Transcriptome Profiling Reveals Transcriptional Regulation by DNA Methyltransferase Inhibitor 5-Aza-2'-Deoxycytidine Enhancing Red Pigmentation in Bagged "Granny Smith" Apples (Malus domestica)

Decoding plant specialized metabolism: new mechanistic insights

Secondary metabolite (SM) production provides biotic and abiotic stress resistance and enables plants to adapt to the environment. Biosynthesis of these metabolites involves a complex interplay between transcription factors (TFs) and regulatory elements, with emerging evidence suggesting an integral role for chromatin dynamics. Here we review key TFs and epigenetic regulators that govern SM biosynthesis in different contexts. We summarize relevant emerging technologies and results from the model species arabidopsis (Arabidopsis thaliana) and outline aspects of regulation that may also function in food, feed, fiber, oil, or industrial crop plants. Finally, we highlight how effective translation of fundamental knowledge from model to non-model species can benefit understanding of SM production in a variety of ecological, agricultural, and pharmaceutical contexts.

DNA methylation regulates biosynthesis of tanshinones and phenolic acids during growth of Salvia miltiorrhiza

DNA methylation plays a crucial role in the regulation of plant growth and the biosynthesis of secondary metabolites. Danshen (Salvia miltiorrhiza) is a valuable Chinese herbal medicine commonly used to treat cardiovascular diseases; its active ingredients are tanshinones and phenolic acids, which primarily accumulate in roots. Here, we conducted a targeted metabolic analysis of S. miltiorrhiza roots at 3 distinct growth stages: 40 d old (r40), 60 d old (r60), and 90 d old (r90). The contents of tanshinones (cryptotanshinone, tanshinone I, tanshinone IIA, and rosmariquinone) and phenolic acids (rosmarinic acid and salvianolic acid B) gradually increased during plant development. Whole-genome bisulfite sequencing and transcriptome sequencing of roots at the 3 growth stages revealed an increased level of DNA methylation in the CHH context (H represents A, T, or C) context at r90 compared with r40 and r60. Increased DNA methylation levels were associated with elevated expression of various genes linked to epigenetic regulations, including CHROMOMETHYLASE2 (SmCMT2), Decrease in DNA Methylation 1 (SmDDM1), Argonaute 4 (SmAGO4), and DOMAINS REARRANGED METHYLTRANSFERASE 1 (SmDRM1). Moreover, expression levels of many genes involved in tanshinone and salvianolic acid biosynthesis, such as copalyldiphosphate synthase 5 (SmCPS5), cytochrome P450-related enzyme (SmCYP71D464), geranylgeranyl diphosphate synthase (SmGGPPS1), geranyl diphosphate synthase (SmGPPS), hydroxyphenylpyruvate reductase (SmHPPR), and hydroxyphenylpyruvate dioxygenase (SmHPPD), were altered owing to hyper-methylation, indicating that DNA methylation plays an important role in regulating tanshinone and phenolic acid accumulation. Our data shed light on the epigenetic regulation of root growth and the biosynthesis of active ingredients in S. miltiorrhiza, providing crucial clues for further improvement of active compound production via molecular breeding in S. miltiorrhiza.

Advances in DNA methylation and demethylation in medicinal plants: a review

DNA methylation and demethylation are widely acknowledged epigenetic phenomena which can cause heritable and phenotypic changes in functional genes without changing the DNA sequence. They can thus affect phenotype formation in medicinal plants. However, a comprehensive review of the literature summarizing current research trends in this field is lacking. Thus, this review aims to provide an up-to-date summary of current methods for the detection of 5-mC DNA methylation, identification and analysis of DNA methyltransferases and demethyltransferases, and regulation of DNA methylation in medicinal plants. The data showed that polyploidy and environmental changes can affect DNA methylation levels in medicinal plants. Changes in DNA methylation can thus regulate plant morphogenesis, growth and development, and formation of secondary metabolites. Future research is required to explore the mechanisms by which DNA methylation regulates the accumulation of secondary metabolites in medicinal plants.

Transcriptomic approach to uncover dynamic events in the development of mid-season sunburn in apple fruit

Apples grown in high heat, high light, and low humidity environments are at risk for sun injury disorders like sunburn and associated crop losses. Understanding the physiological and molecular mechanisms underlying sunburn will support improvement of mitigation strategies and breeding for more resilient varieties. Numerous studies have highlighted key biochemical processes involved in sun injury, such as the phenylpropanoid and reactive oxygen species (ROS) pathways, demonstrating both enzyme activities and expression of related genes in response to sunburn conditions. Most previous studies have focused on at-harvest activity of a small number of genes in response to heat stress. Thus, it remains unclear how stress events earlier in the season affect physiology and gene expression. Here, we applied heat stress to mid-season apples in the field and collected tissue along a time course-24, 48, and 72 h following a heat stimulus-to investigate dynamic gene expression changes using a transcriptomic lens. We found a relatively small number of differentially expressed genes (DEGs) and enriched functional terms in response to heat treatments. Only a few of these belonged to pathways previously described to be involved in sunburn, such as the AsA-GSH pathway, while most DEGs had not yet been implicated in sunburn or heat stress in pome fruit.

Azacytidine-induced hypomethylation delays senescence and coloration in harvested strawberries by stimulating antioxidant enzymes and modulating abscisate metabolism to minimize anthocyanin overproduction

DNA methylation is increasingly known to be essential for fruit ripening and senescence. Currently, 5-azacytidine (AZ) was selected as an effective demethylator and it successfully shaped the genomic hypomethylation in harvested strawberries. This was associated with the reprogramming of global gene expressions, which influenced downstream food traits. The alleviation of decay and softening, as well as the deceleration of soluble solid accumulation, were included. Coloration was also delayed as a result of the AZ-induced hypomethylation. Our examinations of anthocyanin biosynthesis and transport revealed that they were markedly minimized, which was probably involved with the decreased abscisate level and its weakened metabolism. Additionally, under AZ, the retarded postharvest senescence process was observed and it might be induced by the inhibited ROS accumulation accompanying the peroxidase and catalase activities alteration. Overall, these findings underlined the importance of methylation in strawberries and suggested the potential role of epigenetic regulators in the postharvest industry.

DNA methylation reprogramming provides insights into light-induced anthocyanin biosynthesis in red pear

DNA methylation, an epigenetic mark, is proposed to regulate plant anthocyanin biosynthesis. It well known that light induces anthocyanin accumulation, with bagging treatments commonly used to investigate light-controlled anthocyanin biosynthesis. We studied the DNA methylome landscape during pear skin coloration under various conditions (fruits re-exposed to sunlight after bag removal). The DNA methylation level in gene body/TE and its flanking sequence was generally similar between debagged and bagged treatments, however differentially methylated regions (DMRs) were re-modelled after light-exposure. Both DNA demethylase homologs and the RNA-directed DNA methylation (RdDM) pathways contributed to this re-distribution. A total of 310 DEGs were DMR-associated during light-induced anthocyanin biosynthesis between debagged and bagged treatments. The hypomethylated mCHH context was seen within the promoter of PyUFGT, together with other anthocyanin biosynthesis genes (PyPAL, PyDFR and PyANS). This enhanced transcriptional activation and promoted anthocyanin accumulation after light re-exposure. Unlike previous reports on bud sports, we did not detect DMRs within the MYB10 promoter. Instead, we observed the genome-wide re-distribution of methylation patterns, suggesting different mechanisms underlying methylation patterns of differentially accumulated anthocyanins caused by either bud mutation or environment change. We investigate the dynamic landscape of genome-scale DNA methylation, which is the combined effect of DNA demethylation and RdDM pathway, in the process of light-induced fruit colour formation in pear. This process is regulated by methylation changes on promoter regions of several DEGs. These results provide a DMR-associated DEGs set and new insight into the mechanism of DNA methylation involved in light-induced anthocyanin biosynthesis.

Integrative metabolome and transcriptome analyses reveals the black fruit coloring mechanism of Crataegus maximowiczii C. K. Schneid

Crataegus is an economically important plant due to its medicinal and health-promoting properties. Flavonoids are the main functional components of Crataegus fruit. Fruits of naturally pollinated Crataegus maximowiczii possess an extraordinary black skin and are rich in anthocyanins and other flavonoids. However, the composition of anthocyanins and the overall molecular mechanism of anthocyanin biosynthesis in C. maximowiczii fruits have not been fully elucidated. In this study, the metabolome and transcriptome of C. maximowiczii fruits with black and red skin were analyzed. The results revealed that the differential metabolites and genes were enriched in the anthocyanin biosynthesis pathways in C. maximowiczii fruits. In total, 52 differentially accumulated flavonoid metabolites, 12 differentially accumulated anthocyanins and 22 differentially expressed genes were identified. After weighted gene coexpression network analysis, two modules were found to be highly interrelated with the accumulation of anthocyanin components. The coexpression networks of these two modules were used to identify key candidate transcription factors associated with anthocyanin biosynthesis, such as MYB5, MYB113, bHLH60, ERF105, bZIP44, NAC082, and WRKY11. The results revealed that cyanidin-based anthocyanins were the main pigments responsible for the black coloration of C. maximowiczii fruits. Based on these differentially accumulated anthocyanins and key genes, genetic and metabolic regulatory networks of anthocyanin biosynthesis were also proposed. Overall, this study elucidates the molecular basis of the formation of black color in C. maximowiczii fruits, and provides an intensive study on anthocyanin biosynthesis in C. maximowiczii for comprehensive utilization.

Methylation level of potato gene OMT30376 regulates tuber anthocyanin transformations

After anthocyanin synthesis, a variety of anthocyanin compounds are produced through further methylation, glycosylation, and acylation. However, the effect of the potato methylase gene on anthocyanin biosynthesis has not been reported. Red and purple mutation types appear in tubers of the potato cultivar 'Purple Viking' with chimeric skin phenotypes. In this study, transcriptome and anthocyanin metabolome analyses were performed on skin of Purple Viking tubers and associated mutants. According to the metabolome analysis, the transformation of delphinidin into malvidin-3-O-glucoside and petunidin 3-O-glucoside and that of cyanidin into rosinidin O-hexoside and peonidin-3-O-glucoside were hindered in red tubers. Expression of methyltransferase gene OMT30376 was significantly lower in red tubers than in purple ones, whereas the methylation level of OMT30376 was significantly higher in red tubers. In addition, red skin appeared in tubers from purple tuber plants treated with S-adenosylmethionine (SAM), indicating the difference between purple and red was caused by the methylation degree of the gene OMT30376. Thus, the results of the study suggest that the OMT30376 gene is involved in the transformation of anthocyanins in potato tubers. The results also provide an important reference to reveal the regulatory mechanisms of anthocyanin biosynthesis and transformation.

Azacytidine arrests ripening in cultivated strawberry (Fragaria × ananassa) by repressing key genes and altering hormone contents

BACKGROUND

Strawberry ripening involves a number of irreversible biochemical reactions that cause sensory changes through accumulation of sugars, acids and other compounds responsible for fruit color and flavor. The process, which is strongly dependent on methylation marks in other fruits such as tomatoes and oranges, is highly controlled and coordinated in strawberry.

RESULTS

Repeated injections of the hypomethylating compound 5-azacytidine (AZA) into green and unripe Fragaria × ananassa receptacles fully arrested the ripening of the fruit. The process, however, was reversible since treated fruit parts reached full maturity within a few days after AZA treatment was stopped. Transcriptomic analyses showed that key genes responsible for the biosynthesis of anthocyanins, phenylpropanoids, and hormones such as abscisic acid (ABA) were affected by the AZA treatment. In fact, AZA downregulated genes associated with ABA biosynthetic genes but upregulated genes associated with its degradation. AZA treatment additionally downregulated a number of essential transcription factors associated with the regulation and control of ripening. Metabolic analyses revealed a marked imbalance in hormone levels, with treated parts accumulating auxins, gibberellins and ABA degradation products, as well as metabolites associated with unripe fruits.

CONCLUSIONS

AZA completely halted strawberry ripening by altering the hormone balance, and the expression of genes involves in hormone biosynthesis and degradation processes. These results contradict those previously obtained in other climacteric and fleshly fruits, where AZA led to premature ripening. In any case, our results suggests that the strawberry ripening process is governed by methylation marks.

Effect of Paper-Bagging on Apple Skin Patterning Associated with MdMYB10 Promoter Methylation

Paper-bagging is an efficient method to maximize apple skin color, but a relationship between this technique and fruit skin patterning has not been demonstrated. Here, the ‘Fuji’ fruit with red-striped skin changed to red-blushed skin under re-exposure to light after bag treatment. Higher expression of MdMYB10, a transcription factor that regulates anthocyanin biosynthesis in apples, correlated with increased anthocyanin concentration in bag removal fruit. At the mature stage, a comparison of methylation status in the MdMYB10 promoter revealed that the methylation level in the region from −2585 to −2117 bp was reduced in bag removal fruit, especially for CHG context. It can be regulated by the downregulated expression of DNA methyltransferases such as MdMET, MdCMT, and MdDRM. Our results suggest that the bag removal treatment in this cultivar causes a change in skin patterning from striped to blushed pigmentation by inducing DNA demethylation of MdMYB10.

A Data Driven Approach to Assess Complex Colour Profiles in Plant Tissues

The ability to quantify the colour of fruit is extremely important for a number of applied fields including plant breeding, postharvest assessment, and consumer quality assessment. Fruit and other plant organs display highly complex colour patterning. This complexity makes it challenging to compare and contrast colours in an accurate and time efficient manner. Multiple methodologies exist that attempt to digitally quantify colour in complex images but these either require a priori knowledge to assign colours to a particular bin, or fit the colours present within segment of the colour space into a single colour value using a thresholding approach. A major drawback of these methodologies is that, through the process of averaging, they tend to synthetically generate values that may not exist within the context of the original image. As such, to date there are no published methodologies that assess colour patterning using a data driven approach. In this study we present a methodology to acquire and process digital images of biological samples that contain complex colour gradients. The CIE (Commission Internationale de l'Eclairage/International Commission on Illumination) ΔE2000 formula was used to determine the perceptually unique colours (PUC) within images of fruit containing complex colour gradients. This process, on average, resulted in a 98% reduction in colour values from the number of unique colours (UC) in the original image. This data driven procedure summarised the colour data values while maintaining a linear relationship with the normalised colour complexity contained in the total image. A weighted ΔE2000 distance metric was used to generate a distance matrix and facilitated clustering of summarised colour data. Clustering showed that our data driven methodology has the ability to group these complex images into their respective binomial families while maintaining the ability to detect subtle colour differences. This methodology was also able to differentiate closely related images. We provide a high quality set of complex biological images that span the visual spectrum that can be used in future colorimetric research to benchmark colourimetric method development.

PpMYB36 Encodes a MYB-Type Transcription Factor That Is Involved in Russet Skin Coloration in Pear (Pyrus pyrifolia)

Fruit color is one of the most important external qualities of pear (Pyrus pyrifolia) fruits. However, the mechanisms that control russet skin coloration in pear have not been well characterized. Here, we explored the molecular mechanisms that determine the russet skin trait in pear using the F₁ population derived from a cross between russet skin ('Niitaka') and non-russet skin ('Dangshansu') cultivars. Pigment measurements indicated that the lignin content in the skin of the russet pear fruits was greater than that in the non-russet pear skin. Genetic analysis revealed that the phenotype of the russet skin pear is associated with an allele of the PpRus gene. Using bulked segregant analysis combined with the genome sequencing (BSA-seq), we identified two simple sequence repeat (SSR) marker loci linked with the russet-colored skin trait in pear. Linkage analysis showed that the PpRus locus maps to the scaffold NW_008988489.1: 53297-211921 on chromosome 8 in the pear genome. In the mapped region, the expression level of LOC103929640 was significantly increased in the russet skin pear and showed a correlation with the increase of lignin content during the ripening period. Genotyping results demonstrated that LOC103929640 encoding the transcription factor MYB36 is the causal gene for the russet skin trait in pear. Particularly, a W-box insertion at the PpMYB36 promoter of russet skin pears is essential for PpMYB36-mediated regulation of lignin accumulation and russet coloration in pear. Overall, these results show that PpMYB36 is involved in the regulation of russet skin trait in pear.

The R2R3-type MYB transcription factor MdMYB90-like is responsible for the enhanced skin color of an apple bud sport mutant

The anthocyanin content in apple skin determines its red coloration, as seen in a Fuji apple mutant. Comparative RNA-seq analysis was performed to determine differentially expressed genes at different fruit development stages between the wild-type and the skin color mutant. A novel R2R3-MYB transcription factor, MdMYB90-like, was uncovered as the key regulatory gene for enhanced coloration in the mutant. The expression of MdMYB90-like was 21.3 times higher in the mutant. MdMYB90-like regulates anthocyanin biosynthesis directly through the activation of anthocyanin biosynthesis genes and indirectly through the activation of other transcription factors that activate anthocyanin biosynthesis. MdMYB90-like bound to the promoters of both structural genes (MdCHS and MdUFGT) and other transcription factor genes (MdMYB1 and MdbHLH3) in the yeast one-hybrid system, electrophoretic mobility shift assay, and dual-luciferase assay. Transgenic analysis showed that MdMYB90-like was localized in the nucleus, and its overexpression induced the expression of other anthocyanin-related genes, including MdCHS, MdCHI, MdANS, MdUFGT, MdbHLH3, and MdMYB1. The mutant had reduced levels of DNA methylation in two regions (-1183 to -988 and -2018 to -1778) of the MdMYB90-like gene promoter, which might explain the enhanced expression of the gene and the increased anthocyanin content in the mutant apple skin.

Skin Color in Apple Fruit (Malus × domestica): Genetic and Epigenetic Insights

Apple skin color is an important trait for organoleptic quality. In fact, it has a major influence on consumer choice. Skin color is, thus, one of the most important criteria taken into account by breeders. For apples, most novel varieties are so-called "mutants" or "sports" that have been identified in clonal populations. Indeed, many "sports" exist that show distinct phenotypic differences compared to the varieties from which they originated. These differences affect a limited number of traits of economic importance, including skin color. Until recently, the detailed genetic or epigenetic changes resulting in heritable phenotypic changes in sports was largely unknown. Recent technological advances and the availability of several high-quality apple genomes now provide the bases to understand the exact nature of the underlying molecular changes that are responsible for the observed phenotypic changes observed in sports. The present review investigates the molecular nature of sports affected in apple skin color giving arguments in favor of the genetic or epigenetic explanatory models.

DNA demethylation is involved in the regulation of temperature-dependent anthocyanin accumulation in peach

Anthocyanin biosynthesis is induced by low temperatures in a number of plants. However, in peach (cv Zhonghuashoutao), anthocyanin accumulation was observed in fruit stored at 16°C but not at or below 12°C. Fruit stored at 16°C showed elevated transcript levels of genes encoding anthocyanin biosynthetic enzymes, the transport protein glutathione S-transferase and key transcription factors. Higher transcript levels of PpPAL1/2, PpC4H, Pp4CL4/5/8, PpF3H, PpF3'H, PpDFR1/2/3 and PpANS, as well as transcription factor gene PpbHLH3, were associated with lower methylation levels in the promoter of these genes. The DNA methylation level was further highly correlated with the expression of the DNA methyltransferase genes and DNA demethylase genes. The application of DNA methylation inhibitor 5-azacytidine induced anthocyanin accumulation in peach flesh, further implicating a critical role for DNA demethylation in regulating anthocyanin accumulation in peach flesh. Our data reveal that temperature-dependent DNA demethylation is a key factor to the post-harvest temperature-dependent anthocyanin accumulation in peach flesh.

Comparative Proteomic Analysis by iTRAQ Reveals that Plastid Pigment Metabolism Contributes to Leaf Color Changes in Tobacco (Nicotiana tabacum) during Curing

Tobacco (Nicotiana tabacum), is a world's major non-food agricultural crop widely cultivated for its economic value. Among several color change associated biological processes, plastid pigment metabolism is of trivial importance in postharvest plant organs during curing and storage. However, the molecular mechanisms involved in carotenoid and chlorophyll metabolism, as well as color change in tobacco leaves during curing, need further elaboration. Here, proteomic analysis at different curing stages (0 h, 48 h, 72 h) was performed in tobacco cv. Bi'na1 with an aim to investigate the molecular mechanisms of pigment metabolism in tobacco leaves as revealed by the iTRAQ proteomic approach. Our results displayed significant differences in leaf color parameters and ultrastructural fingerprints that indicate an acceleration of chloroplast disintegration and promotion of pigment degradation in tobacco leaves due to curing. In total, 5931 proteins were identified, of which 923 (450 up-regulated, 452 down-regulated, and 21 common) differentially expressed proteins (DEPs) were obtained from tobacco leaves. To elucidate the molecular mechanisms of pigment metabolism and color change, 19 DEPs involved in carotenoid metabolism and 12 DEPs related to chlorophyll metabolism were screened. The results exhibited the complex regulation of DEPs in carotenoid metabolism, a negative regulation in chlorophyll biosynthesis, and a positive regulation in chlorophyll breakdown, which delayed the degradation of xanthophylls and accelerated the breakdown of chlorophylls, promoting the formation of yellow color during curing. Particularly, the up-regulation of the chlorophyllase-1-like isoform X2 was the key protein regulatory mechanism responsible for chlorophyll metabolism and color change. The expression pattern of 8 genes was consistent with the iTRAQ data. These results not only provide new insights into pigment metabolism and color change underlying the postharvest physiological regulatory networks in plants, but also a broader perspective, which prompts us to pay attention to further screen key proteins in tobacco leaves during curing.

Transcriptome analysis of the molecular mechanism of Chrysanthemum flower color change under short-day photoperiods

Chrysanthemum [Dendranthema morifolium Tzvel.] is an ornamental plant grown under long-term artificial cultivation conditions. In production, early Chrysanthemum blossoms are often promoted by artificial short-day treatment. However, we found that the flower colour of Chrysanthemum blossoms induced by artificial short-day treatment was lighter than those induced by the natural photoperiod. To explore the intrinsic mechanism of colour fading in flowers, we performed full-length transcriptome sequencing of Chrysanthemum morifolium cv. 'Jinbeidahong' using single-molecule real-time sequencing and RNA-sequencing under natural daylight (ND) and short daylight (SD) conditions. The clustered transcriptome sequences were assigned to various databases, such as NCBI, Swiss-Prot, Gene Ontology and so on. The comparative results of digital gene expression analysis revealed that there were differentially expressed transcripts (DETs) in the four stages under ND and SD conditions. In addition, the expression patterns of anthocyanin biosynthesis structural genes were verified by quantitative real-time PCR. The major regulators of the light signalling ELONGATED HYPOCOTYL5 genes were markedly upregulated under ND conditions. The patterns of anthocyanin accumulation were consistent with the expression patterns of CHI1 and 3GT1. The results showed that the anthocyanin synthesis is tightly regulated by the photoperiod, which will be useful for molecular breeding of Chrysanthemum.

Transcriptome profiling of anthocyanin biosynthesis in the peel of 'Granny Smith' apples (Malus domestica) after bag removal

Background

Bagging is commonly used to enhance red pigmentation and thereby improve fruit quality of apples (Malus domestica). The green-skinned apple cultivar ‘Granny Smith’ develops red pigmentation after bagging removal, but the signal transduction pathways mediating light-induced anthocyanin accumulation in apple peel are yet to be defined. The aim of this study was to identify the mechanisms underpinning red pigmentation in ‘Granny Smith’ after bag removal based on transcriptome sequencing.

Results

The anthocyanin content in apple peel increased considerably after bag removal, while only trace amounts of anthocyanins were present in the peel of unbagged and bagged fruits. RNA sequencing identified 18,152 differentially expressed genes (DEGs) among unbagged, bagged, and bag-removed fruits at 0, 4, and 10 days after bag removal. The DEGs were implicated in light signal perception and transduction, plant hormone signal transduction, and antioxidant systems. Weighted gene co-expression network analysis of DEGs generated a module of 23 genes highly correlated with anthocyanin content. The deletion of − 2026 to − 1870 bp and − 1062 to − 964 bp regions of the MdMYB1 (LOC103444202) promoter induced a significant decrease in glucuronidase activity and anthocyanin accumulation in apple peel.

Conclusions

Bagging treatment can induce red pigmentation in ‘Granny Smith’ via altering the expression patterns of genes involved in crucial signal transduction and biochemical metabolic pathways. The − 2026 to − 1870 bp and − 1062 to − 964 bp regions of the MdMYB1 promoter are essential for MdMYB1-mediated regulation of anthocyanin accumulation in the ‘Granny Smith’ apple cultivar. The findings presented here provide insight into the mechanisms of coloration in the peel of ‘Granny Smith’ and other non-red apple cultivars.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5730-1) contains supplementary material, which is available to authorized users.