1 through TmHY5. Furthermore, TmHY5 elevates the expression levels of TmbZIP1, which indirectly activates Tm4CL1 expression. In vivo, TmCOP1 directly inhibits the expression of the TmHY5-Tm4CL1 complex. Therefore, we speculate that TmCOP1-TmHY5-mediated blue light signalling effectively activates chicoric acid biosynthesis, providing a foundation for the application of blue light supplementation technology in industrial production.

New insights into the transcription factor regulatory networks driving peel coloration under hormone induction analyzed by transcriptomics and metabolomics in tangor 'Murcot'

Introduction

Fruit color is a crucial quality factor strongly influencing consumer preference for citrus. The coloration of citrus fruit is primarily determined by carotenoids, which produce a range of hues. Gibberellic acid (GA) and ethylene are critical in fruit coloration during the ripening process. Nevertheless, the underlying mechanisms remain poorly understood.

Methods

The present study utilized transcriptomic and metabolomic analyses to investigate the molecular regulatory mechanisms affecting peel pigment metabolism in tangors (Citrus reticulata Blanco×Citrus sinensis L. Osbeck) following GA and ethephon (ETH) treatments.

Results and discussion

Collectively, our findings indicated that GA inhibits chlorophyll degradation and the accumulation of numerous carotenoids, including five violaxanthin esters (violaxanthin palmitate, violaxanthin myristate-caprate, violaxanthin myristate-laurate, violaxanthin dilaurate, violaxanthin myristate) and two β-cryptoxanthin derivatives (β-cryptoxanthin laurate, β-cryptoxanthin myristate), while ETH promotes these processes. Furthermore, GA inhibited the downregulation of lutein, the predominant carotenoid in immature fruits. Notably, integrated transcriptomic and metabolomic analyses identified 33 transcription factors associated with pigment metabolism. Of these, two novel transcription factors, the ethylene-responsive transcription factor ABR1 and the HD-Zip transcription factor ATHB7, were uncovered through both transcriptomic analysis and weighted gene co-expression network analysis. These two transcription factors positively regulated the colouration process, as validated by transient overexpression assays in tobacco. Taken together, our findings elucidated the global carotenoid changes and transcriptional alterations in regulating citrus peel color under hormone induction, with significant implications for improving citrus production.

Comparative Transcriptomic Analyses of Anthocyanin Biosynthesis Genes in Eggplant Under Low Temperature and Weak Light

Low temperature, weak light, and the combination of low temperature and weak light can have an impact on the growth, development, and quality of eggplants. The color of the eggplant peel is affected by the anthocyanin content. To better understand the influence of low temperature, weak light, and the combination of low temperature and weak light on the regulation of anthocyanins in the eggplant peel, four treatments were carried out on the eggplants, respectively: low temperature (18/13 °C, 250 μmol/(m2·s)), weak light intensity (WL, 25/20 °C, 120 μmol/(m2·s)), low temperature combined with weak light intensity (LW, 18/13 °C, 120 μmol/(m2·s)), and the control (CK, 25/20 °C, 250 μmol/(m2·s)). The effects of low temperature and weak light on the anthocyanin content in various parts of the eggplant were analyzed, and transcriptome analysis was performed on the eggplant peel under the treatments of low temperature, weak light, and the combination of low temperature and weak light using RNA sequencing. The anthocyanin content in eggplants increased under low temperature and the combination of low temperature and weak light treatments, while it decreased under weak light. KEGG analysis showed that three pathways, namely phenylpropanoid biosynthesis, flavonoid biosynthesis, and anthocyanin biosynthesis, were involved in the anthocyanin biosynthesis of eggplants. Pearson correlation coefficients indicated that the anthocyanin content in the eggplant peel under low temperature and the combination of low-temperature and weak-light treatments was significantly correlated with SmPAL, Sm4CL, SmCYP73A100, SmCHS, SmCHI, F3H, DFR, ANS, and 3GT, and also significantly correlated with MYB, bHLH, and AP2/ERF. Under low-temperature and the combination of low-temperature and weak-light stress, the anthocyanin content increased due to the significant down-regulation of 3GT.

The inhibition effect of high temperature stress on potato tuber skin coloring mainly occurred in the belowground part of the plant

High temperature stress leads to a dramatic reduction of both the anthocyanin concentration and the appearance quality of colored potatoes. However, it remains uncertain if the high temperature impacts potato tuber skin coloring through only the aerial or belowground parts of the plant, or through their interaction; and it's underlying reason is still unclear. In this study, the red-skin cultivar Qingshu9 (Qs9) was exposed to the high-temperature (30 °C) treatment on the belowground part alone (BH), aerial part alone (AH) and entire plant (EH), and the normal-temperature treatment on entire plant (EN) as control. The results indicated that the total anthocyanin content in tuber skin of the BH treatment was significantly lower than the EN and AH treatment, and there was no accumulation of cyanidin and pelargonidin in BH treatment, only peonidin. Compared with the EN treatment, the decrease rate of total anthocyanin content of the AH treatment was much smaller than the BH treatment, and the composition of anthocyanin did not change. Transcriptome analysis showed the downregulated DEGs of BH vs EN, BH vs AH and AH vs EN were significantly associated with the anthocyanin synthesis and metabolism pathway. High temperature inhibited anthocyanin synthesis by reducing the expression of key genes (StPAL, StF3H, StF3'H, StF3'5'H, StDFR and StANS) in the anthocyanin synthesis pathway. In summary, high temperature inhibits anthocyanin synthesis in tuber skin by downregulating key genes, and this inhibitory effect mainly occurs through the belowground part of the plant.

Genomic analysis provides insights into the origin and divergence of fruit flavor and flesh color of pummelo

Pummelo (Citrus maxima) is one of the most important citrus crops and have genetically contributed sweet orange, lemon and most citrus cultivars. It has been cultivated for c. 4000 years in China and is also distributed in many Southeast Asian countries. Nevertheless, the origin and dispersal of pummelo remain elusive. We conducted whole-genome sequencing for 290 pummelo accessions from China and Southeast Asia (SEA). Our findings indicated that pummelo was originated in Yunnan province. The divergence of the China-SEA accessions occurred c. 2000 years ago and the divergence was likely facilitated through the Maritime Silk Road. We detected the divergence of genomic regions associated with fruit flavor and color, indicating different selection by human activities in different regions. A gene encoding lycopene cyclase 2 (LCYB2) exhibited a high degree of divergence in expression and sequence between red-flesh and white-flesh pummelos. A SNP in the coding region of LCYB2 resulted in a reduction in lycopene β-cyclizing enzyme activity, leading to the accumulation of lycopene and the development of the red-flesh trait. This study reveals the origin and evolutionary history of pummelo and provides insights into the genomic basis for the divergence of fruit flavor and color.

Targeted regulation of 5-aminolevulinic acid enhances flavonoids, anthocyanins and proanthocyanidins accumulation in Vitis davidii callus

BACKGROUND

Spine grape (Vitis davidii) is a promising source of high-quality anthocyanins, with vast potential for application in food, pharmaceutical, and cosmetic industries. However, their availability is limited by resource constraints. Plant cell culture has emerged as a valuable approach for anthocyanin production and serves as an ideal model to investigate the regulation of anthocyanin biosynthesis. Elicitors are employed to achieve targeted enhancement of anthocyanin biosynthesis. The present study investigated the impact of 5-aminolevulinic acid (ALA) as an elicitor on the accumulation of anthocyanins and flavonoids during spine grape callus growth. Specifically, we examined the effects of ALA on anthocyanin and its component accumulation in callus, and biosynthetic anthocyanin gene expression.

RESULTS

ALA at 25 µg/L increased the biomass of spine grape callus. ALA induction enhanced the levels of flavonoids, anthocyanins and proanthocyanidins in callus, with maximum values reaching 911.11 mg/100 g DW, 604.60 mg/100 g DW, and 5357.00 mg/100 g DW, respectively, after callus culture for 45 days. Notably, those levels were 1.47-, 1.93- and 1.83-fold higher than controls. ALA induction modulated the flavonoid profile, and among 97 differential flavonoid metabolites differing from controls, 77 were upregulated and 20 were downregulated. Six kinds of anthocyanins, namely cyanidin (8), delphinidin (6), peonidin (5), malvidin (4), petunidin (3) and pelargonidin (3), were detected in callus, with peonidin most abundant. Compared with controls, anthocyanin components were increased in ALA-treated callus. The key genes PAL1, PAL2, PAL4, CHI, CHS3, F3'H, F3H, FLS, DFR, UFGT, MYBA1, LDOX, OMT3, GT1 and ACT involved in anthocyanin biosynthesis were upregulated following ALA treatment, resulting in anthocyanin accumulation.

CONCLUSION

This study revealed a novel mode of ALA-mediated promotion of plant anthocyanin biosynthesis and accumulation at the cellular level, and a strategy for enhancing anthocyanin content in spine grape callus. The findings advance commercial-scale production of anthocyanins via spine grape callus culture. we also explored the accumulation patterns of flavonoids and anthocyanins under ALA treatment. Augmentation of anthocyanins coincided with elevated expression levels of most genes involved in anthocyanin biosynthesis within spine grape callus following ALA treatment.

A structural variation in the promoter of the leucoanthocyanidin reductase gene AaLAR1 enhances freezing tolerance by modulating proanthocyanidin accumulation in kiwifruit (Actinidia arguta)

Proanthocyanidins (PAs) are important metabolites that enhance freezing tolerance of plants. Actinidia arguta, especially freezing-tolerant germplasms, accumulate abundant PAs in dormant shoots and thereby enhance freezing tolerance, but the underlying mechanism is unknown. In this study, we used two A. arguta with contrasting cold-resistant phenotypes, KL and RB, to explore the mechanisms in response to cold tolerance. We determined that a leucoanthocyanidin reductase gene (AaLAR1) was more highly expressed in freezing-tolerant KL than in freezing-sensitive RB. Moreover, overexpressing AaLAR1 in kiwifruit promoted PAs biosynthesis and enhanced cold tolerance. The AaLAR1 promoters of various A. arguta germplasms differ due to the presence of a 60-bp deletion in cold-tolerant genotypes that forms a functional binding site for MYC-type transcription factor. Yeast one-hybrid and two-hybrid, dual-luciferase reporter, bimolecular fluorescence complementation and coimmunoprecipitation assays indicated that the AaMYC2a binds to the MYC-core cis-element in the AaLAR1 promoter with the assistance of AaMYB5a, thereby promoting PAs accumulation in the shoots of cold-tolerant kiwifruit. We conclude that the variation in the AaLAR1 promoter and the AaMYC2a-AaMYB5a-AaLAR1 module shape freezing tolerance in A. arguta. The identification of a key structural variation in the AaLAR1 promoter offers a new target for resistance breeding of kiwifruit.

Quantitative RUBY reporter assay for gene regulation analysis

Various reporter genes have been developed to study gene expression pattern and gene regulation. The RUBY reporter gene was recently developed and widely used, because of its visible and noninvasive advantages. However, quantitative analysis of RUBY gene expression levels was lacking. In this study, we introduce a novel betalain quantification method in combination with the tobacco transient expression system. The betalain produced in tobacco leaves was extracted and purified, and its concentration was quantitatively measured. We successfully applied this approach in studying the transcriptional regulation of ARC5 gene by transcription factors CPD25 and CPD45. Furthermore, with this method, we showed that the gene expression of RCA and Rbcs1A gene were regulated by light, transcription factors HY5 and PIFs through G-box and I-box elements. The development of this betalain quantification approach with the tobacco transient expression system offers a cost-effective and intuitive strategy for studying the regulatory mechanism of gene expression.

WRKY75 regulates anthocyanin accumulation in juvenile citrus tissues

The anthocyanin accumulation in juvenile tissues can enhance the ornamental value, attract pollinators, and help improve abiotic stress. Although transcriptional regulation studies of anthocyanin have been relatively extensive, there are few reports on the mechanism of anthocyanin accumulation in young tissues. This study reveals that many juvenile citrus tissues (flowers, leaves, and pericarp) undergo transient accumulation of anthocyanins, exhibiting a red coloration. Using weighted gene co-expression network analysis (WGCNA) identified CitWRKY75 as a candidate gene. After detecting the expression levels of CitWRKY75 in various citrus juvenile tissues, the expression trend of CitWRKY75 was highly consistent with the red exhibiting and fading. Overexpression of CitWRKY75 in tobacco significantly increased the anthocyanin content. LUC and yeast one-hybrid assay demonstrated that CitWRKY75 could bind to the promoter of CitRuby1(encoding the key transcription factor promoting anthocyanin accumulation) and promote its expression. Finally, comparing the expression levels of CitWRKY75 and CitRuby1 in the late development stage of blood orange found that CitWRKY75 was not the main regulatory factor for anthocyanin accumulation in the later stage. This study used reverse genetics to identify a transcription factor, CitWRKY75, upstream of CitRuby1, which promotes anthocyanin accumulation in citrus juvenile tissues.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01490-9.

A transcriptional cascade involving BBX22 and HY5 finely regulates both plant height and fruit pigmentation in citrus

Dwarfing is a pivotal agronomic trait affecting both yield and quality. Citrus species exhibit substantial variation in plant height, among which internode length is a core element. However, the molecular mechanism governing internode elongation remains unclear. Here, we unveiled that the transcriptional cascade consisting of B-BOX DOMAIN PROTEIN 22 (BBX22) and ELONGATED HYPOCOTYL 5 (HY5) finely tunes plant height and internode elongation in citrus. Loss-of-function mutations of BBX22 in an early-flowering citrus (Citrus hindsii "SJG") promoted internode elongation and reduced pigment accumulation, whereas ectopic expression of BBX22 in SJG, sweet orange (C. sinensis), pomelo (C. maxima) or heterologous expression of BBX22 in tomato (Solanum lycopersicum) significantly decreased internode length. Furthermore, exogenous application of gibberellin A3 (GA3) rescued the shortened internode and dwarf phenotype caused by BBX22 overexpression. Additional experiments revealed that BBX22 played a dual role in regulation internode elongation and pigmentation in citrus. On the one hand, it directly bound to and activated the expression of HY5, GA metabolism gene (GA2 OXIDASE 8, GA2ox8), carotenoid biosynthesis gene (PHYTOENE SYNTHASE 1, PSY1) and anthocyanin regulatory gene (Ruby1, a MYB DOMAIN PROTEIN). On the other hand, it acted as a cofactor of HY5, enhancing the ability of HY5 to regulate target genes expression. Together, our results reveal the critical role of the transcriptional cascade consisting of BBX22 and HY5 in controlling internode elongation and pigment accumulation in citrus. Unraveling the crosstalk regulatory mechanism between internode elongation and fruit pigmentation provides key genes for breeding of novel types with both dwarf and health-beneficial fortification in citrus.

The R2R3 MYB Ruby1 is activated by two cold responsive ethylene response factors, via the retrotransposon in its promoter, to positively regulate anthocyanin biosynthesis in citrus

Anthocyanins are natural pigments and dietary antioxidants that play multiple biological roles in plants and are important in animal and human nutrition. Low temperature (LT) promotes anthocyanin biosynthesis in many species including blood orange. A retrotransposon in the promoter of Ruby1, which encodes an R2R3 MYB transcription factor, controls cold-induced anthocyanin accumulation in blood orange flesh. However, the specific mechanism remains unclear. In this study, we characterized two LT-induced ETHYLENE RESPONSE FACTORS (CsERF054 and CsERF061). Both CsERF054 and CsERF061 can activate the expression of CsRuby1 by directly binding to a DRE/CRT cis-element within the retrotransposon in the promoter of CsRuby1, thereby positively regulating anthocyanin biosynthesis. Further investigation indicated that CsERF061 also forms a protein complex with CsRuby1 to co-activate the expression of anthocyanin biosynthetic genes, providing a dual mechanism for the upregulation of the anthocyanin pathway. These results provide insights into how LT mediates anthocyanin biosynthesis and increase the understanding of the regulatory network of anthocyanin biosynthesis in blood orange.

For a Colorful Life: Recent Advances in Anthocyanin Biosynthesis during Leaf Senescence

Leaf senescence is the last stage of leaf development, and it is accompanied by a leaf color change. In some species, anthocyanins are accumulated during leaf senescence, which are vital indicators for both ornamental and commercial value. Therefore, it is essential to understand the molecular mechanism of anthocyanin accumulation during leaf senescence, which would provide new insight into autumn coloration and molecular breeding for more colorful plants. Anthocyanin accumulation is a surprisingly complex process, and significant advances have been made in the past decades. In this review, we focused on leaf coloration during senescence. We emphatically discussed several networks linked to genetic, hormonal, environmental, and nutritional factors in regulating anthocyanin accumulation during leaf senescence. This paper aims to provide a regulatory model for leaf coloration and to put forward some prospects for future development.

Promoter replication of grape MYB transcription factor is associated with a new red flesh phenotype

KEY MESSAGE

In our study, we discovered a fragment duplication autoregulation mechanism in 'ZS-HY', which may be the reason for the phenotype of red foliage and red flesh in grapes. In grapes, MYBA1 and MYBA2 are the main genetic factors responsible for skin coloration which are located at the color loci on chromosome 2, but the exact genes responsible for color have not been identified in the flesh. We used a new teinturier grape germplasm 'ZhongShan-HongYu' (ZS-HY) which accumulate anthocyanin both in skin and flesh as experimental materials. All tissues of 'ZS-HY' contained cyanidin 3-O-(6″-p-coumaroyl glucoside), and pelargonidins were detected in skin, flesh, and tendril. Through gene expression analysis at different stage of flesh, significant differences in the expression levels of VvMYBA1 were found. Gene amplification analysis showed that the VvMYBA1 promoter is composed of two alleles, VvMYBA1a and 'VvMYBA1c-like'. An insertion of a 408 bp repetitive fragment was detected in the allele 'VvMYBA1c-like'. In this process, we found the 408 bp repetitive fragment was co-segregated with red flesh and foliage phenotype. Our results revealed that the 408 bp fragment replication insertion in promoter of 'VvMYBA1c-like' was the target of its protein, and the number of repeat fragments was related to the increase of trans-activation of VvMYBA1 protein. The activation of promoter by VvMYBA1 was enhanced by the addition of VvMYC1. In addition, VvMYBA1 interacted with VvMYC1 to promote the expression of VvGT1 and VvGST4 genes in 'ZS-HY'. The discovery of this mutation event provides new insights into the regulation of VvMYBA1 on anthocyanin accumulation in red-fleshed grape, which is of great significance for molecular breeding of red-fleshed table grapes.

Molecular mechanism of abscisic acid signaling response factor VcbZIP55 to promote anthocyanin biosynthesis in blueberry (Vaccinium corymbosum)

A high content of anthocyanin in blueberry (Vaccinium corymbosum) is an important indicator to evaluate fruit quality. Abscisic acid (ABA) can promote anthocyanin biosynthesis, but since the molecular mechanism is unclear, clarifying the mechanism will improve for blueberry breeding and cultivation regulation. VcbZIP55 regulating anthocyanin synthesis in blueberry were screened and mined using the published Isoform-sequencing, RNA-Seq and qRT-PCR at different fruit developmental stages. Blueberry genetic transformation and transgenic experiments confirmed that VcbZIP55 could promote anthocyanin biosynthesis in blueberry adventitious buds, tobacco leaves, blueberry leaves and blueberry fruit. VcbZIP55 responded to ABA signals and its expression was upregulated in blueberry fruit. In addition, using VcbZIP55 for Yeast one hybrid assay (Y1H) and transient expression in tobacco leaves demonstrated an interaction between VcbZIP55 and a G-Box motif on the VcMYB1 promoter to activate the expression of VcMYB1. This study will lay the theoretical foundation for the molecular mechanisms of phytohormone regulation responsible for anthocyanin synthesis and provide theoretical support for blueberry quality improvement.

Genome variation and LTR-RT analyses of an ancient peach landrace reveal mechanism of blood-flesh fruit color formation and fruit maturity date advancement

Peach (Prunus persica) landrace has typical regional characteristics, strong environmental adaptability, and contains many valuable genes that provide the foundation for breeding excellent varieties. Therefore, it is necessary to assemble the genomes of specific landraces to facilitate the localization and utilization of these genes. Here, we de novo assembled a high-quality genome from an ancient blood-fleshed Chinese landrace Tianjin ShuiMi (TJSM) that originated from the China North Plain. The assembled genome size was 243.5 Mb with a contig N50 of 23.7 Mb and a scaffold N50 of 28.6 Mb. Compared with the reported peach genomes, our assembled TJSM genome had the largest number of specific structural variants (SVs) and long terminal repeat-retrotransposons (LTR-RTs). Among the LTR-RTs with the potential to regulate their host genes, we identified a 6688 bp LTR-RT (named it blood TE) in the promoter of NAC transcription factor-encoding PpBL, a gene regulating peach blood-flesh formation. The blood TE was not only co-separated with the blood-flesh phenotype but also associated with fruit maturity date advancement and different intensities of blood-flesh color formation. Our findings provide new insights into the mechanism underlying the development of the blood-flesh color and determination of fruit maturity date and highlight the potential of the TJSM genome to mine more variations related to agronomic traits in peach fruit.

Light regulation of the biosynthesis of phenolics, terpenoids, and alkaloids in plants

Biosynthesis of specialized metabolites (SM), including phenolics, terpenoids, and alkaloids, is stimulated by many environmental factors including light. In recent years, significant progress has been made in understanding the regulatory mechanisms involved in light-stimulated SM biosynthesis at the transcriptional, posttranscriptional, and posttranslational levels of regulation. While several excellent recent reviews have primarily focused on the impacts of general environmental factors, including light, on biosynthesis of an individual class of SM, here we highlight the regulation of three major SM biosynthesis pathways by light-responsive gene expression, microRNA regulation, and posttranslational modification of regulatory proteins. In addition, we present our future perspectives on this topic.

Comprehensive metabolome and transcriptome analyses demonstrate divergent anthocyanin and carotenoid accumulation in fruits of wild and cultivated loquats

Eriobotrya is an evergreen fruit tree native to South-West China and adjacent countries. There are more than 26 loquat species known in this genus, while E. japonica is the only species yet domesticated to produce fresh fruits from late spring to early summer. Fruits of cultivated loquat are usually orange colored, in contrast to the red color of fruits of wild E. henryi (EH). However, the mechanisms of fruit pigment formation during loquat evolution are yet to be elucidated. To understand these, targeted carotenoid and anthocyanin metabolomics as well as transcriptomics analyses were carried out in this study. The results showed that β-carotene, violaxanthin palmitate and rubixanthin laurate, totally accounted for over 60% of the colored carotenoids, were the major carotenoids in peel of the orange colored 'Jiefangzhong' (JFZ) fruits. Total carotenoids content in JFZ is about 10 times to that of EH, and the expression levels of PSY, ZDS and ZEP in JFZ were 10.69 to 23.26 folds to that in EH at ripen stage. Cyanidin-3-O-galactoside and pelargonidin-3-O-galactoside were the predominant anthocyanins enriched in EH peel. On the contrary, both of them were almost undetectable in JFZ, and the transcript levels of F3H, F3'H, ANS, CHS and CHI in EH were 4.39 to 73.12 folds higher than that in JFZ during fruit pigmentation. In summary, abundant carotenoid deposition in JFZ peel is well correlated with the strong expression of PSY, ZDS and ZEP, while the accumulation of anthocyanin metabolites in EH peel is tightly associated with the notably upregulated expressions of F3H, F3'H, ANS, CHS and CHI. This study was the first to demonstrate the metabolic background of how fruit pigmentations evolved from wild to cultivated loquat species, and provided gene targets for further breeding of more colorful loquat fruits via manipulation of carotenoids and anthocyanin biosynthesis.

CsTT8 regulates anthocyanin accumulation in blood orange through alternative splicing transcription

A homologous gene of basic-helix-loop-helix AtTT8 in Arabidopsis thaliana was identified in juice sac cells of pulp tissues from blood orange (Citrus sinensis cv 'Tarocco'), which was designated as CsTT8 in this study. Additionally, the mRNA levels of TT8 with the full-length open reading frame were significantly higher in 'Tarocco' than in mutant fruit lacking pigment in pulp or peel tissues. However, an alternative splicing transcript, Δ15-TT8, with the fourth exon skipped, was also identified from transcripts different in length from that in 'Tarocco'. The mRNA levels of Δ15-TT8 were higher in mutant fruit lacking pigment in pulp or peel tissues than in the wild type. Therefore, the TT8/Δ15-TT8 mRNA level ratio was found to be crucial for sufficient pigment in either pulp or peel tissues. TT8 from blood orange fruit demonstrated the capacity for nucleus localization and binding to other proteins. In contrast, Δ15-TT8, lacking the fourth exon, lost its ability to interact with RUBY1 and to localize at the nucleus. Using a dual luciferase reporter assay and transient overexpression in tobacco, we proved that two regulatory complexes formed by a functional TT8 with different MYB(v-myb avian myeloblastosis viral oncogene homolog)-type partners significantly promoted expression of an anthocyanin biosynthetic gene and a proton pumping gene, leading to anthocyanin and citrate production. Our findings suggest that TT8, rather than dysfunctional Δ15-TT8, is possibly involved in modulating anthocyanin biosynthesis and its transport into vacuoles by proton gradients. However, increased mRNA levels of the dysfunctional alternative splicing transcript may act as a negative feedback to downregulate TT8 expression and limit anthocyanin accumulation in blood oranges.

Light-mediated anthocyanin biosynthesis in rose petals involves a balanced regulatory module comprising transcription factors RhHY5, RhMYB114a, and RhMYB3b

Roses are significant botanical species with both ornamental and economic value, displaying diverse floral traits, particularly an extensive array of petal colors. The red pigmentation of rose petals is predominantly attributed to anthocyanin accumulation. However, the underlying regulatory mechanism of anthocyanin biosynthesis in roses remains elusive. This study presents a novel light-responsive regulatory module governing anthocyanin biosynthesis in rose petals, which involves the transcription factors RhHY5, RhMYB114a, and RhMYB3b. Under light conditions (1000-1500 μmol m-2 s-1), RhHY5 represses RhMYB3b expression and induces RhMYB114a expression, positively regulating anthocyanin biosynthesis in rose petals. Notably, activation of anthocyanin structural genes probably involves an interaction and synergy between RhHY5 and the MYB114a-bHLH3-WD40 complex. Additionally, RhMYB3b is activated by RhMYB114a to prevent excessive accumulation of anthocyanin. Conversely, under low light conditions (<10 μmol m-2 s-1), the degradation of RhHY5 leads to down-regulation of RhMYB114a and up-regulation of RhMYB3b, which in turn inhibits the expression of both RhMYB114a and anthocyanin structural genes. Additionally, RhMYB3b competes with RhMYB114a for binding to RhbHLH3 and the promoters of anthocyanin-related structural genes. Overall, our study uncovers a complex light-mediated regulatory network that governs anthocyanin biosynthesis in rose petals, providing new insights into the molecular mechanisms underlying petal color formation in rose.

Anthocyanins distribution, transcriptional regulation, epigenetic and post-translational modification in fruits

Anthocyanins have indispensable functions in plant resistance, human health, and fruit coloring, which arouse people's favorite. It has been reported that anthocyanins are widely found in fruits, and can be affected by numerous factors. In this review, we systematically summarize anthocyanin functions, classifications, distributions, biosynthesis, decoration, transportation, transcriptional regulation, DNA methylation, and post-translational regulation in fruits.

Postharvest light-induced flavonoids accumulation in mango (Mangifera indica L.) peel is associated with the up-regulation of flavonoids-related and light signal pathway genes

INTRODUCTION

Flavonoids are important secondary metabolites in plants and light is a crucial environmental factor regulating flavonoids biosynthesis. However, effect of light on the different flavonoids compositions accumulation in mango and the relevant molecular mechanism still need to be clarified.

METHODS

In this study, green-mature fruits of red mango cultivar 'Zill' were subjected to postharvest light treatment, and fruit peel color, total soluble solids content, total organic acid, and firmness of flesh were measured. The flavonoids metabolites profile, and the expression of flavonoids-related genes and light signal pathway genes were also analyzed.

RESULTS

Results showed that light treatment promoted the red coloration of fruit peel and increased the total soluble solids content and firmness of flesh. The concentration of flavonols, proanthocyanidins and anthocyanins, and expression of key flavonoids biosynthetic genes including MiF3H, MiFLS, MiLAR, MiANS, MiUFGT1, and MiUFGT3 were significantly induced by light. The MYBs regulating flavonols and proanthocyanidins, i.e. MiMYB22 and MiMYB12, as well as the key light signal pathway transcription factors (TFs) MiHY5 and MiHYH, were identified in mango. The transcription of MiMYB1, MiMYB12, MiMYB22, MiHY5 and MiHYH was up-regulated by light.

DISCUSSION

Our results provide a postharvest technology to improve mango fruit appearance quality, and are helpful to reveal the molecular mechanism of light-induced flavonoids biosynthesis in mango.

Targeting ripening regulators to develop fruit with high quality and extended shelf life

Fruit quality directly impacts fruit marketability and consumer acceptance. Breeders have focused on fruit quality traits to extend shelf life, primarily through fruit texture, but, in some cases, have neglected other qualities such as flavor and nutrition. In recent years, integrative biotechnology and consumer-minded approaches have surfaced, aiding in the development of flavorful, long-lasting fruit. Here, we discussed how specific transcription factors and hormones involved in fruit ripening can be targeted to generate high-quality fruit through traditional breeding and bioengineering. We highlight regulators that can be used to generate novel-colored fruit or biofortify fresh produce with health-promoting nutrients, such as vitamin C. Overall, we argue that addressing grower and industry needs must be balanced with consumer-based traits.

A dual sgRNA-directed CRISPR/Cas9 construct for editing the fruit-specific β-cyclase 2 gene in pigmented citrus fruits

CRISPR/Cas9 genome editing is a modern biotechnological approach used to improve plant varieties, modifying only one or a few traits of a specific variety. However, this technology cannot be easily used to improve fruit quality traits in citrus, due to the lack of knowledge of key genes, long juvenile stage, and the difficulty regenerating whole plants of specific varieties. Here, we introduce a genome editing approach with the aim of producing citrus plantlets whose fruits contain both lycopene and anthocyanins. Our method employs a dual single guide RNA (sgRNA)-directed genome editing approach to knockout the fruit-specific β-cyclase 2 gene, responsible for the conversion of lycopene to beta-carotene. The gene is targeted by two sgRNAs simultaneously to create a large deletion, as well as to induce point mutations in both sgRNA targets. The EHA105 strain of Agrobacterium tumefaciens was used to transform five different anthocyanin-pigmented sweet oranges, belonging to the Tarocco and Sanguigno varietal groups, and 'Carrizo' citrange, a citrus rootstock as a model for citrus transformation. Among 58 plantlets sequenced in the target region, 86% of them were successfully edited. The most frequent mutations were deletions (from -1 to -74 nucleotides) and insertions (+1 nucleotide). Moreover, a novel event was identified in six plantlets, consisting of the inversion of the region between the two sgRNAs. For 20 plantlets in which a single mutation occurred, we excluded chimeric events. Plantlets did not show an altered phenotype in vegetative tissues. To the best of our knowledge, this work represents the first example of the use of a genome editing approach to potentially improve qualitative traits of citrus fruit.

An up-to-date review: differential biosynthesis mechanisms and enrichment methods for health-promoting anthocyanins of citrus fruits during processing and storage

Anthocyanins, naturally found in citrus, play key roles in improving the qualities of citrus fruits and products. Dietary consumption of fruit-derived anthocyanins is concerned increasingly owing to health-promoting properties. However, anthocyanins are vulnerable to many physical and chemical factors during processing and storage, affecting fruit qualities and consumer acceptance. Thus, the aim of this review is to focus on main advances in chemical structures, differential biosynthesis mechanisms, enrichment methods, and bioactivities of anthocyanins in pigmented and unpigmented citrus fruits. In this review, anthocyanin species and concentrations display tissue specificity in citrus, and the chemical structures and contents of main anthocyanins are summarized. For differential biosynthesis mechanisms, the reasons why most citrus fruits lose the ability of anthocyanin biosynthesis compared with pigmented fruits, and the molecular differences of biosynthesis mechanisms in pigmented citrus fruits are both discussed in detail. Furthermore, anthocyanins' enrichment methods (low-temperature stimulus, light irradiation, xenobiotics inductions, and ripeness influence) during processing and storage have been summarized, which achieve quality improvement by promoting structural gene expression, reducing anthocyanin-degrading enzyme activities, or altering DNA methylation status. Meantime, the health benefits of extract from pigmented citrus and their waste are mentioned, which provides a new approach for citrus waste recycling. HIGHLIGHTSChemical structures of individual anthocyanins in citrus are reviewed.Differential anthocyanin biosynthesis in citrus depends on mutations of Ruby genes.Anthocyanins are enriched in response to exogenous stimulus during storage.Health benefits of extract in blood oranges and their waste are summarized.

Comparative transcriptomic analysis identifies KcMYB1 as a R2R3-MYB anthocyanin activator in Kadsura coccinea

Fruit color, as an important appearance attribute, is crucial for attracting consumers. However, the underlying mechanism regulating mature fruit color formation in Kadsura coccinea remains unclear. Here, a comprehensive metabolomics and transcriptomics analysis was performed to investigate the molecular mechanisms of anthocyanin accumulation between two K. coccinea cultivars with different mature fruit colors-'Dahong No. 1' (red) and 'Jinhu' (yellow). Targeted metabolomic analysis revealed high anthocyanin levels, most of which were cyanidin and delphinidin derivatives, in 'Dahong No. 1' mature fruit peel. The SNP analysis indicated that the two different cultivars had similar genetic background. Moreover, comparative transcriptomic analysis demonstrated that differentially expressed genes (DEGs) were related to flavonoid biosynthesis and metabolic process in the two K. coccinea cultivars. Gene expression profiling data showed that the structural and regulatory genes associated with anthocyanin biosynthesis were significantly upregulated in 'Dahong No. 1' mature fruit peel, which was verified by quantitative real-time polymerase chain reaction (qRT-PCR). Notably, the key anthocyanin activator KcMYB1 was identified, which was significantly upregulated in 'Dahong No. 1' compared with 'Jinhu'. We further confirmed that KcMYB1 actively regulated the accumulation of anthocyanin by ectopic expression in vivo. Furthermore, allelic constitution of KcMYB1 in K. coccinea were investigated. The present study can provide insights for understanding the regulatory mechanisms of anthocyanin differential accumulation in the mature fruits of K. coccinea.

Integrated transcriptional and metabolomics signature pattern of pigmented wheat to insight the seed pigmentation and other associated features

Anthocyanin biosynthesis in plants is complex, especially in a polyploid monocot wheat plant. Using whole-genome sequencing, transcriptomics, and LC-MS/MS, we investigated anthocyanin pigmentation patterns in (black, blue, and purple) colored wheat seeds. According to differential gene expression profiling, 2AS-MYC, 7DL-MYB, and WD40 regulatory genes control purple pericarp coloration, 4DL-MYC, 2AS-MYC, 7DL-MYB, WD40 control blue aleurone coloration, and 4DL-MYC, 7DL-MYB, WD40 controls black aleurone color. We hypothesized that at least one MYC and MYB isoform is sufficient to regulate the anthocyanin synthesis in pericarp or aleurone. Transcriptomics and metabolomics revealed that the purple pericarp trait is associated with acylated anthocyanins compared to blue aleurone. Based upon the reduced expressions of the genes belonging to the 4D, SSR molecular marker mapping, variant calling using genome sequencing, and IGV browser gene structure visualization, it was inferred that the advanced black and blue wheat lines were substitution lines (4E{4D}), with very small recombinations. Pericarp anthocyanin pigmentation is controlled by a mutation in chromosome 2AS of purple wheat, and environmental variations influence pigmented pericarp trait. The expression patterns of anthocyanin structural and other genes varied in different colored wheat, corroborating differences in agronomical metrics. Ovate seed shape trait in black and blue wheat dragged with 4E chromosome.

Transcriptomic and Metabolomic Analyses Providing Insights into the Coloring Mechanism of Docynia delavayi

The metabolome and transcriptome profiles of three different variations of mature Docynia delavayi fruit were synthesized to reveal their fruit color formation mechanism. A total of 787 secondary metabolites containing 149 flavonoid metabolites, most of which were flavonoids and flavonols, were identified in the three variations using ultra performance liquid chromatography- tandem mass spectrometry (UPLC-MS/MS), and we found that the secondary metabolites cyanidin-3-O-galactoside and cyanidin-3-O-glucoside were the major coloring substances in D. delavayi. This was associated with the significant upregulation of the structural genes F3H and F3′H in the anthocyanin synthesis pathway and the control genes WRKY, MYB, bZIP, bHLH, and NAC in RP. F3′H expression may play a significant role in the selection of components for anthocyanin synthesis. Our results contribute to breeding and nutritional research in D. delavayi and provide insight into metabolite studies of the anthocyanin biosynthetic pathway.

PIFs- and COP1-HY5-mediated temperature signaling in higher plants

Plants have to cope with the surrounding changing environmental stimuli to optimize their physiological and developmental response throughout their entire life cycle. Light and temperature are two critical environmental cues that fluctuate greatly during day-night cycles and seasonal changes. These two external signals coordinately control the plant growth and development. Distinct spectrum of light signals are perceived by a group of wavelength-specific photoreceptors in plants. PIFs and COP1-HY5 are two predominant signaling hubs that control the expression of a large number of light-responsive genes and subsequent light-mediated development in plants. In parallel, plants also transmit low or warm temperature signals to these two regulatory modules that precisely modulate the responsiveness of low or warm temperatures. The core component of circadian clock ELF3 integrates signals from light and warm temperatures to regulate physiological and developmental processes in plants. In this review, we summarize and discuss recent advances and progresses on PIFs-, COP1-HY5- and ELF3-mediated light, low or warm temperature signaling, and highlight emerging insights regarding the interactions between light and low or warm temperature signal transduction pathways in the control of plant growth.

The red flesh of kiwifruit is differentially controlled by specific activation-repression systems

Anthocyanins are visual cues for pollination and seed dispersal. Fruit containing anthocyanins also appeals to consumers due to its appearance and health benefits. In kiwifruit (Actinidia spp.) studies have identified at least two MYB activators of anthocyanin, but their functions in fruit and the mechanisms by which they act are not fully understood. Here, transcriptome and small RNA high-throughput sequencing were used to comprehensively identify contributors to anthocyanin accumulation in kiwifruit. Stable overexpression in vines showed that both 35S::MYB10 and MYB110 can upregulate anthocyanin biosynthesis in Actinidia chinensis fruit, and that MYB10 overexpression resulted in anthocyanin accumulation which was limited to the inner pericarp, suggesting that repressive mechanisms underlie anthocyanin biosynthesis in this species. Furthermore, motifs in the C-terminal region of MYB10/110 were shown to be responsible for the strength of activation of the anthocyanic response. Transient assays showed that both MYB10 and MYB110 were not directly cleaved by miRNAs, but that miR828 and its phased small RNA AcTAS4-D4(-) efficiently targeted MYB110. Other miRNAs were identified, which were differentially expressed between the inner and outer pericarp, and cleavage of SPL13, ARF16, SCL6 and F-box1, all of which are repressors of MYB10, was observed. We conclude that it is the differential expression and subsequent repression of MYB activators that is responsible for variation in anthocyanin accumulation in kiwifruit species.

TRIPTYCHON-LIKE regulates aspects of both fruit flavor and color in citrus

Deciphering the genetic basis of organoleptic traits is critical for improving the quality of fruits, which greatly shapes their appeal to consumers. Here, we characterize the citrus R3-MYB transcription factor TRIPTYCHON-LIKE (CitTRL), which is closely associated with the levels of citric acid, proanthocyanidins (PAs), and anthocyanins. Overexpression of CitTRL lowered acidity levels and PA contents in citrus calli as well as anthocyanin and PA contents in Arabidopsis leaves and seeds. CitTRL interacts with the two basic helix-loop-helix (bHLH) proteins CitbHLH1 and ANTHOCYANIN 1 (CitAN1) to regulate fruit quality. We show that CitTRL competes with the R2R3-MYB CitRuby1 for binding to CitbHLH1 or CitAN1, thereby repressing their activation of anthocyanin structural genes. CitTRL also competes with a second R2R3-MYB, CitPH4, for binding to CitAN1, thus altering the expression of the vacuolar proton-pump gene PH5 and Leucoanthocyanidin reductase, responsible for vacuolar acidification and proanthocyanidins biosynthesis, respectively. Moreover, CitPH4 activates CitTRL transcription, thus forming an activator-repressor loop to prevent the overaccumulation of citric acid and PAs. Overall, this study demonstrates that CitTRL acts as a repressor of the accumulation of citric acid, PAs, and anthocyanins by a cross-regulation mechanism. Our results provide an opportunity to simultaneously manipulate these key traits as a means to produce citrus fruits that are both visually and organoleptically appealing.

CsNIP5;1 acts as a multifunctional regulator to confer water loss tolerance in citrus fruit

Plant aquaporins facilitate the transport of water across the inner membranes and play an important role in the response to water loss stress. A citrus NOD26-like intrinsic protein, CsNIP5;1, has been investigated to participate in the regulation of water permeability. In the present study, the expression profile indicated that CsNIP5;1 showed high transcription abundance in conducting tissues. Function analysis revealed that CsNIP5;1 reduced water loss of Arabidopsis rosette leaf, as well as promoted the seed germination under hyperosmotic stress. Besides, overexpression of CsNIP5;1 contributed to the alleviation of water loss in citrus fruit and citrus callus during storage. Further metabolomic profiling and RNA-seq analysis of transgenic citrus callus revealed that CsNIP5;1 may modulate the water loss by inducing the accumulation of osmotic adjustment substances and repressing the expression of other AQPs. Moreover, CsWRKY4 and CsWRKY28 were found to directly bind to the promoter and acted as opposite regulators of CsNIP5;1 during the postharvest period. These findings provide new insights into the regulatory mechanism of aquaporins in response to the water loss stress of citrus fruit during postharvest storage.

The UV-B-Induced Transcription Factor HY5 Regulated Anthocyanin Biosynthesis in Zanthoxylum bungeanum

Pericarp color is an important economic characteristic of Zanthoxylum bungeanum. Anthocyanins are the main reason for the pericarp's red appearance in Z. bungeanum. In this study, through the combined analysis of the metabolome and transcriptome, HY5, whose expression is highly correlated to changes in the anthocyanin content, was screened and identified. Under natural ripening conditions, the Z. bungeanum fruit gradually changed in color from green to red, while bagging resulted in the fruit maintaining its green color. After unbagging, the fruit gradually turned red, and the ZbHY5 expression and anthocyanin content increased. In addition, the leaves changed from green to red after exposure to UV-B radiation, and the ZbHY5 expression and anthocyanin content increased. The transient overexpression of ZbHY5 deepened the redness of the Z. bungeanum leaves and promoted the expression of ZbHY5 and ZbMYB113 as well as anthocyanin accumulation. Bimolecular fluorescence complementation (BIFC) showed that there was an interaction between ZbHY5 and ZbMYB113. These results revealed that under UV-B irradiation, ZbHY5 might regulate the expression levels of the structural genes related to anthocyanin biosynthesis through combination with ZbMYB113, thereby affecting anthocyanin accumulation. This finding provides useful insights for further studies focusing on UV-B-induced anthocyanin accumulation in Z. bungeanum.

HY5: A Pivotal Regulator of Light-Dependent Development in Higher Plants

ELONGATED HYPOCOTYL5 (HY5), a bZIP-type transcription factor, acts as a master regulator that regulates various physiological and biological processes in plants such as photomorphogenesis, root growth, flavonoid biosynthesis and accumulation, nutrient acquisition, and response to abiotic stresses. HY5 is evolutionally conserved in function among various plant species. HY5 acts as a master regulator of light-mediated transcriptional regulatory hub that directly or indirectly controls the transcription of approximately one-third of genes at the whole genome level. The transcription, protein abundance, and activity of HY5 are tightly modulated by a variety of factors through distinct regulatory mechanisms. This review primarily summarizes recent advances on HY5-mediated molecular and physiological processes and regulatory mechanisms on HY5 in the model plant Arabidopsis as well as in crops.

Identification, Characterization and Expression Analysis of Anthocyanin Biosynthesis-related bHLH Genes in Blueberry (Vaccinium corymbosum L.)

Basic helix-loop-helix proteins (bHLHs) play very important roles in the anthocyanin biosynthesis of many plant species. However, the reports on blueberry anthocyanin biosynthesis-related bHLHs were very limited. In this study, six anthocyanin biosynthesis-related bHLHs were identified from blueberry genome data through homologous protein sequence alignment. Among these blueberry bHLHs, VcAN1, VcbHLH42-1, VcbHLH42-2 and VcbHLH42-3 were clustered into one group, while VcbHLH1-1 and VcbHLH1-2 were clustered into the other group. All these bHLHs were of the bHLH-MYC_N domain, had DNA binding sites and reported conserved amino acids in the bHLH domain, indicating that they were all G-box binding proteins. Protein subcellular location prediction result revealed that all these bHLHs were nucleus-located. Gene structure analysis showed that VcAN1 gDNA contained eight introns, while all the others contained seven introns. Many light-, phytohormone-, stress- and plant growth and development-related cis-acting elements and transcription factor binding sites (TFBSs) were identified in their promoters, but the types and numbers of cis-elements and TFBSs varied greatly between the two bHLH groups. Quantitative real-time PCR results showed that VcAN1 expressed highly in old leaf, stem and blue fruit, and its expression increased as the blueberry fruit ripened. Its expression in purple podetium and old leaf was respectively significantly higher than in green podetium and young leaf, indicating that VcAN1 plays roles in anthocyanin biosynthesis regulation not only in fruit but also in podetium and leaf. VcbHLH1-1 expressed the highest in young leaf and stem, and the lowest in green fruit. The expression of VcbHLH1-1 also increased as the fruit ripened, and its expression in blue fruit was significantly higher than in green fruit. VcbHLH1-2 showed high expression in stem but low expression in fruit, especially in red fruit. Our study indicated that the anthocyanin biosynthesis regulatory functions of these bHLHs showed certain spatiotemporal specificity. Additionally, VcAN1 might be a key gene controlling the anthocyanin biosynthesis in blueberry, whose function is worth exploring further for its potential applications in plant high anthocyanin breeding.

Citrus Genetic Transformation: An Overview of the Current Strategies and Insights on the New Emerging Technologies

Citrus are among the most prevailing fruit crops produced worldwide. The implementation of effective and reliable breeding programs is essential for coping with the increasing demands of satisfactory yield and quality of the fruit as well as to deal with the negative impact of fast-spreading diseases. Conventional methods are time-consuming and of difficult application because of inherent factors of citrus biology, such as their prolonged juvenile period and a complex reproductive stage, sometimes presenting infertility, self-incompatibility, parthenocarpy, or polyembryony. Moreover, certain desirable traits are absent from cultivated or wild citrus genotypes. All these features are challenging for the incorporation of the desirable traits. In this regard, genetic engineering technologies offer a series of alternative approaches that allow overcoming the difficulties of conventional breeding programs. This review gives a detailed overview of the currently used strategies for the development of genetically modified citrus. We describe different aspects regarding genotype varieties used, including elite cultivars or extensively used scions and rootstocks. Furthermore, we discuss technical aspects of citrus genetic transformation procedures via Agrobacterium, regular physical methods, and magnetofection. Finally, we describe the selection of explants considering young and mature tissues, protoplast isolation, etc. We also address current protocols and novel approaches for improving the in vitro regeneration process, which is an important bottleneck for citrus genetic transformation. This review also explores alternative emerging transformation strategies applied to citrus species such as transient and tissue localized transformation. New breeding technologies, including cisgenesis, intragenesis, and genome editing by clustered regularly interspaced short palindromic repeats (CRISPR), are also discussed. Other relevant aspects comprising new promoters and reporter genes, marker-free systems, and strategies for induction of early flowering, are also addressed. We provided a future perspective on the use of current and new technologies in citrus and its potential impact on regulatory processes.

Emerging roles of brassinosteroids and light in anthocyanin biosynthesis and ripeness of climacteric and non-climacteric fruits

Anthocyanins are important pigments that contribute to fruit quality. The regulation of anthocyanin biosynthesis by several transcription factors via sophisticated regulatory networks has been studied in various plants. Brassinosteroids (BRs), a new class of plant hormone, are involved in regulating anthocyanin biosynthesis in fruits. Furthermore, light directly affects the synthesis and distribution of anthocyanins. Here, we summarize the recent progress toward understanding the impact of BR and light on anthocyanin biosynthesis in climacteric and non-climacteric fruits. We review the BR and light signaling pathways and highlight the important transcription factors that are associated with the synthesis of anthocyanins, such as BZR1 (brassinazole-resistant 1, BR signaling pathway), HY5 (elongated hypocotyl 5) and COP1 (constitutively photomorphogenic 1, light signal transduction pathway), which bind with the target genes involved in anthocyanin synthesis. In addition, we review the mechanism by which light signals interact with hormonal signals to regulate anthocyanin biosynthesis.

Transcriptomics Integrated With Widely Targeted Metabolomics Reveals the Mechanism Underlying Grain Color Formation in Wheat at the Grain-Filling Stage

Colored wheat grains have a unique nutritional value. To elucidate the color formation mechanism in wheat seeds, comprehensive metabolomic and transcriptomic analyses were conducted on purple (Dianmai 20-1), blue (Dianmai 20-8), and white (Dianmai 16) wheat at the grain-filling stage. The results showed that the flavonoid biosynthesis pathway was closely related to grain color formation. Among the 603 metabolites identified in all varieties, there were 98 flavonoids. Forty-six flavonoids were detected in purple and blue wheat, and there were fewer flavonoids in white wheat than in colored wheat. Integrated transcriptomic and metabolomic analyses showed that gene expression modulated the flavonoid composition and content, resulting in different metabolite levels of pelargonidin, cyanidin, and delphinidin, thus affecting the color formation of wheat grains. The present study clarifies the mechanism by which pigmentation develops in wheat grains and provides an empirical reference for colored wheat breeding.

Cold Stress in Citrus: A Molecular, Physiological and Biochemical Perspective

Due to climate change, we are forced to face new abiotic stress challenges like cold and heat waves that currently result from global warming. Losses due to frost and low temperatures force us to better understand the physiological, hormonal, and molecular mechanisms of response to such stress to face losses, especially in tropical and subtropical crops like citrus fruit, which are well adapted to certain weather conditions. Many of the responses to cold stress that are found are also conserved in citrus. Hence, this review also intends to show the latest work on citrus. In addition to basic research, there is a great need to employ and cultivate new citrus rootstocks to better adapt to environmental conditions.

Light dominates the diurnal emissions of herbivore-induced volatiles in wild tobacco

BACKGROUND

Timing is everything when it comes to the fitness outcome of a plant's ecological interactions, and accurate timing is particularly relevant for interactions with herbivores or mutualists that are based on ephemeral emissions of volatile organic compounds. Previous studies of the wild tobacco N. attenuata have found associations between the diurnal timing of volatile emissions, and daytime predation of herbivores by their natural enemies.

RESULTS

Here, we investigated the role of light in regulating two biosynthetic groups of volatiles, terpenoids and green leaf volatiles (GLVs), which dominate the herbivore-induced bouquet of N. attenuata. Light deprivation strongly suppressed terpenoid emissions while enhancing GLV emissions, albeit with a time lag. Silencing the expression of photoreceptor genes did not alter terpenoid emission rhythms, but silencing expression of the phytochrome gene, NaPhyB1, disordered the emission of the GLV (Z)-3-hexenyl acetate. External abscisic acid (ABA) treatments increased stomatal resistance, but did not truncate the emission of terpenoid volatiles (recovered in the headspace). However, ABA treatment enhanced GLV emissions and leaf internal pools (recovered from tissue), and reduced internal linalool pools. In contrast to the pattern of diurnal terpenoid emissions and nocturnal GLV emissions, transcripts of herbivore-induced plant volatile (HIPV) biosynthetic genes peaked during the day. The promotor regions of these genes were populated with various cis-acting regulatory elements involved in light-, stress-, phytohormone- and circadian regulation.

CONCLUSIONS

This research provides insights into the complexity of the mechanisms involved in the regulation of HIPV bouquets, a mechanistic complexity which rivals the functional complexity of HIPVs, which includes repelling herbivores, calling for body guards, and attracting pollinators.

Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh

Radish (Raphanus sativus) is an important vegetable worldwide that exhibits different flesh and skin colors. The anthocyanins responsible for the red and purple coloring in radishes possess nutritional value and pharmaceutical potential. To explore the structural and regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed comparative transcriptome analyses of the skin and flesh of six colored radish accessions. The transcript profiles showed that each accession had a species-specific transcript profile. For radish pigmentation accumulation, the expression levels of anthocyanin biosynthetic genes (RsTT4, RsC4H, RsTT7, RsCCOAMT, RsDFR, and RsLDOX) were significantly upregulated in the red- and purple-colored accessions, but were downregulated or absent in the white and black accessions. The correlation test, combined with metabolome (PCC > 0.95), revealed five structural genes (RsTT4, RsDFR, RsCCOAMT, RsF3H, and RsBG8L) and three transcription factors (RsTT8-1, RsTT8-2, and RsPAR1) to be significantly correlated with flavonoids in the skin of the taproot. Four structural genes (RsBG8L, RsDFR, RsCCOAMT, and RsLDOX) and nine transcription factors (RsTT8-1, RsTT8-2, RsMYB24L, RsbHLH57, RsPAR2L, RsbHLH113L, RsOGR3L, RsMYB24, and RsMYB34L) were found to be significantly correlated with metabolites in the flesh of the taproot. This study provides a foundation for future studies on the gene functions and genetic diversity of radish pigmentation and should aid in the cultivation of new valuable radish varieties.

Recent Insights into Anthocyanin Pigmentation, Synthesis, Trafficking, and Regulatory Mechanisms in Rice (Oryza sativa L.) Caryopsis

Anthocyanins are antioxidants used as natural colorants and are beneficial to human health. Anthocyanins contribute to reactive oxygen species detoxification and sustain plant growth and development under different environmental stresses. They are phenolic compounds that are broadly distributed in nature and are responsible for a wide range of attractive coloration in many plant organs. Anthocyanins are found in various parts of plants such as flowers, leaves, stems, shoots, and grains. Considering their nutritional and health attributes, anthocyanin-enriched rice or pigmented rice cultivars are a possible alternative to reduce malnutrition around the globe. Anthocyanin biosynthesis and storage in rice are complex processes in which several structural and regulatory genes are involved. In recent years, significant progress has been achieved in the molecular and genetic mechanism of anthocyanins, and their synthesis is of great interest to researchers and the scientific community. However, limited studies have reported anthocyanin synthesis, transportation, and environmental conditions that can hinder anthocyanin production in rice. Rice is a staple food around the globe, and further research on anthocyanin in rice warrants more attention. In this review, metabolic and pre-biotic activities, the underlying transportation, and storage mechanisms of anthocyanins in rice are discussed in detail. This review provides potential information for the food industry and clues for rice breeding and genetic engineering of rice.

Integrated metabolic profiling and transcriptome analysis of pigment accumulation in Lonicera japonica flower petals during colour-transition

BACKGROUND

Plants have remarkable diversity in petal colour through the biosynthesis and accumulation of various pigments. To better understand the mechanisms regulating petal pigmentation in Lonicera japonica, we used multiple approaches to investigate the changes in carotenoids, anthocyanins, endogenous hormones and gene expression dynamics during petal colour transitions, i.e., green bud petals (GB_Pe), white flower petals (WF_Pe) and yellow flower petals (YF_Pe).

RESULTS

Metabolome analysis showed that YF_Pe contained a much higher content of carotenoids than GB_Pe and WF_Pe, with α-carotene, zeaxanthin, violaxanthin and γ-carotene identified as the major carotenoid compounds in YF_Pe. Comparative transcriptome analysis revealed that the key differentially expressed genes (DEGs) involved in carotenoid biosynthesis, such as phytoene synthase, phytoene desaturase and ζ-carotene desaturase, were significantly upregulated in YF_Pe. The results indicated that upregulated carotenoid concentrations and carotenoid biosynthesis-related genes predominantly promote colour transition. Meanwhile, two anthocyanins (pelargonidin and cyanidin) were significantly increased in YF_Pe, and the expression level of an anthocyanidin synthase gene was significantly upregulated, suggesting that anthocyanins may contribute to vivid yellow colour in YF_Pe. Furthermore, analyses of changes in indoleacetic acid, zeatin riboside, gibberellic acid, brassinosteroid (BR), methyl jasmonate and abscisic acid (ABA) levels indicated that colour transitions are regulated by endogenous hormones. The DEGs involved in the auxin, cytokinin, gibberellin, BR, jasmonic acid and ABA signalling pathways were enriched and associated with petal colour transitions.

CONCLUSION

Our results provide global insight into the pigment accumulation and the regulatory mechanisms underlying petal colour transitions during the flower development process in L. japonica.

Glutathione S-transferases GhGSTF1 and GhGSTF2 involved in the anthocyanin accumulation in Gossypium hirsutum L

The glutathione S-transferases (GSTs) are important enzymes of secondary metabolism in plants. In this study, two putative GSTs, GhGSTF1 and GhGSTF2, were identified as anthocyanin-related GSTs by the transcriptome data of the leaves of Gossypium hirsutum L. TM-1 and T586. The quantitative real-time PCR showed that GhGSTF1 and GhGSTF2 were highly expressed in red leaves and stems of Gossypium hirsutum L. T586. Orthologous genes of GhGSTF2 in two Gossypium barbadense L. 3-79 and Xinhai21 contain bases deletion in N-terminal (GbGSTF2a) and C-terminal (GbGSTF2b) respectively. Among which, GhGSTF1 and GhGSTF2 can restore pigmentation in hypocotyls of Arabidopsis thaliana mutant tt19-7 while GbGSTF2a and GbGSTF2b cannot. Furthermore, in vitro assays showed the recombinant GhGSTF1 and GhGSTF2 had Glutathione S-transferase activities. Fluorescence quenching assays showed that Cya could obviously quench the fluorescence of GhGSTF1, GhGSTF2, GbGSTF2a and GbGSTF2b to lower levels as compared to C3G. Moreover, the transient dual-luciferase assays showed that the promoters of GhGSTF1 and GhGSTF2 could be activated by GhPAP1D at different levels. GUS staining assays showed that their promoters have different activities to light. This study indicated that GhGSTF1 and GhGSTF2 play important roles in anthocyanin accumulation and the regulatory mechanism of anthocyanin accumulation in allotetraploid Gossypium are complicated.

Target-Genes Reveal Species and Genotypic Specificity of Anthocyanin Pigmentation in Citrus and Related Genera

Background: Anthocyanin pigmentation characterizes a number of tissues of Citrus and its relatives. The gain and loss of pigmentation is intriguing and is inherited variously among species. Methods: Citrus germplasm was used to investigate the anthocyanin pigmentation of tissues never before considered, including stamen, style and stigma, and of young leaves, petals, rind and flesh of 28 genotypes belonging to 14 species. Citrus genotypes encompassed citron, lemon, sweet orange, lime, and Citrus relatives included Microcitrus, Murraya, and Severinia. A relative qRT-PCR analysis was carried out on the structural and regulatory genes: phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3′-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), uridine diphosphate glucose flavonoid glucosyl-transferase (UFGT), glutathione S-transferase (GST), Ruby and Noemi. Image analysis and a genomic approach were employed to evaluate how the red pigmentation is inherited among tissues and species. Results: Pigmentation of young leaves and petals is specific to citron and its hybrids. Ruby controls the pigmentation of petals, but not of leaves. The red color of the rind and flesh is a trait that particularly characterizes a diversity of sweet oranges, citron hybrids and Citrus relatives. Color expression depends on external factors and also on developmental stage. The coloration of stamen and style is citron-specific, while a red stigma is exclusive to Moro orange and its hybrids. Conclusion: It is hypothesized that there is a relationship among Citrus species and genes controlling anthocyanin pigmentation.

FvbHLH9 Functions as a Positive Regulator of Anthocyanin Biosynthesis by Forming a HY5-bHLH9 Transcription Complex in Strawberry Fruits

Anthocyanin accumulation is transcriptionally regulated by the MYB-bHLH-WD40 complex. Light is indispensable for anthocyanin accumulation, and light-inducible MYB and HY5 were considered to promote anthocyanin accumulation in many fruits. Whether and how light-inducible bHLH transcription factor and HY5 regulate anthocyanin synthesis in strawberry is unknown. In this study, we identified a bHLH transcription factor, FvbHLH9, which was induced by light as well as FvHY5, and found that, similar to FvHY5, the transient overexpression and interference FvbHLH9 in strawberry fruits can promote and decrease anthocyanin accumulation, respectively, indicating FvbHLH9 functions as a positive regulator of anthocyanin biosynthesis. Furthermore, we confirmed that both FvHY5 and FvbHLH9 specifically bind to the promoter region of some key enzyme genes, including FvDFR, and the expression of FvDFR was activated through the heterodimer formation between FvHY5 and FvbHLH9. Finally, we confirmed that FvbHLH9-promoted anthocyanin accumulation is dependent on HY5-bHLH heterodimerisation in Arabidopsis. Our findings provide insights into a mechanism involving the synergistic regulation of light-dependent coloration and anthocyanin biosynthesis via a HY5-bHLH heterodimer formed by the interaction of FvHY5 and FvbHLH9 in strawberry fruits.