Anthocyanin Accumulation, Antioxidant Ability and Stability, and a Transcriptional Analysis of Anthocyanin Biosynthesis in Purple Heading Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Genome-Wide Identification of Glutathione S-Transferase Genes in Eggplant (Solanum melongena L.) Reveals Their Potential Role in Anthocyanin Accumulation on the Fruit Peel

Anthocyanins are ubiquitous pigments derived from the phenylpropanoid compound conferring red, purple and blue pigmentations to various organs of horticultural crops. The metabolism of flavonoids in the cytoplasm leads to the biosynthesis of anthocyanin, which is then conveyed to the vacuoles for storage by plant glutathione S-transferases (GST). Although GST is important for transporting anthocyanin in plants, its identification and characterization in eggplant (Solanum melongena L.) remains obscure. In this study, a total of 40 GST genes were obtained in the eggplant genome and classified into seven distinct chief groups based on the evolutionary relationship with Arabidopsis thaliana GST genes. The seven subgroups of eggplant GST genes (SmGST) comprise: dehydroascorbate reductase (DHAR), elongation factor 1Bγ (EF1Bγ), Zeta (Z), Theta(T), Phi(F), Tau(U) and tetra-chlorohydroquinone dehalogenase TCHQD. The 40 GST genes were unevenly distributed throughout the 10 eggplant chromosomes and were predominantly located in the cytoplasm. Structural gene analysis showed similarity in exons and introns within a GST subgroup. Six pairs of both tandem and segmental duplications have been identified, making them the primary factors contributing to the evolution of the SmGST. Light-related cis-regulatory elements were dominant, followed by stress-related and hormone-responsive elements. The syntenic analysis of orthologous genes indicated that eggplant, Arabidopsis and tomato (Solanum lycopersicum L.) counterpart genes seemed to be derived from a common ancestry. RNA-seq data analyses showed high expression of 13 SmGST genes with SmGSTF1 being glaringly upregulated on the peel of purple eggplant but showed no or low expression on eggplant varieties with green or white peel. Subsequently, SmGSTF1 had a strong positive correlation with anthocyanin content and with anthocyanin structural genes like SmUFGT (r = 0.9), SmANS (r = 0.85), SmF3H (r = 0.82) and SmCHI2 (r = 0.7). The suppression of SmGSTF1 through virus-induced gene silencing (VIGs) resulted in a decrease in anthocyanin on the infiltrated fruit surface. In a nutshell, results from this study established that SmGSTF1 has the potential of anthocyanin accumulation in eggplant peel and offers viable candidate genes for the improvement of purple eggplant. The comprehensive studies of the SmGST family genes provide the foundation for deciphering molecular investigations into the functional analysis of SmGST genes in eggplant.

Mutation in BrFLS encoding flavonol synthase induced anthocyanin accumulation in Chinese cabbage

KEY MESSAGE

BrFLS mutation promoted anthocyanin accumulation in Chinese cabbage, which was verified in four allelic mutants. Chinese cabbage is a major vegetable crop in Eastern Asia. Anthocyanin-rich vibrantly colored varieties are increasingly favored by consumers for their higher nutritional and aesthetic value compared to the typical green varieties of Chinese cabbage. Herein, we identified an anthocyanin accumulation mutant aam1 from a mutant library of EMS-mutagenized Chinese cabbage DH line 'FT', which appeared partial purple on leaves, bolting stems and floral buds. This anthocyanin accumulation trait was genetically controlled by a recessive nuclear gene, and through MutMap mapping and KASP genotyping, BraA10g030950.3C was identified as the candidate causal gene with a G202 to A202 non-synonymous SNP variation in exon 1. Three additional mutants allelic to aam1 were obtained via screening of similar-phenotype mutants from the mutant library, namely aam2/3/4, where the causal SNPs reside in the same gene as aam1, corroborating that the mutation of BraA10g030950.3C caused anthocyanin accumulation. BraA10g030950.3C encodes a flavonol synthase that catalyzes dihydroflavonols substrate into flavonols and is homologous to Arabidopsis FLS1 (AT5G08640), named BrFLS. Compared to wildtype, the expression level of BrFLS was significantly reduced in the mutants, while BrDFR, which is involved in the anthocyanin biosynthesis and competes with FLS for the common substrate dihydroflavonols, was increased. The flavonol synthase activity decreased, and dihydroflavonol 4-reductase activity was elevated. Differentially accumulated flavonoid metabolites were detected between wildtype and aam1, which were enriched primarily in flavonol and anthocyanin pathways. Our results revealed that mutations in the BrFLS gene could contribute to anthocyanin accumulation and provide a new target for Chinese cabbage color modification.

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.

HaMYBA-HabHLH1 regulatory complex and HaMYBF fine-tune red flower coloration in the corolla of sunflower (Helianthus annuus L.)

Sunflowers are well-known ornamental plants, while sunflowers with red corolla are rare and the mechanisms underlying red coloration remain unclear. Here, a comprehensive analysis of metabolomics and transcriptomics on flavonoid pathway was performed to investigate the molecular mechanisms underlying the differential color formation between red sunflower Pc103 and two yellow sunflowers (Yr17 and Y35). Targeted metabolomic analysis revealed higher anthocyanin levels but lower flavonol content in Pc103 compared to the yellow cultivars. RNA-sequencing and phylogenetic analysis identified multiple genes involved in the flavonoid pathway, including series of structural genes and three MYB and bHLH genes. Specifically, HaMYBA and HabHLH1 were up-regulated in Pc103, whereas HaMYBF exhibited reduced expression. HaMYBA was found to interact with HabHLH1 in vivo and in vitro, while HaMYBF does not. Transient expression analysis further revealed that HabHLH1 and HaMYBA cooperatively regulate increased expression of dihydroflavonol 4-reductase (DFR), leading to anthocyanin accumulation. On the other hand, ectopic expression of HaMYBF independently modulates flavonol synthase (FLS) expression, but hindered anthocyanin production. Collectively, our findings suggest that the up-regulation of HaMYBA and HabHLH1, as well as the down-regulation of HaMYBF, contribute to the red coloration in Pc103. It offers a theoretical basis for improving sunflower color through genetic engineering.

Effects of long-term blue light irradiation on carotenoid biosynthesis and antioxidant activities in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

The aim of this study was to investigate the impact of long-term exposure to blue light-emitting diodes (LEDs) on the accumulation of indolic glucosinolates and carotenoids, as well as the plant growth and antioxidant activities in both orange and common Chinese cabbage (Brassica rapa L. ssp. pekinensis). Blue light treatment also induced higher ferric-reducing antioxidant power and 2,2-diphenyl-1-picrylhydrazyl by 20.66 % and 30.82 % and antioxidant enzyme activities catalase, peroxidase, superoxide dismutase, and the accumulation of non-enzymatic antioxidant substances (total phenols and total flavonoids) in the orange Chinese cabbage. Furthermore, long-term exposure to blue light had negative effects on the net photosynthetic rate and chlorophyll fluorescence levels. Meanwhile, blue light promoted accumulation of Indol-3-ylmethyl glucosinolate (I3M), β-carotene, lutein and zeaxanthin due to the high expression of regulatory and biosynthetic genes of the above metabolic pathways. In particular, lycopene and β-carotene content in orange Chinese cabbage increased by 60.14 % and 65.33 % compared to the ones in common line. The accumulation of carotenoid and increasing antioxidant levels in the orange cabbage line was influenced by long-term blue light irradiation, leading to better tolerance to low temperature and drought stresses. The up-regulation of transcription factors such as BrHY5-2, BrPIF4 and BrMYB12 may also contribute to the increased tolerance in orange Chinese cabbage to extreme environmental stresses. The BrHY5-2 gene could activate carotenoid biosynthetic genes and induce the accumulation of carotenoids. These findings suggested that long-term blue light irradiation could be a promising technique for increasing the nutrition value and enhancing tolerance to low temperature and drought stresses in Chinese cabbage.

Comparative Transcriptome Analysis of Purple and Green Flowering Chinese Cabbage and Functional Analyses of BrMYB114 Gene

Flowering Chinese cabbage (Brassica rapa var. parachinensis) is one of the most popular vegetables in the south of China. As an antioxidant, anthocyanin is an important quality trait in vegetables, and the gene related to anthocyanin biosynthesis in purple flowering Chinese cabbage is also important. In this study, two flowering Chinese cabbage with extreme colors in the stem were used as materials for transcriptome analysis. RNA-seq analysis showed that 6811 differentially expressed genes (DEGs) were identified, including 295 transcription factors. Phenylpropanoid biosynthesis, flavone and flavanol biosynthesis, and flavonoid biosynthesis pathways were found to be significantly enriched in the purple flowering Chinese cabbage. A total of 25 DEGs associated with anthocyanin biosynthesis were found at a higher expression in purple flowering Chinese cabbage than in green flowering Chinese cabbage. Bioinformatics analysis shows that BrMYB114 is a candidate gene for the regulation of anthocyanin biosynthesis, and heterologous expression analysis of BrMYB114 in Nicotiana benthamiana indicates that BrMYB114 functions in anthocyanin biosynthesis. Therefore, our findings provide vital evidence for elucidating the molecular mechanism in the purple stem in flowering Chinese cabbage.

Research progress and applications of colorful Brassica crops

MAIN CONCLUSION

We review the application and the molecular regulation of anthocyanins in colorful Brassica crops, the creation of new germplasm resources, and the development and utilization of colorful Brassica crops. Brassica crops are widely cultivated: these include oilseed crops, such as rapeseed, mustards, and root, leaf, and stem vegetable types, such as turnips, cabbages, broccoli, and cauliflowers. Colorful variants exist of these crop species, and asides from increased aesthetic appeal, these may also offer advantages in terms of nutritional content and improved stress resistances. This review provides a comprehensive overview of pigmentation in Brassica as a reference for the selection and breeding of new colorful Brassica varieties for multiple end uses. We summarize the function and molecular regulation of anthocyanins in Brassica crops, the creation of new colorful germplasm resources via different breeding methods, and the development and multifunctional utilization of colorful Brassica crop types.

When Cannabis sativa L. Turns Purple: Biosynthesis and Accumulation of Anthocyanins

Environmental cues elicit anthocyanin synthesis in plant vegetative and reproductive tissues. Their accumulation in different organs accounts for their diverse biological functions, mainly related to their antioxidant properties, and it depends on a temporally and spatially regulated mechanism controlled by the action of a well-known multi-transcription factor complex. Despite the highly recognizable value of Cannabis sativa L. as a natural biorefinery of phytochemicals, very little information is known on anthocyanin pigmentation in this species. In this work, a targeted quantification of anthocyanins via HPLC-MS/MS, combined with the transcriptional profile via RT-qPCR of genes encoding for structural and decorating enzymes and regulatory transcription factors in different C. sativa tissues, help gain insights into the anthocyanin pathway in this species. To the best of our knowledge, this is the first report on the identification of cyanidin-3-rutinoside (keracyanin) as the major anthocyanin in C. sativa vegetative and floral tissues. Keracyanin amounts were higher than in small berries, suggesting that Cannabis biomass is a valuable source of colored antioxidants to be exploited in diverse applications. Furthermore, a gene putatively encoding for an anthocyanin DTX35 type transporter and CsTTG1 were identified in silico and their transcriptional levels were assessed via RT-qPCR. The results allow us to provide the first model of anthocyanin regulation in C. sativa, opening a new research scenario in this species for both breeding purposes and phytochemical exploitation.

Prediction of Anthocyanidins Content in Purple Chinese Cabbage Based on Visible/Near Infrared Spectroscopy

Purple Chinese cabbage (PCC) has become a new breeding trend due to its attractive color and high nutritional quality since it contains abundant anthocyanidins. With the aim of rapid evaluation of PCC anthocyanidins contents and screening of breeding materials, a fast quantitative detection method for anthocyanidins in PCC was established using Near Infrared Spectroscopy (NIR). The PCC samples were scanned by NIR, and the spectral data combined with the chemometric results of anthocyanidins contents obtained by high-performance liquid chromatography were processed to establish the prediction models. The content of cyanidin varied from 93.5 mg/kg to 12,802.4 mg/kg in PCC, while the other anthocyanidins were much lower. The developed NIR prediction models on the basis of partial least square regression with the preprocessing of no-scattering mode and the first-order derivative showed the best prediction performance: for cyanidin, the external correlation coefficient (RSQ) and standard error of cross-validation (SECV) of the calibration set were 0.965 and 693.004, respectively; for total anthocyanidins, the RSQ and SECV of the calibration set were 0.966 and 685.994, respectively. The established models were effective, and this NIR method, with the advantages of timesaving and convenience, could be applied in purple vegetable breeding practice.

Identification of CaPs locus involving in purple stripe formation on unripe fruit, reveals allelic variation and alternative splicing of R2R3-MYB transcription factor in pepper (Capsicum annuum L.)

The purple color of unripe pepper fruit is attributed to the accumulation of anthocyanins. Only a few genes controlling the biosynthesis and regulation of anthocyanins have been cloned in Capsicum. In this study, we performed a bulked segregant analysis of the purple striped trait using an F² population derived from a cross between the immature purple striped fruit line Chen12-4-1-1-1-1 and the normal green fruit line Zhongxian101-M-F⁹. We mapped the CaPs locus to an 841.39 kb region between markers M-CA690-Xba and MCA710-03 on chromosome 10. CA10g11690 encodes an R2R3-MYB transcription factor that is involved in the biosynthesis of anthocyanins as the best candidate gene. Overexpression and silencing in transformed tobacco (Nicotiana tabacum) lines indicated that CA10g11690 is involved in the formation of purple stripes in the exocarp. A comparison of parental sequences identified an insertion fragment of 1,926 bp in the second intron region of Chen12-4, and eight SNPs were detected between the two parents. Additionally, there were 49 single nucleotide polymorphic variations, two sequence deletions, and four sequence insertions in the promoter region. We found that CA10g11690 undergoes alternative splicing and generates different transcripts. Thus, the functional transcript of CA10g11690 appeared to be primarily involved in the development of purple phenotype in the exocarp. Our data provide new insight into the mechanism of anthocyanin biosynthesis and a theoretical basis for the future breeding of purple striped pepper varieties.

Comparative Transcriptome and Metabolome Analyses of Broccoli Germplasms with Purple and Green Curds Reveal the Structural Genes and Transitional Regulators Regulating Color Formation

Owing to the high anthocyanin content, broccoli varieties with purple curds have become more popular in food inventories, while the genetic mechanisms of anthocyanin biosynthesis pathways remain largely unknown. We bred a pair of near-isogenic lines (NILs), GB767 and PB767, whose curds exhibited green and purple colors, respectively, due to the purple sepals of florets. RNA sequencing and widely targeted metabolic analyses were conducted. Compared with GB767, eighteen anthocyanin biosynthesis-related genes exhibited significantly higher expressions in PB767, and in turn, the expression level of BolMYBL2.1 was attenuated. A comparison of the metabolites in the flavonoid biosynthetic pathways revealed 142 differentially accumulated metabolites, among which higher content of anthocyanins was responsible for the purple color of PB767. Interestingly, the total cyanidin contents were similar between the curds of NILs, whereas total delphinidin contents were increased by more than 170 times in purple curds, presumably due to a non-canonical F3'H/CYP75B gene, BolC02g015480.2J, with elevated expression in PB767. Furthermore, correlation analysis further confirmed that the identified nineteen DEGs were significantly correlated with seven differentially accumulated anthocyanins in PB767. Together, these results identified the metabolic factors and genes that contribute to the purplish curds, which could lay foundations for the breeding programs of purple broccoli.

Correlation between Parental Transcriptome and Field Data for the Characterization of Heterosis in Chinese Cabbage

In Chinese cabbage breeding, hybrids have made a terrific contribution due to heterosis, the superior performance of offspring compared to their inbred parents. Since the development of new, top-performing hybrids requires a large scale of human and material resources, the prediction of hybrid performance is of utmost interest to plant breeders. In our research, leaf transcriptome data from eight parents were used to investigate if they might be employed as markers to predict hybrid performance and heterosis. In Chinese cabbage, heterosis of plant growth weight (PGW) and heterosis of head weight (HW) were more obvious than other traits. The number of differential expression genes (DEGs) between parents was related to the PGW, length of the biggest outer leaf (LOL), leaf head height (LHH), leaf head width (LHW), HW, leaf number of head (LNH) and plant height (PH) of hybrids, and up-regulated DEGs number was also associated with these traits. Euclidean and binary distances of parental gene expression levels were significantly correlated with the PGW, LOL, LHH, LHW, HW and PH of hybrids. Additionally, there was a significant correlation between the parental expression levels of multiple genes involved in the ribosomal metabolic pathway and hybrid observations and heterosis in PGW, with the BrRPL23A gene showing the highest correlation with the MPH of PGW(r = 0.75). Therefore, leaf transcriptome data can preliminarily predict the hybrid performance and select parents in Chinese cabbage.

Transcriptome Analysis Reveals a Major Gene Expression Pattern and Important Metabolic Pathways in the Control of Heterosis in Chinese Cabbage

Although heterosis is commonly used in Chinese cabbage, its molecular basis is poorly understood. In this study, 16Chinese cabbage hybrids were utilized as test subjects to explore the potential molecular mechanism of heterosis. RNA sequencing revealed 5815-10,252 differentially expressed genes (DEGs) (female parent vs. male parent), 1796-5990 DEGs (female parent-vs-hybrid), and 2244-7063 DEGs (male parent vs. hybrid) in 16 cross combinations at the middle stage of heading. Among of them, 72.83-84.20% DEGs conformed to the dominant expression pattern, which is the predominant expression pattern in hybrids. There were 13 pathways in which DEGs were significantly enriched in most cross combinations. Among them, the plant-pathogen interaction (ko04626) and circadian rhythm-plant (ko04712)were significantly enriched by DEGs in strong heterosis hybrids. WGCNA also proved that the two pathways were significantly related to heterosis in Chinese cabbage.

Investigation of the Key Genes Associated with Anthocyanin Accumulation during Inner Leaf Reddening in Ornamental Kale (Brassica oleracea L. var. acephala)

Ornamental kale (Brassica oleracea L. var. acephala) is a popular decorative plant in late autumn and winter. However, only during low-temperature color-changed periods below rough 15 °C can the plant accumulate anthocyanins and exhibit a diverse array of foliar color patterns. In this study, we probed into the potential mechanism of inner leaf reddening in a red-leaf pure line of ornamental kale by physiological, metabolic, and transcriptomic analyses. Determination of anthocyanin contents in the uncolored new white leaves (S0), the light red leaves (S1) in the reddening period and the red leaves (S2) completing color change, and analysis of anthocyanin metabolites at stage S2, revealed that the coloring of red leaves was mainly attributed to the accumulation of cyanidins. We further used transcriptomic sequencing between the pairwise S0, S1, and S2 stages to identify 21 differentially expressed genes (DEGs) involved in anthocyanin biosynthesis, among which the expression level of 14 DEGs was positively correlated with anthocyanin accumulation, and 6 DEGs were negatively correlated with anthocyanin accumulation. A total of 89 co-expressed genes were screened out, from which three DEGs (BoCHI, Bo4CL3, and BoF3H) were identified as hub genes in co-expression DEGs network. BoDFR and BoCHI were the DEGs with the highest expressions at S2. Moreover, two co-expressed DEGs related to stress response (BoBBX17 and BoCOR47) also exhibited upregulated expressions and positive correlations with anthocyanin accumulation. A deep dive into the underlying regulatory network of anthocyanin accumulation comprising these six upregulated DEGs from S0 to S2 was performed via trend, correlation, and differentially co-expression analysis. This study uncovered the DEGs expression profiles associated with anthocyanin accumulation during ornamental kale inner leaf reddening, which provided a basis for further dissecting the molecular mechanisms of leaf color characteristic change in ornamental kale at low temperatures.

The Flavonoid Biosynthesis and Regulation in Brassica napus: A Review

Brassica napus is an important crop for edible oil, vegetables, biofuel, and animal food. It is also an ornamental crop for its various petal colors. Flavonoids are a group of secondary metabolites with antioxidant activities and medicinal values, and are important to plant pigmentation, disease resistance, and abiotic stress responses. The yellow seed coat, purple leaf and inflorescence, and colorful petals of B. napus have been bred for improved nutritional value, tourism and city ornamentation. The putative loci and genes regulating flavonoid biosynthesis in B. napus have been identified using germplasms with various seed, petal, leaf, and stem colors, or different flavonoid contents under stress conditions. This review introduces the advances of flavonoid profiling, biosynthesis, and regulation during development and stress responses of B. napus, and hopes to help with the breeding of B. napus with better quality, ornamental value, and stress resistances.

Anthocyanins identification and transcriptional regulation of anthocyanin biosynthesis in purple Brassica napus

The main anthocyanin components were identified, and the transcriptional regulation pattern of anthocyanin related genes in leaves and stem bark was elucidated in a purple B. napus. Brassica napus is one of the most important oil crops planted worldwide, and developing varieties of dual-purpose for oil and vegetable is beneficial to improve economic benefits. Anthocyanins are a class of secondary metabolites that not only make plants present beautiful colors, but have a variety of important physiological functions and biological activities. Therefore, increasing the accumulation of anthocyanin in vegetative organs can improve vegetable value of rapeseed. However, anthocyanin enriched varieties in vegetative organs are rare, and there are few studies on category identification and accumulation mechanism of anthocyanin, which limits the utilization of anthocyanins in B. napus. In this study, 157 anthocyanin biosynthesis related genes (ABGs) were identified in B. napus genome by homology comparison and collinearity analysis of genes related to anthocyanin synthesis and regulation in Arabidopsis. Moreover, five anthocyanins were identified in the stem bark and leaves of the purple B. napus PR01 by high performance liquid chromatography-mass spectrometry (HPLC-MS), and the expression characteristics of ABGs in the leaves and stem bark of PR01 were analyzed and compared with the green cultivar ZS11 by RNA-Seq. Combining further weighted gene co-expression network analysis (WGCNA), the up-regulation of transcript factors BnaA07. PAP2 and BnaC06. PAP2 were identified as the key to the up-regulation of most of anthocyanin synthesis genes that promoted anthocyanin accumulation in PR01. This study is helpful to understand the transcriptional regulation of anthocyanin biosynthesis in B. napus and provides the theoretical basis for breeding novel varieties of dual-purpose for oil and vegetable.

Transcriptome and Metabolome Profiling to Explore the Causes of Purple Leaves Formation in Non-Heading Chinese Cabbage (Brassica rapa L. ssp. chinensis Makino var. mutliceps Hort.)

Purple non-heading Chinese cabbage is one of the most popular vegetables, and is rich in various health-beneficial anthocyanins. Research related to genes associated with anthocyanin biosynthesis in non-heading Chinese cabbage is important. This study performed integrative transcriptome and metabolome analysis in the purple non-heading Chinese cabbage wild type (WT) and its green mutant to elucidate the formation of purple leaves. The anthocyanin level was higher in purple than in green plants, while the contents of chlorophyll and carotenoid were higher in the green mutant than in the purple WT. Twenty-five anthocyanins were identified in purple and green cultivars; eleven anthocyanin metabolites were identified specifically in the purple plants. RNA-seq analysis indicated that 27 anthocyanin biosynthetic genes and 83 transcription factors were significantly differentially expressed between the WT and its mutant, most of them with higher expression in the purple than green non-heading Chinese cabbage. Transcriptome and metabolome analyses showed that UGT75C1 catalyzing the formation of pelargonidin-3,5-O-diglucoside and cyanidin-3,5-O-diglucoside may play a critical role in purple leaf formation in non-heading Chinese cabbage. Therefore, these results provide crucial information for elucidating the formation of purple leaves in non-heading Chinese cabbage.

Developing a bioinformatics pipeline for comparative protein classification analysis

BACKGROUND

Protein classification is a task of paramount importance in various fields of biology. Despite the great momentum of modern implementation of protein classification, machine learning techniques such as Random Forest and Neural Network could not always be used for several reasons: data collection, unbalanced classification or labelling of the data.As an alternative, I propose the use of a bioinformatics pipeline to search for and classify information from protein databases. Hence, to evaluate the efficiency and accuracy of the pipeline, I focused on the carotenoid biosynthetic genes and developed a filtering approach to retrieve orthologs clusters in two well-studied plants that belong to the Brassicaceae family: Arabidopsis thaliana and Brassica rapa Pekinensis group. The result obtained has been compared with previous studies on carotenoid biosynthetic genes in B. rapa where phylogenetic analysis was conducted.

RESULTS

The developed bioinformatics pipeline relies on commercial software and multiple databeses including the use of phylogeny, Gene Ontology terms (GOs) and Protein Families (Pfams) at a protein level. Furthermore, the phylogeny is coupled with "population analysis" to evaluate the potential orthologs. All the steps taken together give a final table of potential orthologs. The phylogenetic tree gives a result of 43 putative orthologs conserved in B. rapa Pekinensis group. Different A. thaliana proteins have more than one syntenic ortholog as also shown in a previous finding (Li et al., BMC Genomics 16(1):1-11, 2015).

CONCLUSIONS

This study demonstrates that, when the biological features of proteins of interest are not specific, I can rely on a computational approach in filtering steps for classification purposes. The comparison of the results obtained here for the carotenoid biosynthetic genes with previous research confirmed the accuracy of the developed pipeline which can therefore be applied for filtering different types of datasets.

Benzoic Acid, Chlorine Dioxide, and 1-Methylcyclopropene Induce Flavonoid Metabolic Shifts in Postharvest Flowering Chinese Cabbage Revealed by High-Dimensional Analytical Data

Flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee) is one of the most popular vegetables in China. However, the loss of the functional ingredients in postharvest flowering Chinese cabbage during storage is still serious, owing to the unclear causes of the metabolic shifts. Herein, benzoic acid, chlorine dioxide, and 1-methylcyclopropene (1-MCP) could maintain the quality of postharvest flowering Chinese cabbage, and 1-MCP showed the best effect. Furthermore, transcript-metabolite profiling of the treatments revealed a transcript-metabolite correlation network of the flavonoid biosynthesis pathways with a range of 3 to 3662 differentially expressed genes (DEGs) and a range of 23 to 37 differentially accumulated metabolites (DAMs). Surprisingly, 1-MCP had the best effect on shelf life among the treatments, although chlorine dioxide could stimulate the expression of four critical differential genes (Bra007142, Bra008792, Bra009358, and Bra027457) involved in delaying flavonoid degradation (hesperetin, chalcone, rutin, baicalein). As a result, our findings will help to improve our understanding of the regulation of flavonoid production in relation to the quality of postharvest flowering Chinese cabbage during storage.

Metabolic and RNA sequencing analysis of cauliflower curds with different types of pigmentation

Cauliflower (Brassica oleracea var. botrytis) is a popular vegetable worldwide due to its delicious taste, high nutritional value and anti-cancer properties. Cauliflower normally produces white curds, and natural spontaneous mutations lead to the production of orange, purple or green curds. However, some white cauliflowers show uneven purple pigmentation in their curds, which seriously affects the appearance quality and economic value of this crop. The underlying mechanism is still unclear. In this study, we performed comparative transcriptional and metabolic profiling analysis of light orange, white and purplish cauliflower curds. Metabolite analysis revealed that the pigments conferring purple colouration were delphinin and cyanin. Transcriptome analysis showed that the anthocyanin metabolism-related structural genes DFR, ANS and UGT and the transcription factor genes PAP2, TT8, GL3, EGL3 and TTG1 were upregulated in purplish versus white curds. These findings shed light on the formation of purplish curds, which could facilitate the breeding of purely white or red cauliflower.

The R3-Type MYB Transcription Factor BrMYBL2.1 Negatively Regulates Anthocyanin Biosynthesis in Chinese Cabbage (Brassica rapa L.) by Repressing MYB-bHLH-WD40 Complex Activity

Chinese cabbage (Brassica rapa L.) leaves are purple in color due to anthocyanin accumulation and have nutritional and aesthetic value, as well as antioxidant properties. Here, we identified the R3 MYB transcription factor BrMYBL2.1 as a key negative regulator of anthocyanin biosynthesis. A Chinese cabbage cultivar with green leaves harbored a functional BrMYBL2.1 protein, designated BrMYBL2.1-G, with transcriptional repressor activity of anthocyanin biosynthetic genes. By contrast, BrMYBL2.1 from a Chinese cabbage cultivar with purple leaves carried a poly(A) insertion in the third exon of the gene, resulting in the insertion of multiple lysine residues in the predicted protein, designated BrMYBL2.1-P. Although both BrMYBL2.1 variants localized to the nucleus, only BrMYBL2.1-G interacted with its cognate partner BrTT8. Transient infiltration assays in tobacco leaves revealed that BrMYBL2.1-G, but not BrMYBL2.1-P, actively represses pigment accumulation by inhibiting the transcription of anthocyanin biosynthetic genes. Transient promoter activation assay in Arabidopsis protoplasts verified that BrMYBL2.1-G, but not BrMYBL2.1-P, can repress transcriptional activation of BrCHS and BrDFR, which was activated by co-expression with BrPAP1 and BrTT8. We determined that BrMYBL2.1-P may be more prone to degradation than BrMYBL2.1-G via ubiquitination. Taken together, these results demonstrate that BrMYBL2.1-G blocks the activity of the MBW complex and thus represses anthocyanin biosynthesis, whereas the variant BrMYBL2.1-P from purple Chinese cabbage cannot, thus leading to higher anthocyanin accumulation.

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.

Functional Characterization of BrF3'H, Which Determines the Typical Flavonoid Profile of Purple Chinese Cabbage

Flavonols and anthocyanins are the two major classes of flavonoids in Brassica rapa. To elucidate the flavonoid biosynthetic pathway in Chinese cabbage (B. rapa L. subsp. pekinensis), we analyzed flavonoid contents in two varieties of Chinese cabbage with normal green (5546) and purple (8267) leaves. The 8267 variety accumulates significantly higher levels of quercetin, isorhamnetin, and cyanidin than the 5546 variety, indicating that 3'-dihydroxylated flavonoids are more prevalent in the purple than in the green variety. Gene expression analysis showed that the expression patterns of most phenylpropanoid pathway genes did not correspond to the flavonoid accumulation patterns in 5546 and 8267 varieties, except for BrPAL1.2 while most early and late flavonoid biosynthetic genes are highly expressed in 8267 variety. In particular, the flavanone 3'-hydroxylase BrF3'H (Bra009312) is expressed almost exclusively in 8267. We isolated the coding sequences of BrF3'H from the two varieties and found that both sequences encode identical amino acid sequences and are highly conserved with F3'H genes from other species. An in vitro enzymatic assay demonstrated that the recombinant BrF3'H protein catalyzes the 3'-hydroxylation of a wide range of 4'-hydroxylated flavonoid substrates. Kinetic analysis showed that kaempferol is the most preferred substrate and dihydrokaempferol (DHK) is the poorest substrate for recombinant BrF3'H among those tested. Transient expression of BrF3'H in Nicotiana benthamiana followed by infiltration of naringenin and DHK as substrates resulted in eriodictyol and quercetin production in the infiltrated leaves, demonstrating the functionality of BrF3'H in planta. As the first functional characterization of BrF3'H, our study provides insight into the molecular mechanism underlying purple coloration in Chinese cabbage.

Whole-Genome Identification and Comparative Expression Analysis of Anthocyanin Biosynthetic Genes in Brassica napus

Anthocyanins contribute to most colors of plants and play protective roles in response to abiotic stresses. Brassica napus is widely cultivated worldwide as both an oilseed and a vegetable. However, only several high anthocyanin-containing cultivars have been reported, and the mechanisms of anthocyanin accumulation have not been well-elucidated in B. napus. Here, the phenotype, comparative whole-genome identification, and gene expression analysis were performed to investigate the dynamic change of the anthocyanin content and the gene expression patterns of anthocyanin biosynthetic genes (ABGs) in B. napus. A total of 152 ABGs were identified in the B. napus reference genome. To screen out the critical genes involved in anthocyanin biosynthesis and accumulation, the RNA-seq of young leaves of two B. napus lines with purple leaves (PL) or green leaves (GL), and their F₁ progeny at 41, 91, and 101 days were performed to identify the differentially expressed genes. The comparative expression analysis of these ABGs indicated that the upregulation of TT8 together with its target genes (such as DFR, ANS, UFGT, and TT19) might promote the anthocyanin accumulation in PL at the early developmental stage (41–91 days). While the downregulation of those ABGs and anthocyanin degradation at the late developmental stage (91–101 days) might result in the decrease in anthocyanin accumulation. Our results would enhance the understanding of the regulatory network of anthocyanin dynamic accumulation in B. napus.

Natural variations of BrHISN2 provide a genetic basis for growth-flavour trade-off in different Brassica rapa subspecies

Selection for yield during B. rapa breeding may have unintended consequences for other traits, such as flavour. LYH-type (light yellow head) Chinese cabbage (Brassica rapa ssp. pekinensis) and wucai (Brassica rapa L. ssp. chinensis var. rosularis) varieties are becoming popular because of their unique flavour and yellow leaves. However, the molecular mechanism underlying the interplay for these traits remains unknown. We conducted a fine mapping and genome-wide exploration analysis of the leaf yellowing of LYH and wucai, including transgenic plants, to identify causal genes. We identified that BrHISN2, a rate-limiting enzyme in histidine biosynthesis, causes leaf yellowing by destroying LYH chloroplasts. Normal growing Brhisn2 mutant plants became etiolated and senesced at the cotyledon-seedling stage. Sequence variations in the promoter confers cold-dependent expression on BrHISN2, probably resulting in leaf yellowing in LYH and wucai. Insertions of two DRE cis elements and the subsequent recruitment of two CBF2 proteins by the DREs to the promoter provided the cold-induced expression plasticity of BrHISN2 in plants. Both LYH and wucai are farmed in the fall, in which the temperature gradually decreases, therefore the CBF2-BrHISN2 module probably maximises the benefits of gene-environment interaction for breeding. We determined the mechanistic connections of chlorophyll synthesis and the growth-flavour trade-off in these B. rapa varieties.

Optimization of combined microwave and hot air drying technology for purple cabbage by Response Surface Methodology (RSM)

Purple cabbage is one of the world's most widely consumed vegetables with high nutritional values containing the antioxidants and anti-inflammatory activity of anthocyanins, vitamins, and minerals. But due to rapid postharvest quality decay, novel processing techniques including drying are required. In order to determine the conditions of combined microwave and hot air drying for purple cabbage, factors affecting the drying process including microwave density, hot air temperature, and the dry base water content at conversion point were investigated using the anthocyanin content, DPPH antioxidant capacity, chewiness, △E, rehydration ratio, and average drying rate as responses. The combined drying conditions were optimized considering three independent variables at three different levels by response surface methodology. The results showed that the processing parameters of purple cabbage with combined microwave and hot air drying technology were microwave density at 2.5 W/g, moisture content of conversion point at 4.0 g/g, and hot air temperature at 55°C. Under these conditions, the anthocyanin content, DPPH antioxidant capacity, chewiness, △E, rehydration ratio, average drying rate, and overall score of the dried purple cabbage were 175.87 mg/100 g, 87.59%, 4,521.468 g, 26.5, 4.3, 0.76 g/min, and 0.785, respectively. Therefore, combined microwave and hot air drying technology is an effective, suitable method for drying purple cabbage.

Red-Fleshed Apple Anthocyanin Extracts Attenuate Male Reproductive System Dysfunction Caused by Busulfan in Mice

In this research, we analyzed the effect of an intragastrical oral administration of red-fleshed apple anthocyanin extract (RAAE) on busulfan-treated mice. First, we showed that the most abundant component in RAAE was cyanidin 3-O-galactoside. To determine the effect of the RAAE, the mice were divided into control and four other different concentrations of RAAE feeding treatment groups (BA0, no RAAE; BA.1, 0.1 mg/kg; BA1, 1 mg/kg; and BA5, 5 mg/kg) following busulfan injection. We observed that RAAE treatments displayed ameliorative effects on male reproductive system dysfunction caused by busulfan, such as recovering the irregular arrangements of seminiferous tubules, increasing the number of spermatogonia and spermatocytes, improving sperm concentration by 3-fold in BA.1, and improving sperm motility by 2-fold in BA1. The liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis showed significant up- or downregulation of certain metabolites, such as lysophosphatidylcholine (LysoPC), L-arginine, glycine, anandamide, and L-carnitine, which could contribute to the positive effects of RAAE, especially in PBA1 (plasma of BA1) and PBA5 (plasma of BA5). Taken together, the results indicate that 1 mg/kg of RAAE is a suitable concentration for rescuing spermatogenesis in mice. The research suggests that RAAE could be a potential nutraceutical for protecting spermatogenesis after busulfan therapy in cancer.

Transcriptome analysis reveals the mechanism of anthocyanidins biosynthesis during grains development in purple corn (Zea mays L.)

Anthocyanidins are important pigments that cause plant tissues to develop colors. They have attracted much attention due to their crucial regulatory roles in plant growth as well as their health benefits. In order to reveal the molecular mechanism of anthocyanidin synthesis and regulation in purple corn (Zea mays L.) in this study, purple corn 963 was used to compare differences in gene expression during three stages of grain development by transcriptome analysis. A total of 17,168 differentially expressed genes (DEGs) (7564 up-regulated and 9604 down-regulated DGEs) were identified. The DEGs were significantly enriched in "Phenylpropanoid biosynthesis", "Biosynthesis of secondary metabolites", and "Plant hormone signal transduction". In addition, 72 % of the structural genes that regulate anthocyanidin synthesis were up-regulated, and the transcription factors related to the accumulation of anthocyanidins were enriched during grain development. Moreover, the differential expression of phytohormone genes might also be an important factor in anthocyanidin accumulation. Transcriptomic analysis presents a molecular basis for the study of grain color changes in the three stages of grain development, and provides information for further research on the mechanism of anthocyanidin synthesis.

The dihydroflavonol 4-reductase BoDFR1 drives anthocyanin accumulation in pink-leaved ornamental kale

Overexpression and virus-induced gene silencing verified BoDFR1 conferred the anthocyanin accumulation in pink-leaved ornamental kale. Leaf color is an essential trait in the important horticultural biennial plant ornamental kale (Brassica oleracea var. acephala). The identity of the gene conferring this striking trait and its mode of inheritance are topics of debate. Based on an analysis of F₁, F₂, BC₁P₁, and BC₁P₂ ornamental kale populations derived from a cross between a pink-leaved P28 and white-leaved D10 line, we determined that the pink leaf trait is controlled by a semi-dominant gene. We cloned two genes potentially involved in anthocyanin biosynthesis in ornamental kale: Bo9g058630 and Bo6g100940. Based on their variation in sequence, we speculated that Bo9g058630, encoding the kale dihydroflavonol-4 reductase (BoDFR1) enzyme, plays a critical role in the development of the pink leaf trait. Indeed, an InDel marker specific for BoDFR1 completely co-segregated with the pink leaf trait in our F₂ population. We then generated the 35Spro: DFR-GUS overexpression vector, which we transformed into D10. Overexpression of BoDFR1 indeed restored some anthocyanin accumulation in this white-leaved parental line. In addition, we targeted BoDFR1 in P28 using virus-induced gene silencing. Again, silencing of BoDFR1 resulted in a substantial decrease in anthocyanin accumulation. This work lays the foundation for further exploration of the mechanism underlying anthocyanin accumulation in pink-leaved ornamental kale.

Dynamic Changes of the Anthocyanin Biosynthesis Mechanism During the Development of Heading Chinese Cabbage (Brassica rapa L.) and Arabidopsis Under the Control of BrMYB2

Chinese cabbage is an important vegetable mainly planted in Asian countries, and mining the molecular mechanism responsible for purple coloration in Brassica crops is fast becoming a research hotspot. In particular, the anthocyanin accumulation characteristic of purple heading Chinese cabbage, along with the plant's growth and head developing, is still largely unknown. To elucidate the dynamic anthocyanin biosynthesis mechanism of Chinese cabbage during its development processes, here we investigated the expression profiles of 86 anthocyanin biosynthesis genes and corresponding anthocyanin accumulation characteristics of plants as they grew and their heads developed, between purple heading Chinese cabbage 11S91 and its breeding parents. Anthocyanin accumulation of 11S91 increased from the early head formation period onward, whereas the purple trait donor 95T2-5 constantly accumulated anthocyanin throughout its whole plant development. Increasing expression levels of BrMYB2 and BrTT8 together with the downregulation of BrMYBL2.1, BrMYBL2.2, and BrLBD39.1 occurred in both 11S91 and 95T2-5 plants during their growth, accompanied by the significantly continuous upregulation of a phenylpropanoid metabolic gene, BrPAL3.1; a series of early biosynthesis genes, such as BrCHSs, BrCHIs, BrF3Hs, and BrF3'H; as well as some key late biosynthesis genes, such as BrDFR1, BrANS1, BrUF3GT2, BrUF5GT, Br5MAT, and Brp-Cout; in addition to the transport genes BrGST1 and BrGST2. Dynamic expression profiles of these upregulated genes correlated well with the total anthocyanin contents during the processes of plant growth and leaf head development, and results supported by similar evidence for structural genes were also found in the BrMYB2 transgenic Arabidopsis. After intersubspecific hybridization breeding, the purple interior heading leaves of 11S91 inherited the partial purple phenotypes from 95T2-5 while the phenotypes of seedlings and heads were mainly acquired from white 94S17; comparatively in expression patterns of investigated anthocyanin biosynthesis genes, cotyledons of 11S91 might inherit the majority of genetic information from the white type parent, whereas the growth seedlings and developing heading tissues of 11S91 featured expression patterns of these genes more similar to 95T2-5. This comprehensive set of results provides new evidence for a better understanding of the anthocyanin biosynthesis mechanism and future breeding of new purple Brassica vegetables.

Bok choy (Brassica rapa) grown in copper oxide nanoparticles-amended soils exhibits toxicity in a phenotype-dependent manner: Translocation, biodistribution and nutritional disturbance

The comparative toxicity of nano/bulk cupric oxide (CuO) and ionic copper (Cu) in Rosie and Green bok choy (Brassica rapa) varieties, with higher and lower anthocyanin contents, respectively, was investigated. Both phenotypes were cultivated for 70 days in natural soil amended with nano CuO (nCuO), bulk CuO (bCuO), and Cu chloride (CuCl₂) at 75, 150, 300, and 600 mg Cu/kg soil. Essential elements in tissues, agronomical parameters, chlorophyll content, and Cu distribution in leaf were determined. In both varieties, nCuO treatments significantly increased Cu uptake in roots, compared with bCuO and CuCl₂ (p ≤ 0.05). At all treatment concentrations, Rosie variety had more Cu than Green. More physiological impairments such as chlorophyll and leaf biomass reduction were observed in treated-Rosie varieties, compared to Green plants. The adverse effects were higher in nCuO-treated plants than their bCuO- or ionic Cu-exposed counterparts. Different distribution patterns of the translocated Cu in leaf midrib and parenchyma depended on particle size and plant phenotype, as demonstrated by two-photon microscopy. The different effects of CuO-based compounds in Rosie and Green varieties may be related to the anthocyanin content. These findings help to understand the factors involved in nanoparticles uptake and translocation to plant edible parts.

Study of the Relationship between Leaf Color Formation and Anthocyanin Metabolism among Different Purple Pakchoi Lines

Purple pakchoi (Brassica rapa ssp. Chinensis) is particularly appreciated due to its high edible quality and ornamental value, but there are few studies on the underlying mechanisms of leaf color formation. To comprehensively assess the differences in purple formation in pakchoi, four lines of pakchoi with different purple leaves were used in this experiment to determine the pigment content and to investigate the distribution and components of anthocyanin using LCMS (Liquid Chromatography Mass Spectrometry) and leaf cross-sections. Moreover, the expression levels of anthocyanin synthesis-related genes in four lines were calculated by qRT-PCR. The results showed that three new purple lines rich in anthocyanin and of high-quality were bred, and the anthocyanin were mainly distributed in both the upper epidermis and lower epidermis of leaves. Thirteen anthocyanin components were separated and identified, all the anthocyanins were acylated and glycosylated cyanidins; the main anthocyanins in purple pakchoi were a diacylated form of cyanidin 3-trans-(feruloyl)diglucoside-5-(malonyl)glucoside. Both the ratio of non-aromatic acylated cyanidin to aromatic acylated cyanidin and the ratio of anthocyanin content to chlorophyll content were responsible for the color formation in different purple pakchoi lines. When the ratio was high, the leaf appeared reddish purple, and when the ratio was low, the leaf appeared deep purple, even blackish purple. The expression level of BrF3H was significantly correlated with the content of anthocyanin through the correlation coefficient, which was speculated to be the main anthocyanin synthesis-related gene resulting in color differences among the four purple pakchoi lines. These results will enhance our understanding for the cultivation of new purple pakchoi varieties.

A review of the interaction between anthocyanins and proteins

Anthocyanins have good physiological functions, but they are unstable. The interaction between anthocyanins and proteins can improve the stability, nutritional and functional properties of the complex. This paper reviews the structural changes of complex of anthocyanins interacting with proteins from different sources. By circular dichroism (CD) spectroscopy, it was found that the contents of α-helix (from 15.90%-42.40% to 17.60%-52.80%) or β-sheet (from 29.00%-50.00% to 29.40%-57.00%) of the anthocyanins-proteins complex increased. Fourier transform infrared spectroscopy showed that the regions of amide I (from 1627.87-1641.41 cm^-1 to 1643.34-1651.02 cm^-1) and amide II (from 1537.00-1540.25 cm^-1 to 1539.00-1543.75 cm^-1) of anthocyanins-proteins complex were shifted. Fluorescence spectroscopy showed that the fluorescence intensity of the complex decreased from 150-5100 to 40-3900 a.u. The thermodynamic analysis showed that there were hydrophobic interactions, electrostatic and hydrogen bonding interactions between anthocyanins and proteins. The kinetic analysis showed that the half-life and activation energy of the complex increased. The stability, antioxidant, digestion, absorption, and emulsification of the complex were improved. This provides a reference for the study and application of anthocyanins and proteins interactions.

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

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

The novel gene BrMYB2, located on chromosome A07, with a short intron 1 controls the purple-head trait of Chinese cabbage (Brassica rapa L.)

Anthocyanins are important secondary metabolites in plants, but information on anthocyanin biosynthesis mechanisms in Chinese cabbage is limited. The new purple head Chinese cabbage cultivar 11S91 was analyzed, and an R2R3-MYB regulatory gene BrMYB2, located on chromosome A07, controlling the dominant purple-head trait was isolated. High expression of BrMYB2 generated a large accumulation of anthocyanins in 11S91, accompanied by highly upregulated BrTT8, BrF3'H, BrDFR1, BrANS1, BrUGTs, BrATs, and BrGSTs. 11S91 inherited the purple locus from purple trait donor 95T2-5, and they shared consensus CDSs and gDNAs with those of BrMYB2 (cBrMYB2 and gBrMYB2). Two SNPs in cBrMYB2 in 11S91 did not cause loss of function; in addition to several SNPs at both ends of intron 1, a large deletion had occurred in intron 1 of gBrMYB2 in 11S91. Genetic transformation of Arabidopsis showed that gBrMYB2 overexpression lines presented deeper purple color and higher expression than did the cBrMYB2 and cBrmyb2 lines, whereas gBrmyb2 with a long intron 1 did not cause the purple phenotype. We first show that BrMYB2 promotes anthocyanin biosynthesis under the control of the short intron 1 of gBrMYB2 in purple head Chinese cabbage, and gBrmyb2 with a long intron 1 represses anthocyanin production in white head Chinese cabbage. This evidence provides a new understanding of anthocyanin biosynthesis and purple germplasm generation in Brassica vegetables.

Red Chinese Cabbage Transcriptome Analysis Reveals Structural Genes and Multiple Transcription Factors Regulating Reddish Purple Color

Reddish purple Chinese cabbage (RPCC) is a popular variety of Brassica rapa (AA = 20). It is rich in anthocyanins, which have many health benefits. We detected novel anthocyanins including cyanidin 3-(feruloyl) diglucoside-5-(malonoyl) glucoside and pelargonidin 3-(caffeoyl) diglucoside-5-(malonoyl) glucoside in RPCC. Analyses of transcriptome data revealed 32,395 genes including 3345 differentially expressed genes (DEGs) between 3-week-old RPCC and green Chinese cabbage (GCC). The DEGs included 218 transcription factor (TF) genes and some functionally uncharacterized genes. Sixty DEGs identified from the transcriptome data were analyzed in 3-, 6- and 9-week old seedlings by RT-qPCR, and 35 of them had higher transcript levels in RPCC than in GCC. We detected cis-regulatory motifs of MYB, bHLH, WRKY, bZIP and AP2/ERF TFs in anthocyanin biosynthetic gene promoters. A network analysis revealed that MYB75, MYB90, and MYBL2 strongly interact with anthocyanin biosynthetic genes. Our results show that the late biosynthesis genes BrDFR, BrLDOX, BrUF3GT, BrUGT75c1-1, Br5MAT, BrAT-1,BrAT-2, BrTT19-1, and BrTT19-2 and the regulatory MYB genes BrMYB90, BrMYB75, and BrMYBL2-1 are highly expressed in RPCC, indicative of their important roles in anthocyanin biosynthesis, modification, and accumulation. Finally, we propose a model anthocyanin biosynthesis pathway that includes the unique anthocyanin pigments and genes specific to RPCC.

Low Temperature Promotes Anthocyanin Biosynthesis and Related Gene Expression in the Seedlings of Purple Head Chinese Cabbage (Brassica rapa L.)

To elucidate the effect of low temperature on anthocyanin biosynthesis in purple head Chinese cabbage, we analyzed anthocyanin accumulation and related gene expression in the seedlings of purple head Chinese cabbage, white head parent Chinese cabbage, and its purple male parent under a normal 25 °C temperature and a low 12 °C temperature. Anthocyanin accumulation in purple lines was strongly induced by low temperature, and the total anthocyanin content of seedlings was significantly enhanced. In addition, nearly all phenylpropanoid metabolic pathway genes (PMPGs) were down-regulated, some early biosynthesis genes (EBGs) were up-regulated, and nearly all late biosynthesis genes (LBGs) directly involved in anthocyanin biosynthesis showed higher expression levels in purple lines after low-temperature induction. Interestingly, a R2R3-MYB transcription factor (TF) gene 'BrMYB2' and a basic-helix-loop-helix (bHLH) regulatory gene 'BrTT8' were highly up-regulated in purple lines after low temperature induction, and two negative regulatory genes 'BrMYBL2.1' and 'BrLBD38.2' were up-regulated in the white line. BrMYB2 and BrTT8 may play important roles in co-activating the anthocyanin structural genes in purple head Chinese cabbage after low-temperature induction, whereas down-regulation of BrMYB2 and up-regulation of some negative regulators might be responsible for white head phenotype formation. Data presented here provide new understanding into the anthocyanin biosynthesis mechanism during low temperature exposure in Brassica crops.

Genomic Variance and Transcriptional Comparisons Reveal the Mechanisms of Leaf Color Affecting Palatability and Stressed Defense in Tea Plant

Leaves are one of the most important organs of plants, and yet, the association between leaf color and consumable traits remains largely unclear. Tea leaves are an ideal study system with which to investigate the mechanism of how leaf coloration affects palatability, since tea is made from the leaves of the crop Camellia sinensis. Our genomic resequencing analysis of a tea cultivar ZiJuan (ZJ) with purple leaves and altered flavor revealed genetic variants when compared with the green-leaf, wild type cultivar YunKang(YK). RNA-Seq based transcriptomic comparisons of the bud and two youngest leaves in ZJ and YK identified 93%, 9% and 5% expressed genes that were shared in YK- and ZJ-specific cultivars, respectively. A comparison of both transcript abundance and particular metabolites revealed that the high expression of gene UFGT for anthocyanin biosynthesis is responsible for purple coloration, which competes with the intermediates for catechin-like flavanol biosynthesis. Genes with differential expression are enriched in response to stress, heat and defense, and are casually correlated with the environmental stress of ZJ plant origin in the Himalayas. In addition, the highly expressed C4H and LDOX genes for synthesizing flavanol precursors, ZJ-specific CLH1 for degrading chlorophyll, alternatively spliced C4H and FDR and low photosynthesis also contributed to the altered color and flavor of ZJ. Thus, our study provides a better molecular understanding of the effect of purple coloration on leaf flavor, and helps to guide future engineering improvement of palatability.

Transcriptional regulation of anthocyanin biosynthesis in a high-anthocyanin resynthesized Brassica napus cultivar

BACKGROUND

Anthocyanins are plant secondary metabolites with key roles in attracting insect pollinators and protecting against biotic and abiotic stresses. They have potential health-promoting effects as part of the human diet. Anthocyanin biosynthesis has been elucidated in many species, enabling the development of anthocyanin-enriched fruits, vegetables, and grains; however, few studies have investigated Brassica napus anthocyanin biosynthesis.

RESULTS

We developed a high-anthocyanin resynthesized B. napus line, Rs035, by crossing anthocyanin-rich B. rapa (A genome) and B. oleracea (C genome) lines, followed by chromosome doubling. We identified and characterized 73 and 58 anthocyanin biosynthesis genes in silico in the A and C genomes, respectively; these genes showed syntenic relationships with 41 genes in Arabidopsis thaliana and B. napus. Among the syntenic genes, twelve biosynthetic and six regulatory genes showed transgressively higher expression in Rs035, and eight structural genes and one regulatory gene showed additive expression. We identified three early-, four late-biosynthesis pathways, three transcriptional regulator genes, and one transporter as putative candidates enhancing anthocyanin accumulation in Rs035. Principal component analysis and Pearson's correlation coefficients corroborated the contribution of these genes to anthocyanin accumulation.

CONCLUSIONS

Our study lays the foundation for producing high-anthocyanin B. napus cultivars. The resynthesized lines and the differentially expressed genes we have identified could be used to transfer the anthocyanin traits to other commercial rapeseed lines using molecular and conventional breeding.

Developmental Stage and Shape of Embryo Determine the Efficacy of Embryo Rescue in Introgressing Orange/Yellow Color and Anthocyanin Genes of Brassica Species

Vegetables in Brassica are some of the world's most commonly cultivated plants and have a wide range of consumable plant organs. Improvement of this group of vegetables is limited at the species level due to limited genetic variability. Interspecies hybridization could be a powerful alternate tool for broadening the genetic variability of target traits. Embryo rescue technique is necessarily practiced in interspecies hybridization for protecting embryos from premature abortion. However, its success depends on the age of ovaries, shape of embryos, and the effect of female genotype. In this study, we carried out a wide range of interspecies crossing for introgressing target traits (orange/yellow color in cabbage and anthocyanin in Chinese cabbage) and optimizing the appropriate age of ovaries, the shape of embryo, and the suitable genotypes of such crosses. We observed that 15 DAP (days after pollination) was the best for embryo rescue in the diploid-diploid (Brassica rapa × B. oleracea) crosses, while 20 DAP was optimum for amphidiploid-diploid (B. napus/B. juncea × B. rapa) crosses. Cotyledonary shape of embryos and genotypes of amphidiploid species were the best for successful plant regeneration in interspecies crosses. We successfully selected plants with desired orange/yellow inner leaves for cabbage and higher anthocyanin in Chinese cabbage. The results of this study have the potential to be applied for the efficient production of interspecific hybrids and to develop Brassica vegetables with new traits, which could have potential for the enrichment of the human diet.

Looking at Flavonoid Biodiversity in Horticultural Crops: A Colored Mine with Nutritional Benefits

Flavonoids represent a wide group of plant secondary metabolites implicated in many physiological roles, from the attraction of pollinators to the protection against biotic or abiotic stresses. Flavonoids are synthetized in a number of horticultural crops that are important components of our daily diet. In the last decades, the consumption of vegetables rich in antioxidants has been strongly promoted from the perspective of prevention/protection against chronic diseases. Therefore, due to their nutritional importance, several attempts have been made to enhance flavonoid levels in species of agronomic interest. In this review, we focus on the flavonoid biodiversity among the major horticultural species, which is responsible of differences among closely related species and influences the qualitative/quantitative composition. We also review the role of flavonoids in the nutritional quality of plant products, contributing to their organoleptic and nutritional properties, and the main strategies of biofortification to increase their content.

Roles of R2R3-MYB transcription factors in transcriptional regulation of anthocyanin biosynthesis in horticultural plants

This review contains functional roles of MYB transcription factors in the transcriptional regulation of anthocyanin biosynthesis in horticultural plants. This review describes potential uses of MYB TFs as tools for metabolic engineering for anthocyanin production. Anthocyanins (ranging from red to blue) are controlled by specific branches of the anthocyanin biosynthetic pathway and are mostly visible in ornamentals, fruits, and vegetables. In the present review, we describe which R2R3-MYB transcription factors (TFs) control the transcriptional regulation of anthocyanin structural genes involved in the specific branches of the anthocyanin biosynthetic pathway in various horticultural plants (e.g., ornamentals, fruits, and vegetables). In addition, some MYBs responsible for anthocyanin accumulation in specific tissues are described. Moreover, we highlight the phylogenetic relationships of the MYBs that suppress or promote anthocyanin synthesis in horticultural crops. Enhancement of anthocyanin synthesis via metabolic genetic engineering of anthocyanin MYBs, which is described in the review, is indicative of the potential use of the mentioned anthocyanin-related MYBs as tools for anthocyanin production. Therefore, the MYBs would be suitable for metabolic genetic engineering for improvement of flower colors, fruit quality, and vegetable nutrients.

Correlation Analysis of Phenolic Contents and Antioxidation in Yellow- and Black-Seeded Brassica napus

Brassica napus L. is rich in phenolic components and it has natural antioxidant characteristics which are important to human health. In the present study, the total phenolic and flavonoid contents of developing seeds of yellow- and black-seeded B. napus were compared. Both phenolic and flavonoid contents were significantly higher at 5 weeks after flowering (WAF) in black seeds (6.44 ± 0.97 mg EE/g phenolics and 3.78 ± 0.05 mg EE/g flavonoids) than yellow seeds (2.80 ± 0.13 mg/g phenolics and 0.83 ± 0.01 mg/g flavonoids). HPLC–DAD–ESI/MS analysis revealed different content of 56 phenolic components between yellow and black-seeded B. napus, including kaempferol-3-O-glucoside, isorhamnetin-3-O-glucoside, quercetin-3-O-sophoroside, procyanidin B2 ([DP 2]), which were significantly reduced in yellow seeds compared with black seeds. Applying the 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical assay, we found maximum clearance of DPPH and ABTS in the late developmental stages of yellow and black seeds. Additionally, the ferric reducing antioxidant power (FRAP) value maximized at 5 WAF in black seeds (432.52 ± 69.98 μmol Fe (II)/g DW) and 6 WAF in yellow seeds (274.08 ± 2.40 μmol Fe (II)/g DW). Generally, antioxidant ability was significantly reduced in yellow-seeded B. napus compared to black rapeseed, and positive correlations between antioxidation and flavonoid content were found in both yellow- and black-seeded B. napus.

Protection of Anthocyanin from Myrica rubra against Cerebral Ischemia-Reperfusion Injury via Modulation of the TLR4/NF-κB and NLRP3 Pathways

Myrica rubra (MR) is rich in anthocyanins, and it has good anti-cancer, anti-aging, antioxidant, and antiviral effects. The proportion of disability and death caused by ischemic stroke gradually increased, becoming a major disease that is harmful to human health. However, research on effects of anthocyanin from MR on cerebral ischemia-reperfusion (I/R) injury is rare. In this study, we prepared eight purified anthocyanin extracts (PAEs) from different types of MR, and examined the amounts of total anthocyanin (TA) and cyanidin-3-O-glucoside (C-3-G). After one week of PAE treatment, the cerebral infarction volume, disease damage, and contents of nitric oxide and malondialdehyde were reduced, while the level of superoxide dismutase was increased in I/R mice. Altogether, our results show that Boqi¹ MR contained the most TA (22.07%) and C-3-G (21.28%), and that PAE isolated from Dongkui MR can protect the brain from I/R injury in mice, with the mechanism possibly related to the Toll-like receptor 4 (TLR4)/ nuclear factor-κB (NF-κB) and NOD-like receptor pyrin domain-containing 3 protein (NLRP3) pathways.

Production of red-flowered oilseed rape via the ectopic expression of Orychophragmus violaceus OvPAP2

Oilseed rape (Brassica napus L.), which has yellow flowers, is both an important oil crop and a traditional tourism resource in China, whereas the Orychophragmus violaceus, which has purple flowers, likely possesses a candidate gene or genes to alter the flower colour of oilseed rape. A previously established B. napus line has a particular pair of O. violaceus chromosomes (M4) and exhibits slightly red petals. In this study, the transcriptomic analysis of M4, B. napus (H3), and O. violaceus with purple petals (OvP) and with white petals (OvW) revealed that most anthocyanin biosynthesis genes were up-regulated in both M4 and OvP. Read assembly and sequence alignment identified a homolog of AtPAP2 in M4, which produced the O. violaceus transcript (OvPAP2). The overexpression of OvPAP2 via the CaMV35S promoter in Arabidopsis thaliana led to different levels of anthocyanin accumulation in most organs, including the petals. However, the B. napus overexpression plants showed anthocyanin accumulation primarily in the anthers, but not the petals. However, when OvPAP2 was driven by the petal-specific promoter XY355, the transgenic B. napus plants produced red anthers and red petals. The results of metabolomic experiments showed that specific anthocyanins accumulated to high levels in the red petals. This study illustrates the feasibility of producing red-flowered oilseed rape, thereby enhancing its ornamental value, via the ectopic expression of the OvPAP2 gene. Moreover, the practical application of this study for insect pest management in the crop is discussed.

Health-Promoting Phytochemicals from 11 Mustard Cultivars at Baby Leaf and Mature Stages

Mustard is a Brassica vegetable that provides a number of phytonutrients. However, the phytonutrient profile of mustard has been relatively limited. We analyzed the glucosinolates and their hydrolysis products, carotenoids, total anthocyanin and phenolic contents, and antioxidant capacity of the leaves of 11 mustard cultivars grown in a greenhouse at the baby leaf and mature stages. An aliphatic glucosinolate sinigrin and its hydrolysis products allyl isothiocyanate and 1-cyano-2,3-epithiopropane were the major phytonutrients in the mustard leaves. Carotenoids β-carotene, lutein, violaxanthin, and neoxanthin were detected. We found phytonutrient concentration and their change with plant growth were cultivar-dependent. The %RDA value for vitamin A calculated using β-carotene content and retinol activity equivalents suggests that mustard cultivars used in this study can be a good source of vitamin A. Phenolic contents and antioxidant capacity also varied among cultivars and between physiological stages. Our results suggest that mustard leaves are rich in various phytochemicals and their composition depends on cultivar and the physiological stage. This is the first report on phytochemical composition in various mustard cultivars at different physiological stages.