Increased accumulation of anthocyanins in Fragaria chiloensis fruits by transient suppression of FcMYB1 gene

Mutation in FvPAL2 leads to light red strawberry fruits and yellow-green petioles

In recent years, light red or white strawberries have attracted much attention because of their unusual color, however, the mechanism of strawberry color formation, especially light red strawberry color, is not well understood. By EMS mutagenesis of woodland strawberry (Fragaria vesca), we identified two mutants, rg40 and rg120, with light red fruit and yellow-green petiole, and allelic hybridization and BSA mixed-pool sequencing revealed that the phenotype was caused by mutation in the FvPAL2 protein in the anthocyanin synthesis pathway. Enzyme activity experiments showed that the mutant FvPAL2 protein barely catalyzed the substrate conversion normally, thus blocking anthocyanin synthesis, which in turn led to a decrease in anthocyanin accumulation in fruits and petioles. Analysis of the active pockets of the wild-type and mutant FvPAL2 proteins revealed that the mutant FvPAL2 could not bind to the substrate properly. The specific transcription factors FvMYB10 and FvMYB10L were further found to bind and activate the expression of FvPAL1 and FvPAL2 in both fruit and petiole. The discovery of the key site of FvPAL2 protein activity provides a clear modification target for the breeding of light red strawberry varieties, which has important application value.

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

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

Unraveling the Anthocyanin Regulatory Mechanisms of White Mutation in Verbena stricta by Integrative Transcriptome and Metabolome Analysis

Background: Verbena stricta is a perennial herb of the Verbenaceae family, known for its medicinal properties, wide adaptability, and high resistance. Methods: This research investigated the metabolic pathways of flower color change by combining transcriptome and metabolomics analyses. Results: In purple flowers and white variants, a total of 118 differentially accumulated metabolites (DAMs), including 20 anthocyanins, and 7627 differentially expressed genes (DEGs) were found. The downregulation of delphinidin-3-O-galactoside, delphinidin-3-O-glucoside, and delphinidin-3-O-(6″-O-p-coumaroyl) glucoside, along with the absence of petunidin and malvidin derivatives, may explain the loss of pigmentation in the white-flower mutant. Fourteen candidate genes involved in anthocyanin biosynthesis were identified, among which the expression of Flavonoid 3', 5'-hydroxylase (F3'5'H) was significantly downregulated, notably limiting flux through the delphinidin pathway and reducing delphinidin accumulation. This limitation in upstream reactions, coupled with the multi-shunt process in downstream reactions, completely blocked the production of petunidin and malvidin. Conclusions: These findings offer new opinions on the anthocyanin metabolites and key genes responsible for the floral pigmentation in V. stricta. Additionally, the white variant provides a valuable platform for future research into the ornamental flower color of the Verbenaceae family.

Characterization of FchAGL9 and FchSHP, two MADS-boxes related to softening of Fragaria chiloensis fruit

Fragaria chiloensis is a Chilean native species that softens intensively during its ripening. Its softening is related to cell wall disassembly due to the participation of cell wall degrading enzymes. Softening of F. chiloensis fruit can be accelerated by ABA treatment which is accompanied by the increment in the expression of key cell wall degrading genes, however the molecular machinery involved in the transcriptional regulation has not been studied until now. Therefore, the participation of two MADS-box transcription factors belonging to different subfamilies, FchAGL9 and FchSHP, was addressed. Both TFs are members of type-II MADS-box family (MIKC-type) and localized in the nucleus. FchAGL9 and FchSHP are expressed only in flower and fruit tissues, rising as the fruit softens with the highest expression level at C3-C4 stages. EMSA assays demonstrated that FchAGL9 binds to CArG sequences of RIN and SQM, meanwhile FchSHP interacts only with RIN. Bimolecular fluorescence complementation and yeast two-hybrid assays confirmed FchAGL9-FchAGL9 and FchAGL9-FchSHP interactions. Hetero-dimer structure was built through homology modeling concluding that FchSHP monomer binds to DNA. Functional validation by Luciferase-dual assays indicated that FchAGL9 transactivates FchRGL and FchPG's promoters, meanwhile FchSHP transactivates those of FchEXP2, FchRGL and FchPG. Over-expression of FchAGL9 in C2 F. chiloensis fruit rises FchEXP2 and FchEXP5 transcripts, meanwhile the over-expression of FchSHP also increments FchXTH1 and FchPL; in both cases there is a down-regulation of FchRGL and FchPG. In summary, we provided evidence of FchAGL9 and FchSHP participating in the transcription regulation associated to F. chiloensis's softening.

Loss-of-function mutation in anthocyanidin reductase activates the anthocyanin synthesis pathway in strawberry

Fruit color substantially affects consumer preferences, with darker red strawberries being economically more valuable due to their higher anthocyanin content. However, the molecular basis for the dark red coloration remains unclear. Through screening of an ethyl methanesulfonate mutant library, we identified a rg418 mutant, that demonstrated anthocyanin accumulation during early fruit development stages. Furthermore, the ripening fruits of this mutant had higher anthocyanin content than wild-type (WT) fruits. An analysis of flavonoid content in WT and rg418 mutant fruits revealed substantial changes in metabolic fluxes, with the mutant exhibiting increased levels of anthocyanins and flavonols and decreased levels of proanthocyanidins. Bulked sergeant analysis sequencing indicated that the mutant gene was anthocyanidin reductase (ANR), a key gene in the proanthocyanidin synthesis pathway. Furthermore, transcriptome sequencing revealed the increased expression of MYB105 during the early development stage of mutant fruits, which promoted the expression of UFGT (UDP-glucose flavonoid 3-O-glucosyltransferase), a key gene involved in anthocyanin synthesis, thus substantially enhancing the anthocyanin content in the mutant fruits. Additionally, mutating ANR in a white-fruited strawberry variant (myb10 mutant) resulted in appealing pink-colored fruits, suggesting the diverse roles of ANR in fruit color regulation. Our study provides valuable theoretical insights for improving strawberry fruit color.

Unveiling the mysteries of HvANS: a study on anthocyanin biosynthesis in qingke (hordeum vulgare L. var. Nudum hook. f.) seeds

BACKGROUND

Based on our previous research, a full-length cDNA sequence of HvANS gene was isolated from purple and white Qingke. The open reading frame (ORF) in the purple variety Nierumuzha was 1320 base pairs (bp), encoding 439 amino acids, while the ORF in the white variety Kunlun 10 was 1197 bp, encoding 398 amino acids. A nonsynonymous mutation was found at the position of 1195 bp (T/C) in the coding sequence (CDS) of the HvANS gene. We carried out a series of studies to further clarify the relationship between the HvANS gene and anthocyanin synthesis in Qingke.

RESULTS

The conservative structural domain prediction results showed that the encoded protein belonged to the PLN03178 superfamily. Multiple comparisons showed that this protein had the highest homology with Hordeum vulgare, at 88.61%. The approximately 2000 bp promoter sequence of the HvANS gene was identical in both varieties. The real-time fluorescence PCR (qRT-PCR) results revealed that HvANS expression was either absent or very low in the roots, stems, leaves, and awns of Nierumuzha. In contrast, the HvANS expression was high in the seed coats and seeds of Nierumuzha. Likewise, in Kunlun 10, HvANS expression was either absent or very low, indicating a tissue-specific and variety-specific pattern for HvANS expression. The subcellular localization results indicated that HvANS was in the cell membrane. Metabolomic results indicated that the HvANS gene is closely related to the synthesis of three anthocyanin substances (Idaein chloride, Kinetin 9-riboside, and Cyanidin O-syringic acid). Yeast single hybridization experiments showed that the HvANS promoter interacted with HvANT1, which is the key anthocyanin regulatory protein. In a yeast two-hybrid experiment, we obtained two significantly different proteins (ZWY2020 and POMGNT2-like) and verified the results by qRT-PCR.

CONCLUSIONS

These results provide a basis for further studies on the regulatory mechanism of HvANS in the synthesis of anthocyanins in Qingke purple grains.

Image analysis and polyphenol profiling unveil red-flesh apple phenotype complexity

BACKGROUND

The genetic basis of colour development in red-flesh apples (Malus domestica Borkh) has been widely characterised; however, current models do not explain the observed variations in red pigmentation intensity and distribution. Available methods to evaluate the red-flesh trait rely on the estimation of an average overall colour using a discrete class notation index. However, colour variations among red-flesh cultivars are continuous while development of red colour is non-homogeneous and genotype-dependent. A robust estimation of red-flesh colour intensity and distribution is essential to fully capture the diversity among genotypes and provide a basis to enable identification of loci influencing the red-flesh trait.

RESULTS

In this study, we developed a multivariable approach to evaluate the red-flesh trait in apple. This method was implemented to study the phenotypic diversity in a segregating hybrid F1 family (91 genotypes). We developed a Python pipeline based on image and colour analysis to quantitatively dissect the red-flesh pigmentation from RGB (Red Green Blue) images and compared the efficiency of RGB and CIEL*a*b* colour spaces in discriminating genotypes previously classified with a visual notation. Chemical destructive methods, including targeted-metabolite analysis using ultra-high performance liquid chromatography with ultraviolet detection (UPLC-UV), were performed to quantify major phenolic compounds in fruits' flesh, as well as pH and water contents. Multivariate analyses were performed to study covariations of biochemical factors in relation to colour expression in CIEL*a*b* colour space. Our results indicate that anthocyanin, flavonol and flavanol concentrations, as well as pH, are closely related to flesh pigmentation in apple.

CONCLUSTION

Extraction of colour descriptors combined to chemical analyses helped in discriminating genotypes in relation to their flesh colour. These results suggest that the red-flesh trait in apple is a complex trait associated with several biochemical factors.

The R2R3-MYB Transcriptional Repressor TgMYB4 Negatively Regulates Anthocyanin Biosynthesis in Tulips (Tulipa gesneriana L.)

Anthocyanins play a paramount role in color variation and significantly contribute to the economic value of ornamental plants. The conserved activation complex MYB-bHLH-WD40 (MBW; MYB: v-myb avian myeloblastosis viral oncogene homolog; bHLH: basic helix-loop-helix protein; WD40:WD-repeat protein) involved in anthocyanin biosynthesis has been thoroughly researched, but there have been limited investigations into the function of repressor factors. In this study, we characterized TgMYB4, an R2R3-MYB transcriptional repressor which is highly expressed during petal coloration in red petal cultivars. TgMYB4-overexpressing tobaccos exhibited white or light pink petals with less anthocyanin accumulation compared to control plants. TgMYB4 was found to inhibit the transcription of ANTHOCYANIDIN SYNTHASE (TfANS1) and DIHYDRO-FLAVONOL-4-REDUCTASE (AtDFR), although it did not bind to their promoters. Moreover, the TgMYB4 protein was able to compete with the MYB activator to bind to the :bHLHprotein, thereby suppressing the function of the activator MBW complex. These findings demonstrate that TgMYB4 plays a suppressive role in the regulation of anthocyanin synthesis during flower pigmentation.

Deciphering the genetic architecture of fruit color in strawberry

Fruits of Fragaria species usually have an appealing bright red color due to the accumulation of anthocyanins, water-soluble flavonoid pigments. Octoploid cultivated strawberry (Fragaria × ananassa) is a major horticultural crop for which fruit color and associated nutritional value are main breeding targets. Great diversity in fruit color intensity and pattern is observed not only in cultivated strawberry but also in wild relatives such as its octoploid progenitor F. chiloensis or the diploid woodland strawberry F. vesca, a model for fruit species in the Rosaceae. This review examines our understanding of fruit color formation in strawberry and how ongoing developments will advance it. Natural variations of fruit color as well as color changes during fruit development or in response to several cues have been used to explore the anthocyanin biosynthetic pathway and its regulation. So far, the successful identification of causal genetic variants has been largely driven by the availability of high-throughput genotyping tools and high-quality reference genomes of F. vesca and F. × ananassa. The current completion of haplotype-resolved genomes of F. × ananassa combined with QTL mapping will accelerate the exploitation of the untapped genetic diversity of fruit color and help translate the findings into strawberry improvement.

Molecular bases of strawberry fruit quality traits: Advances, challenges, and opportunities

The strawberry is one of the world's most popular fruits, providing humans with vitamins, fibers, and antioxidants. Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid and highly heterozygous, making it a challenge for breeding, quantitative trait locus (QTL) mapping, and gene discovery. Some wild strawberry relatives, such as Fragaria vesca, have diploid genomes and are becoming laboratory models for the cultivated strawberry. Recent advances in genome sequencing and CRISPR-mediated genome editing have greatly improved the understanding of various aspects of strawberry growth and development in both cultivated and wild strawberries. This review focuses on fruit quality traits that are most relevant to the consumers, including fruit aroma, sweetness, color, firmness, and shape. Recently available phased-haplotype genomes, single nucleotide polymorphism (SNP) arrays, extensive fruit transcriptomes, and other big data have made it possible to locate key genomic regions or pinpoint specific genes that underlie volatile synthesis, anthocyanin accumulation for fruit color, and sweetness intensity or perception. These new advances will greatly facilitate marker-assisted breeding, the introgression of missing genes into modern varieties, and precise genome editing of selected genes and pathways. Strawberries are poised to benefit from these recent advances, providing consumers with fruit that is tastier, longer-lasting, healthier, and more beautiful.

Identification of key genes responsible for green and white colored spathes in Anthurium andraeanum (Hort.)

Modern anthuriums, Anthurium andraeanum (Hort.) are among the most popular flowering plants and widely used for interior decoration. Their popularity is largely attributed to the exotic spathes with different colors. Previous studies have reported color development in red spathe cultivars, but limited information is available on key genes regulating white and green colored spathes. This study analyzed anthocyanin, chlorophyll, and carotenoid contents as well as transcript differences in spathes of eight cultivars that differed in spathe colors ranging from red to white and green. Results showed that increased expression of a transcription factor AaMYB2 was associated with elevated levels of anthocyanin in spathes, but decreased expression of AaMYB2 and increased expression of AaLAR (leucoanthocyanidin reductase) and AaANR (anthocyanidin reductase) were accompanied with the accumulation of colorless proanthocyanidin, thus the white spathe. As to the green colored spathe, chlorophyll content in the green spathe cultivar was substantially higher than the other cultivars. Correspondingly, transcripts of chlorophyll biosynthesis-related genes AaHemB (porphobilinogen synthase) and AaPor (protochlorophyllide oxidoreductase) were highly upregulated but almost undetectable in white and red spathes. The increased expression of AaHemB and AaPor was correlated with the expression of transcription factor AaMYB124. Subsequently, qRT-PCR analysis confirmed their expression levels in nine additional cultivars with red, white, and green spathes. A working model for the formation of white and green spathes was proposed. White colored spathes are likely due to the decreased expression of AaMYB2 which results in increased expression of AaLAR and AaANR, and the green spathes are attributed to AaMYB124 enhanced expression of AaHemB and AaPor. Further research is warranted to test this working model.

Physicochemical Quality, Polyphenol Profiles, and Postharvest Performance of Florida Pearl® 'FL 16.78-109' White Strawberries Compared to the Red Cultivar 'Florida Brilliance'

White-fruited strawberry cultivars have recently become popular due to their exotic appearance and flavor, but more needs to be known about their overall quality and postharvest performance. The objective of this study was to characterize and compare the overall quality of the white-fruited strawberry Florida Pearl® 'FL 16.78-109' against the commercial, red-fruited strawberry 'Florida Brilliance' at harvest and during cold storage (1 °C). Results showed that harvest date and weather conditions contributed to significant differences in fruit quality, regardless of the cultivar. However, Pearl was softer at harvest and had lower total phenolic and anthocyanin contents but was less acidic and had higher total sugars and ascorbic acid contents than Brilliance. Pearl major polyphenols were kaempferol 3-glucoside, quercetin 3-glucoside, quercetin, and gallic acid, while for Brilliance epicatechin, pelargonidin, pelargonidin 3-glucoside, and ferulic acid were the major polyphenol compounds identified. After cold storage, Pearl lost less weight than Brilliance and showed a less dramatic decline in individual polyphenols. Pearl and Brilliance anthocyanins and phenolic acids were the polyphenol groups most affected by cold storage because they showed the highest decline from harvest to the end of storage. Cold storage also had different effects on other polyphenols, but the effect was cultivar-dependent. Overall, white strawberries have a unique appearance, are sweet, have an excellent bioactive profile, and can maintain good postharvest quality.

Insight into the Molecular Mechanism of Flower Color Regulation in Rhododendron latoucheae Franch: A Multi-Omics Approach

Rhododendron latoucheae Franch. (R. latoucheae) is a valuable woody plant known for its high ornamental value. While purple flowers are a distinct and attractive variant phenotype of R. latoucheae, the underlying mechanism regulating its flower color is still poorly understood. To investigate the molecular regulatory mechanism responsible for the variation in flower color, we selected plants with white-pink and purple petals as the object and conducted analyses of metabolites, key genes, and transcription factors associated with flower color. A combined metabolome-transcriptome analysis was performed, and the expression of key genes was subsequently verified through qRT-PCR experiments. The results of our study demonstrated a significant enrichment of differential metabolites in the flavonoid metabolic pathway. Changes in anthocyanin content followed the same trend as the observed flower color variations, specifically showing significant correlations with the contents of malvidin-3-O-glucoside, dihydromyricetin, gallocatechin, and peonidin-3-O-glucoside. Furthermore, we identified three key structural genes (F3GT1, LAR, ANR) and four transcription factors (bHLH130, bHLH41, bHLH123, MYB4) that are potentially associated with the biosynthesis of flavonoid compounds, thereby influencing the appearance of purple flower color in R. latoucheae.

FaMYB5 Interacts with FaBBX24 to Regulate Anthocyanin and Proanthocyanidin Biosynthesis in Strawberry (Fragaria × ananassa)

MYB and BBX transcription factors play important roles in flavonoid biosynthesis. Here, we obtained transgenic woodland strawberry with stable overexpression of FaMYB5, demonstrating that FaMYB5 can increase anthocyanin and proanthocyanidin content in roots, stems and leaves of woodland strawberry. In addition, bimolecular fluorescence complementation assays and yeast two-hybridization demonstrated that the N-terminal (1-99aa) of FaBBX24 interacts with FaMYB5. Transient co-expression of FaBBX24 and FaMYB5 in cultivated strawberry 'Xiaobai' showed that co-expression strongly promoted the expression of F3'H, 4CL-2, TT12, AHA10 and ANR and then increased the content of anthocyanin and proanthocyanidin in strawberry fruits. We also determined that FaBBX24 is also a positive regulator of anthocyanin and proanthocyanidin biosynthesis in strawberry. The results reveal a novel mechanism by which the FaMYB5-FaBBX24 module collaboratively regulates anthocyanin and proanthocyanidin in strawberry fruit.

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

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

Regulation of flavonoids in strawberry fruits by FaMYB5/FaMYB10 dominated MYB-bHLH-WD40 ternary complexes

Anthocyanins endowing strawberry fruit red color are regulated by the MYB-bHLH-WD40 complex. By analyzing the MYBs involved in the flavonoid biosynthesis in strawberry, we found that R2R3-FaMYB5 promoted the content of anthocyanin and proanthocyanidins in strawberry fruits. Yeast two-hybrid and BiFC assays confirmed that MBW complexes connected with flavonoid metabolism were FaMYB5/FaMYB10-FaEGL3 (bHLH)-FaLWD1/FaLWD1-like (WD40). Transient overexpression and qRT-PCR analysis revealed that disparate MBW models hold different patterns in the regulation of flavonoid biosynthesis in strawberry fruits. Compared with FaMYB10, FaMYB5 and its dominant complexes showed a more specific regulatory range on strawberry flavonoid biosynthetic pathway, while FaMYB10 was more extensive. In addition, the complexes involved in FaMYB5 facilitated PAs accumulation primarily through the LAR tributary while FaMYB10 mainly by the ANR branch. FaMYB9 and FaMYB11 tremendously elicited the accumulation of proanthocyanidins by up-regulating the expression levels of both LAR and ANR, and also affected anthocyanin metabolism by changing the ratio of Cy3G and Pg3G which were constituted as two major anthocyanin monomers in strawberries. Our study also illustrated that FaMYB5-FaEGL3-FaLWD1-like directly targeted the promoters of F3'H, LAR, and AHA10 thus committing to flavonoid accumulation. These results allow the specific members involved in the MBW complex to be deciphered and provide new insights into the regulatory mechanisms of anthocyanins and proanthocyanidins regulated by the MBW complex.

Visualization of Sugar Content Distribution of White Strawberry by Near-Infrared Hyperspectral Imaging

In this study, an approach to visualize the spatial distribution of sugar content in white strawberry fruit flesh using near-infrared hyperspectral imaging (NIR-HSI; 913-2166 nm) is developed. NIR-HSI data collected from 180 samples of "Tochigi iW1 go" white strawberries are investigated. In order to recognize the pixels corresponding to the flesh and achene on the surface of the strawberries, principal component analysis (PCA) and image processing are conducted after smoothing and standard normal variate (SNV) pretreatment of the data. Explanatory partial least squares regression (PLSR) analysis is performed to develop an appropriate model to predict Brix reference values. The PLSR model constructed from the raw spectra extracted from the flesh region of interest yields high prediction accuracy with an RMSEP and R2p values of 0.576 and 0.841, respectively, and with a relatively low number of PLS factors. The Brix heatmap images and violin plots for each sample exhibit characteristics feature of sugar content distribution in the flesh of the strawberries. These findings offer insights into the feasibility of designing a noncontact system to monitor the quality of white strawberries.

Proanthocyanidins Delay Fruit Coloring and Softening by Repressing Related Gene Expression during Strawberry (Fragaria × ananassa Duch.) Ripening

Proanthocyanidins (PAs), also known as condensed tannins, are widespread throughout the plant kingdom, presenting diverse biological and biochemical activities. Being one of the most abundant groups of natural polyphenolic antioxidant, PAs are applied to improve plant tolerance to (a)biotic stresses and delay the senescence of fruit by scavenging the reactive oxygen species (ROS) and enhancing antioxidant responses. The effects of PAs on coloring and softening of strawberries (Fragaria × ananassa Duch.), a worldwide demanded edible fruit and typical material for studying non-climacteric fruit ripening, were firstly assessed in this work. The results showed that exogenous PAs delayed the decrease in fruit firmness and anthocyanins accumulation but improved the fruit skin brightness. Strawberries treated with PAs had similar total soluble solids, total phenolics, and total flavonoids, but lower titratable acidity content. Moreover, the contents of endogenous PAs, abscisic acid and sucrose, were somehow increased by PA treatment, while no obvious change was found in fructose and glucose content. In addition, the anthocyanin- and firmness-related genes were significantly repressed, while the PA biosynthetic gene (anthocyanin reductase, ANR) was highly up-regulated by PA treatment at the key point for fruit softening and coloring. In summary, the results presented in this study suggest that PAs slow down strawberry coloration and softening by inhibiting the expression of related genes, which could be helpful for a better understanding of the biological role of PAs and provide a new strategy to regulate strawberry ripening.

Anthocyanin metabolism in Nelumbo: translational and post-translational regulation control transcription

BACKGROUND

Lotus (Nelumbo Adans.) is used as an herbal medicine and the flowers are a source of natural flavonoids. 'Da Sajin', which was firstly found in the plateau area, is a natural mutant in flower color with red streamers dyeing around white petals.

RESULTS

The LC-MS-MS results showed that eight anthocyanin compounds, including cyanidin 3-O-glucoside, cyanidin 3-O-galactoside, malvidin 3-O-galactoside, and malvidin 3-O-glucoside, were differentially enriched in red-pigmented tissues of the petals, whereas most of these metabolites were undetected in white tissues of the petals. Transcriptome profiling indicated that the relative high expression levels of structural genes, such as NnPAL, NnF3H, and NnANS, was inconsistent with the low anthocyanin concentration in white tissues. Members of the NnMYB and NnbHLH transcription factor families were presumed to play a role in the metabolic flux in the anthocyanin and proanthocyanidin biosynthetic pathway. The expression model of translational initiation factor, ribosomal proteins and SKP1-CUL1-F-box protein complex related genes suggested an important role for translational and post-translational network in anthocyanin biosynthesis. In addition, pathway analysis indicated that light reaction or photo destruction might be an important external cause for floral color determination in lotus.

CONCLUSIONS

In this study, it is supposed that the natural lotus mutant 'Da Sajin' may have originated from a red-flowered ancestor. Partial loss of anthocyanin pigments in petals may result from metabolic disorder caused by light destruction. This disorder is mainly regulated at post translation and translation level, resulting in a non-inherited phenotype. These results contribute to an improved understanding of anthocyanin metabolism in lotus, and indicate that the translational and post-translational regulatory network determines the metabolic flux of anthocyanins and proanthocyanidins under specific environmental conditions.

Interplay between R2R3 MYB-type activators and repressors regulates proanthocyanidin biosynthesis in banana (Musa acuminata)

Proanthocyanidins are oligomeric flavonoids that promote plant disease resistance and benefit human health. Banana is one of the world's most extensively farmed crops and its fruit pulp contain proanthocyanidins. However, the transcriptional regulatory network that fine tunes proanthocyanidin biosynthesis in banana remains poorly understood. We characterised two proanthocyanidin-specific R2R3 MYB activators (MaMYBPA1-MaMYBPA2) and four repressors (MaMYBPR1-MaMYBPR4) to elucidate the mechanisms underlying the transcriptional regulation of proanthocyanidin biosynthesis in banana. Heterologous expression of MaMYBPA1 and MaMYBPA2 partially complemented the Arabidopsis thaliana proanthocyanidin-deficient transparent testa2 mutant. MaMYBPA1 and MaMYBPA2 interacted physically with MaMYCs to transactivate anthocyanin synthase, leucoanthocyanidin reductase, and anthocyanidin reductase genes in vitro and form functional MYB-bHLH-WD Repeat (MBW) complexes with MaTTG1 to transactivate these promoters in vivo. Overexpression of MaMYBPAs alone or with MaMYC in banana fruits induced proanthocyanidin accumulation and transcription of proanthocyanidin biosynthesis-related genes. MaMYBPR repressors are also shown to interact with MaMYCs forming repressing MBW complexes, and diminished proanthocyanidin accumulation. Interestingly overexpression of MaMYBPA induces the expression of MaMYBPR, indicating an agile regulation of proanthocyanidin biosynthesis through the formation of competitive MBW complexes. Our results reveal regulatory modules of R2R3 MYB- that fine tune proanthocyanidin biosynthesis and offer possible targets for genetic manipulation for nutritional improvement of banana.

Insights into transcription factors controlling strawberry fruit development and ripening

Fruit ripening is a highly regulated and complex process involving a series of physiological and biochemical changes aiming to maximize fruit organoleptic traits to attract herbivores, maximizing therefore seed dispersal. Furthermore, this process is of key importance for fruit quality and therefore consumer acceptance. In fleshy fruits, ripening involves an alteration in color, in the content of sugars, organic acids and secondary metabolites, such as volatile compounds, which influence flavor and aroma, and the remodeling of cell walls, resulting in the softening of the fruit. The mechanisms underlying these processes rely on the action of phytohormones, transcription factors and epigenetic modifications. Strawberry fruit is considered a model of non-climacteric species, as its ripening is mainly controlled by abscisic acid. Besides the role of phytohormones in the regulation of strawberry fruit ripening, a number of transcription factors have been identified as important regulators of these processes to date. In this review, we present a comprehensive overview of the current knowledge on the role of transcription factors in the regulation of strawberry fruit ripening, as well as in compiling candidate regulators that might play an important role but that have not been functionally studied to date.

RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit

Fragaria chiloensis (Chilean strawberry) is a native species that produces fruit with an exotic pinkish color and a fruity aroma. It has a non-climacteric pattern of fruit ripening, and it is the mother of the commercial Fragaria x ananassa. The ripening of F. chiloensis fruit seems stimulated by ABA, and a complete set of genes participate in its softening, color, and aroma development. In addition, a set of transcription factors regulate the entire process, but few of them have been described. Over the last two decades, RNA-seq was used to identify genes at three fruit development/ripening stages, named C2 (unripe, large green) to C4 (full ripe), in whole fruit and fruit without achenes. A total of 204,754 contigs were assembled considering all samples, obtaining an N50 of 1.125 bp. Differentially expressed genes (DEGs) between two samples were identified, obtaining a total of 77,181 DEGs. Transcripts for genes involved in ABA biosynthesis present high and differential expression during the C2, C3, and C4 stages. Besides, contigs corresponding to ABA receptors, which interact with a regulatory network, are also differentially expressed. Genes associated with cell wall remodeling and those involved in flavonoid synthesis were also differentially expressed. An interaction network was built considering differentially expressed genes for the phenylpropanoid and flavonoid molecular pathways and having FcMYB1 as a transcription factor regulator. Identifying key genes could give an option to control the ripening of this non-climacteric fruit.

Transcriptome-wide N6-methyladenosine (m6A) methylation in soybean under Meloidogyne incognita infection

N6-methyladenosine (m6A) is a reversible epigenetic modification of mRNA and other RNAs that plays a significant role in regulating gene expression and biological processes. However, m6A abundance, dynamics, and transcriptional regulatory mechanisms remain unexplored in the context of soybean resistance to Meloidogyne incognita. In this study, we performed a comparative analysis of transcriptome-wide m6A and metabolome profiles of soybean root tissues with and without M. incognita infection. Global m6A hypermethylation was widely induced in response to M. incognita infection and was enriched around the 3' end of coding sequences and in 3' UTR regions. There were 2069 significantly modified m6A sites, 594 differentially expressed genes, and 103 differentially accumulated metabolites between infected and uninfected roots, including coumestrol, psoralidin, and 2-hydroxyethylphosphonate. Among 101 m6A-modified DEGs, 34 genes were hypomethylated and upregulated, and 39 genes were hypermethylated and downregulated, indicating a highly negative correlation between m6A methylation and gene transcript abundance. A number of these m6A-modified DEGs, including WRKY70, ERF60, POD47 and LRR receptor-like serine/threonine-protein kinases, were involved in plant defense responses. Our study provides new insights into the critical role of m6A modification in early soybean responses to M. incognita.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-022-00077-2.

Comparative transcriptome analysis of purple-fleshed sweet potato and its yellow-fleshed mutant provides insight into the transcription factors involved in anthocyanin biosynthesis in tuberous root

In various plant species, many transcription factors (TFs), such as MYB, bHLH, and WD40, have been identified as regulators of anthocyanin biosynthesis in underground organs. However, the regulatory elements of anthocyanin biosynthesis in the tuberous roots of sweet potato have not been elucidated yet. Here, we selected the purple-fleshed sweet potato cultivar "Zhezi1" (ZZ ^P ) and its spontaneous yellow-fleshed mutant "Xinli" (XL ^Y ) to investigate the regulatory mechanism of the anthocyanin biosynthesis in the tuberous roots of sweet potato. By analyzing the IbMYB1 genotype in ZZ ^P and XL ^Y , we found that the IbMYB1-2, a MYB TF involved in anthocyanin biosynthesis, was missing in the XL ^Y genome, which might lead to an extreme decrease in anthocyanins in XL ^Y . A comparative transcriptome analysis of ZZ ^P and XL ^Y was conducted to find the TFs involved in anthocyanin biosynthesis in ZZ ^P and XL ^Y . The anthocyanin structural genes were significantly enriched among the differentially expressed genes. Moreover, one MYB activator (IbMYB1), one bHLH (IbbHLH2), three WRKY activator candidates (IbWRKY21, IbWRKY24, and IbWRKY44), and two MYB repressors (IbMYB27 and IbMYBx-ZZ) were highly expressed in ZZ ^P accompanied with anthocyanin structural genes. We also tested the expression of these TFs in six purple- and two orange-fleshed sweet potato cultivars. Interestingly, most of these TFs were significantly positively correlated with anthocyanin contents in these cultivars. The function of the anthocyanin biosynthesis repression of IbMYB27 and IbMYBx-ZZ was verified through transient co-transformation with IbMYB1 into tobacco leaves. Further functional verification of the above TFs was conducted by Y2H, BiFC, and dual-luciferase assays. These tests showed that the MYB-bHLH-WD40/MYB-bHLH-WD40-WRKY complex activated the promoter of anthocyanin structural gene IbDFR and promoters for IbWRKY44, IbMYB27, and IbMYBx-ZZ, indicating reinforcement and feedback regulation to maintain the level of anthocyanin accumulation in the tuberous roots of purple-fleshed sweet potato. These results may provide new insights into the regulatory mechanism of anthocyanin biosynthesis and accumulation in underground organs of sweet potatoes.

Evaluation of reference genes for transcript normalization in Fragaria chiloensis fruit and vegetative tissues

Quantitative real-time PCR (RT-qPCR) is used extensively in gene expression studies. For adequate comparisons, the identification and use of reliable reference genes are crucial. Nevertheless, the availability of such genes in strawberry species is limited and has yet to be described for the Chilean strawberry, Fragaria chiloensis. In this study, the expression dynamics of a set of 10 candidate reference genes were analyzed in various F. chiloensis vegetative tissues (root, runners, stem, leaf, and flower), and fruits at different ripening stages or subjected to different hormonal treatments (ABA, auxin). The expression stability of candidate genes was examined by a series of algorithms, such as geNorm, NormFinder, BestKeeper, and ΔCt, for comparisons and rankings. Finally, by using RefFinder, a comprehensive and comparative ranking of the four methods was achieved. The results highlight that the expression stability of candidate reference genes fluctuates depending on tissue type, fruit stage, and hormonal treatment. As reference genes, the use of FcCHP2 and FcACTIN1 is recommended for F. chiloensis vegetative tissues; FcDBP and FcCHP1 for fruit ripening stages; FcGAPDH and FcDBP for fruit subjected to ABA and NDGA treatments; FcCHP1 and FcCHP2 for fruit under AUXIN and TIBA treatments; and FcDBP and FcCHP2 when all fruit stages and hormonal treatments are compared. If just one reference gene is employed as a normalizer, FcDBP should be chosen as it is the most stable internal control in most conditions. Therefore, the present study delivers a set of reliable reference genes for RT-qPCR expression analysis in F. chiloensis tissues and fruits subjected to several hormonal treatments.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01227-y.

Molecular Cloning and Functional Analysis of DXS and FPS Genes from Zanthoxylum bungeanum Maxim

Zanthoxylum bungeanum Maxim. (Z. bungeanum) has attracted attention for its rich aroma. The aroma of Z. bungeanum is mainly volatile terpenes synthesized by plant terpene metabolic pathways. However, there is little information on Z. bungeanum terpene metabolic gene. In this study, the coding sequence of 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and farnesyl pyrophosphate synthase (FPS) were cloned from Z. bungeanum cv. 'Fengxiandahongpao.' ZbDXS and ZbFPS genes from Z. bungeanum with CDS lengths of 2172 bp and 1029 bp, respectively. The bioinformatics results showed that Z. bungeanum was closely related to citrus, and it was deduced that ZbFPS were hydrophilic proteins without the transmembrane domain. Subcellular localization prediction indicated that ZbDXS was most likely to be located in chloroplasts, and ZbFPS was most likely to be in mitochondria. Meanwhile, the 3D protein structure showed that ZbDXS and ZbFPS were mainly composed of α-helices, which were folded into a single domain. In vitro enzyme activity experiments showed that purified proteins ZbDXS and ZbFPS had the functions of DXS enzyme and FPS enzyme. Transient expression of ZbDXS and ZbFPS in tobacco significantly increased tobacco's terpene content. Moreover, ZbDXS and ZbFPS were expressed in different tissues of Z. bungeanum, and the relative expression of the two genes was the highest in fruits. Therefore, this suggests that ZbDXS and ZbFPS are positively related to terpene synthesis. This study could provide reference genes for improving Z. bungeanum breeding as well as for the Rutaceae research.

The yellowhorn AGL transcription factor gene XsAGL22 contributes to ABA biosynthesis and drought tolerance in poplar

Regulation of abscisic acid (ABA) biosynthesis helps plants adapt to drought stress, but the underlying molecular mechanisms are largely unclear. Here, a drought-induced transcription factor XsAGL22 was isolated from yellowhorn (Xanthoceras sorbifolium Bunge). Yeast one-hybrid and electrophoretic mobility shift assays indicated that XsAGL22 can physically bind to the promoters of the ABA biosynthesis-related genes XsNCED6 and XsBG1, and a dual-luciferase assay showed that XsAGL22 activates the promoters of the later two genes. Transient overexpression of XsAGL22 in yellowhorn leaves also increased the expression of XsNCED6 and XsBG1 and increased cellular ABA levels. Finally, heterologous overexpression of XsAGL22 in poplar increased ABA content, reduced stomatal aperture and increased drought resistance. Our results suggest that XsAGL22 is a powerful regulator of ABA biosynthesis and plays a critical role in drought resistance in plants.

Metabolomic and transcriptomic analyses reveal the effects of self- and hetero-grafting on anthocyanin biosynthesis in grapevine

Grafting, which joins a scion from a cultivar with the stem of a rootstock from a grapevine wild relative, is commonly used in viticulture. Grafting has crucial effects on various phenotypes of the cultivar, including its phenology, biotic and abiotic resistance, berry metabolome, and coloration, but the underlying genetics and regulatory mechanisms are largely unexplored. In this study, we investigated the phenotypic, metabolomic, and transcriptomic profiles at three developmental stages (45, 75, and 105 days after flowering) of the Crimson Seedless cultivar (Vitis vinifera) grafted onto four rootstocks (three heterografts, CS/101-14, CS/SO4, and CS/110R and one self-graft, CS/CS) with own-rooted graft-free Crimson Seedless (CS) as the control. All the heterografts had a significant effect on berry reddening as early as ~45 days after flowering. The grafting of rootstocks promoted anthocyanin biosynthesis and accumulation in grape berries. The metabolomic features showed that cyanidin 3-O-glucoside, delphinidin 3-O-glucoside, malvidin 3-O-glucoside, peonidin 3-O-glucoside, and petunidin 3-O-glucoside were the pigments responsible for the purplish-red peel color. Transcriptomic analyses revealed that anthocyanin biosynthesis-related genes, from upstream (phenylalanine ammonia-lyase) to downstream (anthocyanidin 3-O-glucosyltransferase and anthocyanidin synthase), were upregulated with the accumulation of anthocyanins in the heterografted plants. At the same time, all these genes were also highly expressed and more anthocyanin was accumulated in self-grafted CS/CS samples compared with own-rooted graft-free CS samples, suggesting that self-grafting may also have promoted berry reddening in grapevine. Our results reveal global transcriptomic and metabolomic features in berry color regulation under different grafting conditions that may be useful for improving berry quality in viticulture.

Transcriptome Analysis of MYB Genes and Patterns of Anthocyanin Accumulation During Seed Development in Wheat

Plants accumulate key metabolites as a response of biotic/abiotic stress conditions. In seed coats, anthocyanins, carotenoids, and chlorophylls can be found. They have been associated as important antioxidants that affect germination. In wheat, anthocyanins can impart the seed coat color which have been recognized as health-promoting nutrients. Transcription factors act as master regulators of cellular processes. Transcription complexes such as MYB-bHLH-WD40 (MBW) regulate the expression of multiple target genes in various plant species. In this study, the spatiotemporal accumulation of seed coat pigments in different developmental stages (10, 20, 30, and 40 days after pollination) was analyzed using cryo-cuts. Moreover, the accumulation of phenolic, anthocyanin, and chlorophyll contents was quantified, and the expression of flavonoid biosynthetic genes was evaluated. Finally, transcriptome analysis was performed to analyze putative MYB genes related to seed coat color, followed by further characterization of putative genes. TaTCL2, an MYB gene, was cloned and sequenced. It was determined that TaTCL2 contains a SANT domain, which is often present in proteins participating in the response to anthocyanin accumulation. Moreover, TaTCL2 transcript levels were shown to be influenced by anthocyanin accumulation during grain development. Interaction network analysis showed interactions with GL2 (HD-ZIP IV), EGL3 (bHLH), and TTG1 (WD40). The findings of this study elucidate the mechanisms underlying color formation in Triticum aestivum L. seed coats.

ABA Speeds Up the Progress of Color in Developing F. chiloensis Fruit through the Activation of PAL, CHS and ANS, Key Genes of the Phenylpropanoid/Flavonoid and Anthocyanin Pathways

Phenolic compounds with antioxidant properties have risen in interest due to their benefits for human health. Fragaria chiloensis is a native wild berry species from Chile that develops a white/pink receptacle and white flesh at the ripe stage. Changes in color parameters, anthocyanins, secondary metabolites (phenolics, flavonoids), and total antioxidant capacity were followed during the development and ripening of F. chiloensis fruit. The increment in color ‘a’ index takes place in parallel with anthocyanins rise and the reduction in phenolics, flavonoids, and antioxidant capacity. Good correlations were determined between color development, anthocyanins, and the expression of key phenylpropanoid/flavonoid and anthocyanin pathway genes. To investigate the role of ABA on color development, detached immature fruit (C2 stage) were treated with exogenous ABA and stored at 20 °C. Fruit color development was accelerated by ABA treatment compared to non-treated fruit, and consistent with that, the increment in the accumulation of anthocyanins and transcripts of phenylpropanoid/flavonoid, and anthocyanin pathways genes such as FcPAL, FcCHS, and FcANS were observed. This suggests that ABA promotes transcriptional changes that lead to the color formation on this non-climacteric fruit.

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

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

Ethylene precisely regulates anthocyanin synthesis in apple via a module comprising MdEIL1, MdMYB1, and MdMYB17

Ethylene regulates anthocyanin synthesis in ripening apple fruit via the antagonistic activities of the R2R3-MYB repressors and activators. However, the molecular mechanism underlying this process remains unknown. In this study, ethylene significantly induced the expression of the R2R3-MYB gene MdMYB17 in apple fruit. Moreover, MdMYB17 was revealed to be an important repressor of anthocyanin synthesis. Specifically, MdMYB17 binds directly to the promoters of the ethylene-induced genes MdMYB1 and MdEIL1, which encode positive regulators of anthocyanin synthesis, and represses their expression. Additionally, MdMYB1 and MdEIL1 bind to the MdMYB17 promoter to activate its expression. Thus, MdMYB17, MdMYB1, and MdEIL1 form a regulatory module that controls the expression of the corresponding genes. MdMYB17 interacts with MdEIL1. The interaction between MdMYB17 and MdEIL1 attenuates the regulatory effects of MdMYB17 on MdMYB1 and MdEIL1 as well as the regulatory effects of MdEIL1 on MdMYB17. Overall, our results reveal the molecular mechanisms by which MdMYB17, MdMYB1, and MdEIL1 finely mediate ethylene-regulated anthocyanin synthesis in apple fruit.

High Resolution Quantitative Trait Locus Mapping and Whole Genome Sequencing Enable the Design of an Anthocyanidin Reductase-Specific Homoeo-Allelic Marker for Fruit Colour Improvement in Octoploid Strawberry (Fragaria × ananassa)

Fruit colour is central to the sensorial and nutritional quality of strawberry fruit and is therefore a major target in breeding programmes of the octoploid cultivated strawberry (Fragaria × ananassa). The red colour of the fruit is caused by the accumulation of anthocyanins, which are water-soluble flavonoids. To facilitate molecular breeding, here we have mapped with high resolution fruit colour quantitative trait loci (QTLs) (COLOUR, scored visually as in selection programmes) and associated flavonoid metabolic QTLs (5 anthocyanins compounds together with 8 flavonols and flavan-3-ols) to specific subgenomes of cultivated strawberry. Two main colour-related QTLs were located on the LG3A linkage group (Fragaria vesca subgenome). Genetic mapping, transcriptome analysis and whole genome sequencing enabled the detection of a homoeo-allelic variant of ANTHOCYANIDIN REDUCTASE (ANR) underlying the major male M3A COLOUR and pelargonidin-3-glucoside (PgGs) QTLs (up to ∼20% of explained variance). Consistent with previously published functional studies, ANR transcript abundance was inversely related with PgGs content in contrasted progeny individuals. Genetic segregation analyses further indicated that a molecular marker designed using an 18 bp deletion found in the 5'UTR of the candidate ANR homoeo-allelic variant is effective in identifying genotypes with intense red fruit colour. Our study provides insights into the genetic and molecular control of colour-related traits in strawberry and further defines a genetic marker for marker-assisted selection of new strawberry varieties with improved colour. The QTLs detected and the underlying candidate genes are different from those described to date, emphasising the importance of screening a wide diversity of genetic resources in strawberry.

Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)

Strawberry (Fragaria spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past 10 y. Here, we report chromosome-scale reference genomes for five strawberry species, including three newly sequenced species' genomes, and genome resequencing data for 128 additional accessions to estimate the genetic diversity, structure, and demographic history of key Fragaria species. Our analyses obtained fully resolved and strongly supported phylogenies and divergence times for most diploid strawberry species. These analyses also uncovered a new diploid species (Fragaria emeiensis Jia J. Lei). Finally, we constructed a pan-genome for Fragaria and examined the evolutionary dynamics of gene families. Notably, we identified multiple independent single base mutations of the MYB10 gene associated with white pigmented fruit shared by different strawberry species. These reference genomes and datasets, combined with our phylogenetic estimates, should serve as a powerful comparative genomic platform and resource for future studies in strawberry.

Recent Advanced Metabolic and Genetic Engineering of Phenylpropanoid Biosynthetic Pathways

The MYB transcription factors (TFs) are evolving as critical role in the regulation of the phenylpropanoid and tanshinones biosynthetic pathway. MYB TFs relate to a very important gene family, which are involved in the regulation of primary and secondary metabolisms, terpenoids, bioactive compounds, plant defense against various stresses and cell morphology. R2R3 MYB TFs contained a conserved N-terminal domain, but the domain at C-terminal sorts them different regarding their structures and functions. MYB TFs suppressors generally possess particular repressive motifs, such as pdLNLD/ELxiG/S and TLLLFR, which contribute to their suppression role through a diversity of complex regulatory mechanisms. A novel flower specific "NF/YWSV/MEDF/LW" conserved motif has a great potential to understand the mechanisms of flower development. In the current review, we summarize recent advanced progress of MYB TFs on transcription regulation, posttranscriptional, microRNA, conserved motif and propose directions to future prospective research. We further suggest there should be more focus on the investigation for the role of MYB TFs in microalgae, which has great potential for heterologous protein expression system for future perspectives.

Identification of candidate genes influencing anthocyanin biosynthesis during the development and ripening of red and white strawberry fruits via comparative transcriptome analysis

Strawberries are one of the most economically important berry fruits worldwide and exhibit colours ranging from white to dark red, providing a rich genetic resource for strawberry quality improvement. In the present study, we conducted transcriptome analyses of three strawberry cultivars, namely, 'Benihoppe', 'Xiaobai', and 'Snow White', and compared their gene expression profiles. Among the high-quality sequences, 5,049 and 53,200 differentially expressed genes (DEGs) were obtained when comparing the diploid and octoploid strawberry genomes and analysed to identify anthocyanin-related candidate genes. Sixty-five DEGs in the diploid genome (transcriptome data compared to the diploid strawberry genome) and 317 DEGs in the octoploid genome (transcriptome data compared to the octoploid strawberry genome) were identified among the three cultivars. Among these DEGs, 19 and 70 anthocyanin pathway genes, six and 42 sugar pathway genes, 23 and 101 hormone pathway genes, and 17 and 104 transcription factors in the diploid and octoploid genomes, respectively, correlated positively or negatively with the anthocyanin accumulation observed among the three cultivars. Real-time qPCR analysis of nine candidate genes showed a good correlation with the transcriptome data. For example, the expression of PAL was higher in 'Benihoppe' and 'Xiaobai' than in 'Snow White', consistent with the RNA-seq data. Thus, the RNA-seq data and candidate DEGs identified in the present study provide a sound basis for further studies of strawberry fruit colour formation.

Fine Mapping of the "black" Peel Color in Pomegranate (Punica granatum L.) Strongly Suggests That a Mutation in the Anthocyanidin Reductase (ANR) Gene Is Responsible for the Trait

Anthocyanins are important dietary and health-promoting substances present in high quantities in the peel and arils of the pomegranate (Punica granatum L.) fruit. Yet, there is a high variation in the content of anthocyanin among different pomegranate varieties. The 'Black' pomegranate variety (P.G.127-28) found in Israel contains exceptionally high levels of anthocyanins in its fruit peel which can reach up to two orders of magnitude higher content as compared to that of other pomegranate varieties' peel anthocyanins. Biochemical analysis reveals that delphinidin is highly abundant in the peel of 'Black' variety. The pattern of anthocyanin accumulation in the fruit peel during fruit development of 'Black' variety differs from that of other pomegranates. High anthocyanin levels are maintained during all developmental stages. Moreover, the accumulation of anthocyanin in the fruit peel of 'Black' variety is not dependent on light. Genetic analysis of an F₂ population segregating for the "black" phenotype reveals that it is determined by a single recessive gene. Genetic mapping of the F₂ population using single nucleotide polymorphism (SNP) markers identified few markers tightly linked to the "black" phenotype. Recombination analysis of the F₂ population and F₃ populations narrowed the "black" trait to an area of 178.5 kb on the draft genome sequence of pomegranate cv. 'Dabenzi.' A putative anthocyanidin reductase (ANR) gene is located in this area. Only pomegranate varieties displaying the "black" trait carry a base pair deletion toward the end of the gene, causing a frame shift resulting in a shorter protein. We propose that this mutation in the ANR gene is responsible for the different anthocyanin composition and high anthocyanin levels of the "black" trait in pomegranate.

Transcriptome profiling provides insights into the fruit color development of wild Lycium ruthenicum Murr. from Qinghai-Tibet Plateau

Lycium ruthenicum Murr. is an important ecological and economic species in the Qaidam Basin of Qinghai-Tibet Plateau. Its black fruits (BF) are rich in anthocyanins, which have health-promoting properties for humans and thus provide nutritional benefits for this plant. Although the fruit quality of natural white fruit (WF) is affected by the disappearance of pigmentation in phenotypes, this phenomenon provides an opportunity to unravel the complex color metabolic networks. In this study, anthocyanin profiling confirmed that WF was formed due to anthocyanin loss. Transcriptome analysis of BF and WF revealed 101,466 unigenes, 261 of which were identified as the putative homologs of color-related genes in other species. Genes encoding the enzymes involved in flavonoid biosynthesis were also identified systematically. The structural gene expression levels of chalcone synthase (CHS), chalcone isomerase (CHI), flavonoid 3'5'-hydroxylase (F3'5'H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), and anthocyanidin 3-O-glucosyltransferase (UFGT) were highly similar and significantly positively correlated with anthocyanin accumulation rate in BF. In particular, F3'5'H, UFGT, ANS, and DFR expression levels in BF were 2391, 119, 96, and 85 times higher than those in WF at S3 (35 days after anthesis), respectively. This result strongly suggests that the low expression of these genes in WF is responsible for the anthocyanin loss. Meanwhile, the expression patterns of the anthocyanin regulatory genes were also investigated by qRT-PCR. Mass sequencing data were obtained and annotated by deep sequencing and provided a platform for future function and molecular biological research on L. ruthenicum Murr.

Genetic analysis of phenylpropanoids and antioxidant capacity in strawberry fruit reveals mQTL hotspots and candidate genes

Phenylpropanoids are a large class of plant secondary metabolites, which play essential roles in human health mainly associated with their antioxidant activity. Strawberry (Fragaria × ananassa) is a rich source of phytonutrients, including phenylpropanoids, which have been shown to have beneficial effects on human health. In this study, using the F. × ananassa '232' × '1392' F₁ segregating population, we analyzed the genetic control of individual phenylpropanoid metabolites, total polyphenol content (TPC) and antioxidant capacity (TEAC) in strawberry fruit over two seasons. We have identified a total of 7, 9, and 309 quantitative trait loci (QTL) for TPC, TEAC and for 77 polar secondary metabolites, respectively. Hotspots of stable QTL for health-related antioxidant compounds were detected on linkage groups LG IV-3, LG V-2 and V-4, and LG VI-1 and VI-2, where associated markers represent useful targets for marker-assisted selection of new varieties with increased levels of antioxidant secondary compounds. Moreover, differential expression of candidate genes for major and stable mQTLs was studied in fruits of contrasting lines in important flavonoids. Our results indicate that higher expression of FaF3'H, which encodes the flavonoid 3'-hydroxylase, is associated with increased content of these important flavonoids.

Genetic and Physical Localization of the Gene Controlling Leaf Pigmentation Pattern in Medicago truncatula

In Medicago truncatula, some ecotypes form a black or purple stain in the middle of adaxial leaf surface due to accumulation of anthocyanins. However, this morphological marker is missing in some other ecotypes, although anthocyanin biosynthesis pathway is not disrupted. Genetic analysis indicated that the lack of the leaf spot of anthocyanins accumulation is a dominant trait, which is controlled by a single gene, LPP1. Genetic mapping indicated that the LPP1 gene was delimited to a 280 kb-region on Chromosome 7. A total of 8 protein-coding genes were identified in the LPP1 locus through gene annotation and sequence analysis. Of those, two genes, putatively encoding MYB-transcriptional suppressors, were selected as candidates for functional validation.

The strawberry transcription factor FaRAV1 positively regulates anthocyanin accumulation by activation of FaMYB10 and anthocyanin pathway genes

The RAV (related to ABI3/viviparous 1) group of transcription factors (TFs) play multifaceted roles in plant development and stress responses. Here, we show that strawberry (Fragaria × ananassa) FaRAV1 positively regulates anthocyanin accumulation during fruit ripening via a hierarchy of activation processes. Dual-luciferase assay screening of all fruit-expressed AP2/ERFs showed FaRAV1 had the highest transcriptional activation of the promoter of FaMYB10, a key activator of anthocyanin biosynthesis. Yeast one-hybrid and electrophoretic mobility shift assays indicated that FaRAV1 could directly bind to the promoter of FaMYB10. Transient overexpression of FaRAV1 in strawberry fruit increased FaMYB10 expression and anthocyanin production significantly. Correspondingly, transient RNA interference-induced silencing of FaRAV1 led to decreases in FaMYB10 expression and anthocyanin content. Transcriptome analysis of FaRAV1-overexpressing strawberry fruit revealed that transcripts of phenylpropanoid and flavonoid biosynthesis pathway genes were up-regulated. Luciferase assays showed that FaRAV1 could also activate the promoters of strawberry anthocyanin biosynthetic genes directly, revealing a second level of FaRAV1 action in promoting anthocyanin accumulation. These results show that FaRAV1 stimulates anthocyanin accumulation in strawberry both by direct activation of anthocyanin pathway gene promoters and by up-regulation of FaMYB10, which also positively regulates these genes.

Multiple MYB Activators and Repressors Collaboratively Regulate the Juvenile Red Fading in Leaves of Sweetpotato

Juvenile red fading describes the phenomenon in plants whereby red young leaves gradually turn green as they mature. While this phenomenon is commonly observed, the underlying molecular mechanism is still obscure as the classic model plants do not exhibit this process. Here, the molecular mechanism for the loss of anthocyanins during juvenile red fading were explored in the sweetpotato (Ipomoea batatas L.) cultivar "Chuanshan Zi". The MYB-bHLH-WDR (MBW) regulatory complexes for anthocyanins were examined with five stages of leaf development from C1 to C5. Alternating accumulation of anthocyanins and chlorophylls caused the leaf color change. Five anthocyanin components were identified by ultra performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS), and their contents were highest at stage C2. Transcriptomic analysis showed massive gene expression alteration during leaf development. The anthocyanin structural genes expressed in sweetpotato leaves were screened and found to be highly comparable with those identified in morning glories. The screened anthocyanin regulatory genes included one bHLH (IbbHLH2), one WDR (IbWDR1), three MYB activators (IbMYB1, IbMYB2, and IbMYB3), and five MYB repressors (IbMYB27, IbMYBx, IbMYB4a, IbMYB4b, and IbMYB4c). The expression trends of MYBs were key to the red fading process: the activators were highly expressed in early red leaves and were all accompanied by simultaneously expressed MYB repressors, which may act to prevent excessive accumulation of anthocyanins. The only antagonistic repressor, IbMYB4b, was highly expressed in green leaves, and may be critical for declined anthocyanin content at later stages. Further functional verification of the above transcription factors were conducted by promoter activation tests. These tests showed that the MBW complexes of IbMYB1/IbMYB2/IbMYB3-IbbHLH2-IbWDR1 not only activated promoters of anthocyanin structural genes IbCHS-D and IbDFR-B, but also promoters for IbbHLH2 and IbMYB27, indicating both hierarchical and feedback regulations. This study outlines the elaborate regulatory network of MBW complexes involving multiple MYBs which allow for the timely accumulation of anthocyanins in sweetpotato leaves. These results may also provide clues for similar studies of juvenile red fading in other plant species.

R2R3-MYB Transcription Factors Regulate Anthocyanin Biosynthesis in Grapevine Vegetative Tissues

Anthocyanins with important physiological functions mainly accumulate in grape berry, but teinturier grape cultivars can accumulate anthocyanins in both reproductive and vegetative tissues. The molecular regulatory mechanisms of anthocyanin biosynthesis in grapevine reproductive and vegetative tissues are different. Therefore, teinturier grapevine cultivar provides opportunities to investigate transcriptional regulation of vegetative anthocyanins, and to compare with mechanisms that regulate grape berry anthocyanins. Yan73 is a teinturier Vitis vinifera variety with vegetative tissues able to accumulate anthocyanins, but the anthocyanin pattern and the molecular mechanism regulating anthocyanin biosynthesis in these tissues remain uncharacterized. We analyzed the anthocyanin metabolic and transcriptome profiles of the vegetative tissues of Yan73 and its male parent with HPLC-ESI-MS/MS and RNA-sequencing technologies. Yan73 vegetative tissues had relatively high 3'-OH, acylated, and methoxylated anthocyanins. Furthermore, peonidin-3-O-(trans-6-coumaryl)-glucoside is the most abundant anthocyanin in Yan73 grapevine vegetative tissues. A total of 30,17 and 10 anthocyanin biosynthesis genes showed up-regulated expression in Yan73 leaf, stem and tendril, respectively, indicating anthocyanin biosynthesis in Yan73 vegetative tissues is regulated by transcription factors. The up-regulated expression of VvMYBA1 on chromosome 2 and VvMYBA5, VvMYBA6, and VvMYBA7 on chromosome 14 are responsible for the anthocyanin patterns of Yan73 vegetative tissues. The expression of a set of R2R3-MYB C2 repressor genes is activated and may negatively regulate anthocyanin biosynthesis in Yan73 vegetative tissues. These findings enhance our understanding of anthocyanin biosynthesis in grapevine.

A roadmap for research in octoploid strawberry

The cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, originating nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry has become the most widely cultivated fruit crop in the world, universally appealing due to its sensory qualities and health benefits. The recent publication of the first high-quality chromosome-scale octoploid strawberry genome (cv. Camarosa) is enabling rapid advances in genetics, stimulating scientific debate and provoking new research questions. In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture. Among these are the origins of the genome, characterization of genetic variants, and big data approaches to breeding. Key areas of research in molecular biology will include the control of flowering, fruit development, fruit quality, and plant-pathogen interactions. In order to realize this potential as a global community, investments in genome resources must be continually augmented.

Fragaria Genus: Chemical Composition and Biological Activities

The strawberries represent in our days one of the main fresh fruits consumed globally, inevitably leading to large amounts of by-products and wastes. Usually appreciated because of their specific flavor, the strawberries also possess biological properties, including antioxidant, antimicrobial, or anti-inflammatory effects. In spite of the wide spread of the Fragaria genus, few species represent the subject of the last decade scientific research. The main components identified in the Fragaria species are presented, as well as several biological properties, as emerging from the scientific papers published in the last decade.

Differential expression after UV-B radiation and characterization of chalcone synthase from the Patagonian hairgrass Deschampsia antarctica

Deschampsiaantarctica inhabits the maritime territory of Antarctica and South Patagonia. It grows under very harsh environmental conditions. The survival of this species in low freezing temperatures and under high levels of UV-B radiation may constitute some of the most remarkable adaptive plant responses and suggests that this plant possesses genes associated with cold and UV tolerance. Frequently, increased levels of flavonoids have been linked to highly UV-B irradiated plants. Studies examining the biosynthesis of flavonoids in D. antarctica may provide clues to its success in this extreme environment. In this study, we characterized the family of genes encoding chalcone synthase, a key enzyme of the flavonoid biosynthetic pathway. DaCHS was cloned, sequenced and characterized by using software tools. CHS contains two domains, the N-terminal domain ranges from amino acid 8 to 231 and the C-terminal domain ranges from amino acid 241 to 391. Sequence analysis of the three family members revealed a high degree of identity after comparison with other monocotyledons such as Oryza sativa L., Zea mays L. and Hordeum vulgare L. According to these results, DaCHS can be grouped together with H. vulgare CHS1 in the same branch. The phylogenetic tree was built using MEGA software and the neighbour join method with 1000 bootstrap replicates. A model of DaCHS was constructed by way of structural tools and key amino acid residues were identified at the active motif site.

An atypical HLH transcriptional regulator plays a novel and important role in strawberry ripened receptacle

BACKGROUND

In soft fruits, the differential expression of many genes during development and ripening is responsible for changing their organoleptic properties. In strawberry fruit, although some genes involved in the metabolic regulation of the ripening process have been functionally characterized, some of the most studied genes correspond to transcription factors. High throughput transcriptomics analyses performed in strawberry red receptacle (Fragaria x ananassa) allowed us to identify a ripening-related gene that codes an atypical HLH (FaPRE1) with high sequence homology with the PACLOBUTRAZOL RESISTANCE (PRE) genes. PRE genes are atypical bHLH proteins characterized by the lack of a DNA-binding domain and whose function has been linked to the regulation of cell elongation processes.

RESULTS

FaPRE1 sequence analysis indicates that this gene belongs to the subfamily of atypical bHLHs that also includes ILI-1 from rice, SlPRE2 from tomato and AtPRE1 from Arabidopsis, which are involved in transcriptional regulatory processes as repressors, through the blockage by heterodimerization of bHLH transcription factors. FaPRE1 presented a transcriptional model characteristic of a ripening-related gene with receptacle-specific expression, being repressed by auxins and activated by abscisic acid (ABA). However, its expression was not affected by gibberellic acid (GA₃). On the other hand, the transitory silencing of FaPRE1 transcription by agroinfiltration in receptacle produced the down-regulation of a group of genes related to the ripening process while inducing the transcription of genes involved in receptacle growth and development.

CONCLUSIONS

In summary, this work presents for the first time experimental data that support an important novel function for the atypical HLH FaPRE1 during the strawberry fruit ripening. We hypothesize that FaPRE1 modulates antagonistically the transcription of genes related to both receptacle growth and ripening. Thus, FaPRE1 would repress the expression of receptacle growth promoting genes in the ripened receptacle, while it would activate the expression of those genes related to the receptacle ripening process.