Identification of key gene networks controlling anthocyanin biosynthesis in peach flower

AaMYB61-like and AabHLH137 jointly regulate anthocyanin biosynthesis in Actinidia arguta

BACKGROUND

Red Actinidia arguta has recently become highly popular because of its red appearance resulting from anthocyanin accumulation, and has gradually become an important breeding direction. However, regulators involved in anthocyanin biosynthesis have not been fully characterized in A. arguta.

RESULTS

Here, we demonstrated that a key R2R3-MYB transcription factor, AaMYB61-like, plays a crucial role in A. arguta anthocyanin biosynthesis. The RT-qPCR results revealed that transient overexpression of AaMYB61-like in A. arguta fruit at 90-100 DAFB significantly promoted anthocyanin biosynthesis, as did the gene expression levels of AaCHS, AaCHI, AaF3H, AaLDOX, and AaF3GT, whereas the result of VIGS revealed the opposite results in A. arguta fruit at 105-115 DAFB. A transcriptional activation assay indicated that AaMYB61-like exhibited transcriptional activation activity. Y1H and LUC assays revealed that AaMYB61-like activates the promoters of AaCHS, AaLDOX, and AaF3GT. In addition, AabHLH137 was found to be related to fruit color from the transcriptome data. We demonstrated that AaMYB61-like promotes anthocyanin biosynthesis by interacting with AabHLH137 via Y2H, BiFC, and Agrobacterium-mediated co-transformation.

CONCLUSIONS

Our study not only reveals the functions of AaMYB61-like and AabHLH137 in anthocyanin regulation, but also broadly enriches color regulation theory, establishing a foundation for clarifying the molecular mechanism of fruit coloration in kiwifruit.

Transcriptome sequencing and anthocyanin metabolite analysis involved in leaf red color formation of Cinnamomum camphora

Cinnamomum camphora, a key multifunctional tree species, primarily serves in landscaping. Leaf color is crucial for its ornamental appeal, undergoing a transformation to red that enhances the ornamental value of C. camphora. However, the molecular mechanisms underlying this transformation remain largely unexplored. In this study, green leaf (GL), color turning red leaf (RL) and whole red leaf (WRL) were obtained to measure pigment contents, while GL and RL were analyzed for transcriptomic alterations. A decline in chlorophyll content and a rise in anthocyanins were observed during the transition from green to red leaves. Using LC MS/MS, 11 types of anthocyanins showed significant accumulative differences, with cyanidin-3,5-O-diglucoside exhibiting the greatest disparity. Comparative RNA-seq identified 22,948 genes against reference genes, revealing 544 novel genes. Of these, 3,222 genes were up-regulated and 7,391 genes were down-regulated when the FPKM mean value > 1 in at least one group. The ribosome was identified as the most abundant KEGG term, with a substantial number of down-regulated differentially expressed genes (DEGs). The results indicated a downward trend in protein content, with GL exhibiting the highest protein concentration. 22, 4, and 29 DEGs were associated with chlorophyll biosynthesis, chlorophyll degradation, and anthocyanin biosynthesis, respectively. Most DEGs related to chlorophyll biosynthesis were down-regulated. SGR and SGRL, which are associated with chlorophyll degradation, exhibited opposite differential expression, resulting in a significant decrease in chlorophyll content in RL. The significantly up-regulated genes ANS and UFGT are advantageous for anthocyanin biosynthesis, contributing to the red coloration observed. Additionally, differential expression was noted in 40 R2R3-MYBs. Two MYB90 (Ccam01G003512 and Ccam01G003515) homologs of AtMYB113 were also identified showed high levels of up-regulation in RL. These findings suggest a strong correlation between pigment metabolism and transcriptome data, elucidating the mechanism that leads to the red coloration of leaves in C. camphora.

Research advances of coloring mechanism regulated by MicroRNAs in plants

In plants, microRNAs (miRNAs) are a class of important small RNAs involved in their growth and development, and play a very significant role in regulating their tissue coloring. In this paper, the mechanisms on miRNA regulation of plant coloring are mainly reviewed from three aspects: macroscopic physiological and molecular foundations related to tissue coloring, miRNA biosynthesis and function, and specific analysis of miRNA regulation studies on leaf color, flower color, fruit color, and other tissue color formation in plants. Furthermore, we also systematically summarize the miRNA regulatory mechanisms identified on pigments biosynthesis and color formation in plants, and the regulatory mechanisms of these miRNAs mentioned on the existing researches can be divided into four main categories: directly targeting the related transcription factors, directly targeting the related structural genes, directly targeting the related long noncoding RNAs (LncRNAs) and miRNA-mediated production of trans-acting small interfering RNAs (ta-siRNAs). Together, these research results aim to provide a theoretical reference for the in-depth study of plant coloring mechanism and molecular breeding study of related plants in the future.

Integrated transcriptomic and WGCNA analyses reveal candidate genes regulating mainly flavonoid biosynthesis in Litsea coreana var. sinensis

Litsea coreana Levl. var. sinensis (Allen) Yang et P. H. Huang is a popular ethnic herb and beverage plant known for its high flavonoid content, which has been linked to a variety of pharmacological benefits and crucial health-promoting impacts in humans. The progress in understanding the molecular mechanisms of flavonoid accumulation in this plant has been hindered due to the deficiency of genomic and transcriptomic resources. We utilized a combination of Illumina and Oxford Nanopore Technology (ONT) sequencing to generate a de novo hybrid transcriptome assembly. In total, 126,977 unigenes were characterized, out of which 107,977 were successfully annotated in seven public databases. Within the annotated unigenes, 3,781 were categorized into 58 transcription factor families. Furthermore, we investigated the presence of four valuable flavonoids-quercetin-3-O-β-D-galactoside, quercetin-3-O-β-D-glucoside, kaempferol-3-O-β-D-galactoside, and kaempferol-3-O-β-D-glucoside in 98 samples, using high-performance liquid chromatography. A weighted gene co-expression network analysis identified two co-expression modules, MEpink and MEturquoise, that showed strong positive correlation with flavonoid content. Within these modules, four transcription factor genes (R2R3-MYB, NAC, WD40, and ARF) and four key enzyme-encoding genes (CHI, F3H, PAL, and C4H) emerged as potential hub genes. Among them, the R2R3-MYB (LcsMYB123) as a homologous gene to AtMYB123/TT2, was speculated to play a significant role in flavonol biosynthesis based on phylogenetic analysis. Our findings provided a theoretical foundation for further research into the molecular mechanisms of flavonoid biosynthesis. Additionally, The hybrid transcriptome sequences will serve as a valuable molecular resource for the transcriptional annotation of L. coreana var. sinensis, which will contribute to the improvement of high-flavonoid materials.

A decade of advances in the study of buckwheat for organic farming and agroecology (2013-2023)

During the last decade, research has shown the environment and human health benefits of growing buckwheat (Fagopyrum spp.). This comprehensive review aims to summarize the major advancements made in the study of buckwheat from 2013 to 2023, focusing on its agronomic characteristics, nutritional value, and potential applications in sustainable agriculture. The review examines the diverse applications of buckwheat in organic and agroecological farming systems, and discusses the ability of buckwheat to control weeds through allelopathy, competition, and other sustainable farming methods, such as crop rotation, intercropping and green manure, while improving soil health and biodiversity. The review also explores the nutritional value of buckwheat. It delves into the composition of buckwheat grains, emphasizing their high protein content, and the presence of essential amino acids and valuable micronutrients, which is linked to health benefits such as lowering cholesterol levels, controlling diabetes and acting against different types of cancer, among others. Finally, the review concludes by highlighting the gaps in current knowledge, and proposing future research directions to further optimize buckwheat production in organic or agroecological farming systems. It emphasizes the need for interdisciplinary collaboration, and the integration of traditional knowledge with modern scientific approaches to unlock the full potential of buckwheat as a sustainable crop.

The PpMYB75-PpDFR module reveals the difference between 'SR' and its bud variant 'RMHC' in peach red flesh

'Red Meat Honey Crisp (RMHC)' has been widely cultivated by growers in recent years due to its early maturity, and red meat type characteristics. As a bud variant of 'Super Red (SR)' peach, red flesh is the most distinctive characteristic of 'Red Meat Honey Crisp (RMHC)'. However, the mechanism of red flesh formation in 'RMHC' remains unclear. In this study, 79 differentially produced metabolites were identified by metabolomics analysis. The anthocyanin content in 'RMHC' was significantly higher than that in 'SR' during the same period, such as cyanidin O-syringic acid and cyanidin 3-O-glucoside. Other flavonoids also increased during the formation of red flesh, including flavonols (6-hydroxykaempferol-7-O-glucoside, hyperin), flavanols (protocatechuic acid, (+)-gallocatechin), and flavonoids (chrysoeriol 5-O-hexoside, tricetin). In addition, transcriptomic analysis and RT-qPCR showed that the expression levels of the flavonoid synthesis pathway transcription factor MYB75 and some structural genes, such as PpDFR, PpCHS, PpC4H, and PpLDOX increased significantly in 'RMHC'. Subcellular localization analysis revealed that MYB75 was localized to the nucleus. Yeast single hybridization assays showed that MYB75 bound to the cis-acting element CCGTTG of the PpDFR promoter region. The MYB75-PpDFR regulatory network was identified to be a key pathway in the reddening of 'RMHC' flesh. Moreover, this is the first study to describe the cause for red meat reddening in 'RMHC' compared to 'SR' peaches using transcriptomics, metabolomics and molecular methods. Our study identified a key transcription factor involved in the regulation of the flavonoid synthetic pathway and contributes to peach breeding-related efforts as well as the identification of genes involved in color formation in other species.

Advancing tree genomics to future proof next generation orchard production

The challenges facing tree orchard production in the coming years will be largely driven by changes in the climate affecting the sustainability of farming practices in specific geographical regions. Identifying key traits that enable tree crops to modify their growth to varying environmental conditions and taking advantage of new crop improvement opportunities and technologies will ensure the tree crop industry remains viable and profitable into the future. In this review article we 1) outline climate and sustainability challenges relevant to horticultural tree crop industries, 2) describe key tree crop traits targeted for improvement in agroecosystem productivity and resilience to environmental change, and 3) discuss existing and emerging genomic technologies that provide opportunities for industries to future proof the next generation of orchards.

Genome sequencing revealed the red-flower trait candidate gene of a peach landrace

Peach (Prunus persica) is an economically important fruit crop globally and an excellent material for genomic studies. While considerable progress has been made in unveiling trait-associated genes within cultivars and wild relatives, certain novel genes controlling valuable traits in peach landraces, such as the red-flowering gene, remained unclear. In this study, we sequenced and assembled the diploid genome of the red-flower landrace 'Yingzui' (abbreviated as 'RedY'). Multi-omics profiling of red petals of 'RedY' revealed the intensified red coloration associated with anthocyanins accumulation and concurrent decline in flavonols. This phenomenon is likely attributed to a natural variant of Flavonol Synthase (FLS) harboring a 9-bp exonic insertion. Intriguingly, the homozygous allelic configurations of this FLS variant were only observed in red-flowered peaches. Furthermore, the 9-bp sequence variation tightly associated with pink/red petal color in genome-wide association studies (GWAS) of collected peach germplasm resources. Functional analyses of the FLS variant, purified from procaryotic expression system, demonstrated its diminished enzymatic activity in flavonols biosynthesis, impeccably aligning with the cardinal trait of red flowers. Therefore, the natural FLS variant was proposed as the best candidate gene for red-flowering trait in peach. The pioneering unveiling of the red-flowered peach genome, coupled with the identification of the candidate gene, expanded the knowledge boundaries of the genetic basis of peach traits and provided valuable insights for future peach breeding efforts.

Chromosome-scale genome assembly provides insights into flower coloration mechanisms of Canna indica

Canna indica, which produce conspicuous and colorful flowers, are widely appreciated as ornamental plants. We used Pacific Biosciences sequencing (PacBio) and chromosome conformation capture (Hi-C) genome scaffolding to build a high-quality chromosome-scale genome assembly of C. indica and the genome assembly was 821Mb with a contig N50 of 48Mb assembled into nine chromosomes. The genome of C. indica was predicted to contain 31,130 genes and 30,816 genes were functionally annotated. Genome annotation identified 522 Mb (63.59 %) as repetitive sequences. Genome evolution analysis showed that whole-genome duplication occurred 53.4 million years ago. Transcriptome analysis revealed that petal coloration was linked with the expression of genes encoding enzymes involved in anthocyanin biosynthesis, carotenoid biosynthesis, and the methylerythritol phosphate (MEP) pathway. Furthermore, modules of co-expressed genes and hub genes were identified via weighted gene co-expression network analysis. These results suggested that, in Canna indica, deep red petal coloration was regulated by CHS2 and yellow petal coloration was associated with expression of ARF6 and NAC14. Considered together, the current study revealed a high-quality reference genome which may provide new insights into the molecular basis of flower coloration in Canna indica and help enhance the conservation and breeding of ornamental plants in general.

Integrated analyses of metabolomics and transcriptomics reveal the potential regulatory roles of long non-coding RNAs in gingerol biosynthesis

BACKGROUND

As the characteristic functional component in ginger, gingerols possess several health-promoting properties. Long non-coding RNAs (lncRNAs) act as crucial regulators of diverse biological processes. However, lncRNAs in ginger are not yet identified so far, and their potential roles in gingerol biosynthesis are still unknown. In this study, metabolomic and transcriptomic analyses were performed in three main ginger cultivars (leshanhuangjiang, tonglingbaijiang, and yujiang 1 hao) in China to understand the potential roles of the specific lncRNAs in gingerol accumulation.

RESULTS

A total of 744 metabolites were monitored by metabolomics analysis, which were divided into eleven categories. Among them, the largest group phenolic acid category contained 143 metabolites, including 21 gingerol derivatives. Of which, three gingerol analogs, [8]-shogaol, [10]-gingerol, and [12]-shogaol, accumulated significantly. Moreover, 16,346 lncRNAs, including 2,513, 1,225, and 2,884 differentially expressed (DE) lncRNA genes (DELs), were identified in all three comparisons by transcriptomic analysis. Gene ontology enrichment (GO) analysis showed that the DELs mainly enriched in the secondary metabolite biosynthetic process, response to plant hormones, and phenol-containing compound metabolic process. Correlation analysis revealed that the expression levels of 11 DE gingerol biosynthesis enzyme genes (GBEGs) and 190 transcription factor genes (TF genes), such as MYB1, ERF100, WRKY40, etc. were strongly correlation coefficient with the contents of the three gingerol analogs. Furthermore, 7 and 111 upstream cis-acting lncRNAs, 1,200 and 2,225 upstream trans-acting lncRNAs corresponding to the GBEGs and TF genes were identified, respectively. Interestingly, 1,184 DELs might function as common upstream regulators to these GBEGs and TFs genes, such as LNC_008452, LNC_006109, LNC_004340, etc. Furthermore, protein-protein interaction networks (PPI) analysis indicated that three TF proteins, MYB4, MYB43, and WRKY70 might interact with four GBEG proteins (PAL1, PAL2, PAL3, and 4CL-4).

CONCLUSION

Based on these findings, we for the first time worldwide proposed a putative regulatory cascade of lncRNAs, TFs genes, and GBEGs involved in controlling of gingerol biosynthesis. These results not only provide novel insights into the lncRNAs involved in gingerol metabolism, but also lay a foundation for future in-depth studies of the related molecular mechanism.

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.

Involvement of a MYB Transcription Factor in Anthocyanin Biosynthesis during Chinese Bayberry (Morella rubra) Fruit Ripening

Anthocyanin is a class of water-soluble flavonoids found in Chinese bayberry (Morella rubra) that is not only responsible for the variety of colors visible in nature but also has numerous health-promoting benefits in humans. Through comparative transcriptomics, we isolated and identified a transcription factor (TF) of the R2R3-MYB type, MrMYB9, in order to explore the anthocyanin biosynthesis pathway in red and white Chinese bayberries. MrMYB9 transcript was positively correlated with anthocyanin level and anthocyanin biosynthetic gene expression during Chinese bayberry fruit maturation (R-values in the range 0.54-0.84, p < 0.05). Sequence analysis revealed that MrMYB9 shared a similar R2R3 domain with MYB activators of anthocyanin biosynthesis in other plants. MrMYB9 substantially transactivated promoters of anthocyanin biosynthesis-related EBGs (MrCHI, MrF3'H, and MrANS) and LBGs (MrUFGT) upon co-expression of the AtEGL3 gene. Our findings indicated that MrMYB9 may positively modulate anthocyanin accumulation in Chinese bayberry.

The MYB transcription factor RcMYB1 plays a central role in rose anthocyanin biosynthesis

Rose (Rosa hybrida) is one of most famous ornamental plants in the world, and its commodity value largely depends on its flower color. However, the regulatory mechanism underlying rose flower color is still unclear. In this study, we found that a key R2R3-MYB transcription factor, RcMYB1, plays a central role in rose anthocyanin biosynthesis. Overexpression of RcMYB1 significantly promoted anthocyanin accumulation in both white rose petals and tobacco leaves. In 35S:RcMYB1 transgenic lines, a significant accumulation of anthocyanins occurred in leaves and petioles. We further identified two MBW complexes (RcMYB1-RcBHLH42-RcTTG1; RcMYB1-RcEGL1-RcTTG1) associated with anthocyanin accumulation. Yeast one-hybrid and luciferase assays showed that RcMYB1 could active its own gene promoter and those of other EBGs (early anthocyanin biosynthesis genes) and LBGs (late anthocyanin biosynthesis genes). In addition, both of the MBW complexes enhanced the transcriptional activity of RcMYB1 and LBGs. Interestingly, our results also indicate that RcMYB1 is involved in the metabolic regulation of carotenoids and volatile aroma. In summary, we found that RcMYB1 widely participates in the transcriptional regulation of ABGs (anthocyanin biosynthesis genes), indicative of its central role in the regulation of anthocyanin accumulation in rose. Our results provide a theoretical basis for the further improvement of the flower color trait in rose by breeding or genetic modification.

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

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

Biostimulants promote the accumulation of carbohydrates and biosynthesis of anthocyanins in 'Yinhongli' plum

Biostimulants play an important role in promoting crop growth and development and improving fruit yield, but their influence on fruit quality in horticulture plants is still unclear. In this study, four types of biostimulants, Ainuo (AN), Aigefu (AG), Weiguo (WG), and Guanwu Shuang (GS) were applied to the fruit surface of 'Yinhongli' plum at 60 and 75 days after anthesis to investigate their effect on carbohydrates and biosynthesis of anthocyanins, and also analyze the relationship between sugar and anthocyanin accumulation during fruit color change to ripening. Results showed that all biostimulant treatments significantly improved fruit appearance quality, and increased single fruit weight and TSS/TA. Cyanidin 3-O-glucoside and cyanidin 3-O-rutinoside, are the most important anthocyanins in the red skin of the 'Yinhongli' plum, and no anthocyanin was detected in the green skin. In addition, WG and GS treatments significantly increased the expression of structural genes involved in anthocyanin biosynthesis compared with the control, especially chalcone synthase (CHS) and flavonoid 3-O-glucosyltransferase (UFGT) at 95-105 d after anthesis, leading to anthocyanin accumulation 10 days earlier than the control. Correlation analysis showed that there was a significant correlation between total sugar and anthocyanin content during fruit coloring and ripening.

Genome-wide characterization and functional identification of MYB genes in Malus sieversii infected by Valsa mali

Among the most important transcription factors in plants, the v-myb avian myeloblastosis viral oncogene homolog (MYB) regulates the expression network of response genes under stresses such as fungal infection. In China, the canker disease Valsa mali threatens the survival of Malus sieversii, an ancestor of cultivated apples. Using the M. sieversii genome, we identified 457 MsMYB and 128 R2R3-MsMYB genes that were randomly distributed across 17 chromosomes. Based on protein sequence and structure, the R2R3-MsMYB genes were phylogenetically divided into 29 categories, and 26 conserved motifs were identified. We further predicted cis-elements in the 2000-kb promoter region of R2R3-MsMYBs based on the genome. Transcriptome analysis of M. sieversii under V. mali infection showed that 27 R2R3-MsMYBs were significantly differentially expressed, indicating their key role in the response to V. mali infection. Using transient transformation, MsMYB14, MsMYB24, MsMYB39, MsMYB78, and MsMYB108, which were strongly induced by V. mali infection, were functionally identified. Among the five MsMYBs, MsMYB14 and MsMYB78 were both important in enhancing resistance to diseases, whereas MsMYB24 inhibited resistance. Based on the results of this study, we gained a better understanding of the MsMYB transcription factor family and laid the foundation for a future research program on disease prevention strategies in M. sieversii.

Comparative Transcriptome Analysis Unveils the Molecular Mechanism Underlying Sepal Colour Changes under Acidic pH Substratum in Hydrangea macrophylla

The hydrangea (Hydrangea macrophylla (Thunb). Ser.), an ornamental plant, has good marketing potential and is known for its capacity to change the colour of its inflorescence depending on the pH of the cultivation media. The molecular mechanisms causing these changes are still uncertain. In the present study, transcriptome and targeted metabolic profiling were used to identify molecular changes in the RNAome of hydrangea plants cultured at two different pH levels. De novo assembly yielded 186,477 unigenes. Transcriptomic datasets provided a comprehensive and systemic overview of the dynamic networks of the gene expression underlying flower colour formation in hydrangeas. Weighted analyses of gene co-expression network identified candidate genes and hub genes from the modules linked closely to the hyper accumulation of Al³⁺ during different stages of flower development. F3'5'H, ANS, FLS, CHS, UA3GT, CHI, DFR, and F3H were enhanced significantly in the modules. In addition, MYB, bHLH, PAL6, PAL9, and WD40 were identified as hub genes. Thus, a hypothesis elucidating the colour change in the flowers of Al³⁺-treated plants was established. This study identified many potential key regulators of flower pigmentation, providing novel insights into the molecular networks in hydrangea flowers.

Transcriptome and chemical analyses revealed the mechanism of flower color formation in Rosa rugosa

Rosa rugosa is a famous Chinese traditional flower with high ornamental value and well environmental adapt ability. The cultivation of new colorful germplasms to improve monotonous flower color could promote its landscape application. However, the mechanism of flower color formation in R. rugosa remains unclear. In this study, combined analyses of the chemical and transcriptome were performed in the R. rugosa germplasms with representative flower colors. Among the identified anthocyanins, cyanidin 3,5-O-diglucoside (Cy3G5G) and peonidin 3,5-O-diglucoside (Pn3G5G) were the two dominant anthocyanins in the petals of R. rugosa. The sum content of Cy3G5G and Pn3G5G was responsible for the petal color intensity, such as pink or purple, light- or dark- red. The ratio of Cy3G5G to Pn3G5G was contributed to the petal color hue, that is, red or pink/purple. Maintaining both high relative and high absolute content of Cy3G5G may be the precondition for forming red-colored petals in R. rugosa. Cyanidin biosynthesis shunt was the dominant pathway for anthocyanin accumulation in R. rugosa, which may be the key reason for the presence of monotonous petal color in R. rugosa, mainly pink/purple. In the upstream pathway of cyanidin biosynthesis, 35 differentially expressed structural genes encoding 12 enzymes co-expressed to regulate the sum contents of Cy3G5G and Pn3G5G, and then determined the color intensity of petals. RrAOMT, involved in the downstream pathway of cyanidin biosynthesis, regulated the ratio of Cy3G5G to Pn3G5G via methylation and then determined the color hue of petals. It was worth mentioning that significantly higher delphinidin-3,5-O-diglucoside content and RrF3'5'H expression were detected from deep purple-red-flowered 8-16 germplasm with somewhat unique and visible blue hue. Three candidate key transcription factors identified by correlation analysis, RrMYB108, RrC1, and RrMYB114, might play critical roles in the control of petal color by regulating the expression of both RrAOMT and other multiple structural genes. These results provided novel insights into anthocyanin accumulation and flower coloration mechanism in R. rugosa, and the candidate key genes involved in anthocyanin biosynthesis could be valuable resources for the breeding of ornamental plants in future.

Identification of microRNAs and their target genes related to the accumulation of anthocyanin in purple potato tubers (Solanum tuberosum)

MicroRNAs (miRNAs) are types of endogenous non-coding small RNAs found in eukaryotes that are 18-25 nucleotides long. miRNAs are considered to be key regulatory factors of the expression of target mRNA. The roles of miRNAs involved in the regulation of anthocyanin accumulation in pigmented potatoes have not been systematically reported. In this study, the differentially expressed miRNAs and their target genes involved in the accumulation of anthocyanin during different developmental stages in purple potato (Solanum tuberosum L.) were identified using small RNA (sRNA) and degradome sequencing. A total of 275 differentially expressed miRNAs were identified in the sRNA libraries. A total of 69,387,200 raw reads were obtained from three degradome libraries. The anthocyanin responsive miRNA-mRNA modules were analyzed, and 37 miRNAs and 23 target genes were obtained. Different miRNAs regulate the key enzymes of anthocyanin synthesis in purple potato. The structural genes included phenylalanine ammonia lyase, chalcone isomerase, flavanone 3-hydroxylase, and anthocyanidin 3-O-glucosyltransferase. The regulatory genes included WD40, MYB, and SPL9. stu-miR172e-5p_L-1R-1, stu-miR828a, stu-miR29b-4-5p, stu-miR8019-5p_L-4R-3, stu-miR396b-5p, stu-miR5303f_L-7R + 2, stu-miR7997a_L-3, stu-miR7997b_L-3, stu-miR7997c_L + 3R-5_2ss2TA3AG, stu-miR156f-5p_L + 1, stu-miR156a, stu-miR156a_R-1, stu-miR156e, stu-miR858, stu-miR5021, stu-miR828 and their target genes were validated by qRT-PCR. They play important roles in the coloration and accumulation of purple potatoes. These results provide new insights into the biosynthesis of anthocyanins in pigmented potatoes.

PpMYB39 Activates PpDFR to Modulate Anthocyanin Biosynthesis during Peach Fruit Maturation

Anthocyanins are a class of water-soluble flavonoids widely present in fruits and vegetablesresponsible for the red flesh formation of peach fruit. Previously, several genes of the MYB family have been reported as transcriptional regulators of the anthocyanin biosynthetic pathway of structural genes in plants. In this study, through comparative transcriptome analysis of the white and red flesh peach cultivars of Harrow Blood and Asama Hakuto, a predicted transcription factor of the R2R3MYB family, PpMYB39, was identified to be associated with anthocyanin biosynthesis in peach fruit. In red-fleshed peach cultivars, the maximum amount of anthocyanin accumulated 95 days after full bloom (DAFB), at full maturity near ripening. Our results showed that, at this stage, PpMYB39 had the highest expression level among the 13 differentially expressed genes (DEGs) found in both red- and white-fleshed fruits, as well as a high correlation with total anthocyanin content throughout fruit development. Moreover, the expression analysis of the structural genes of the anthocyanin biosynthetic pathway in peach fruit revealed that Prunus persica Dihydroflavonol-4-reductase (PpDFR) was co-expressed and up-regulated with PpMYB39 at 95 DAFB, suggesting its possible role as a transcriptional activator of MYB39. This was further confirmed by a yeast one-hybrid assay and a dual luciferase reporter assay. Our results will be helpful in the breeding of peach cultivars and the identification and significance of color in peaches and related fruit species, in addition to providing an understanding of color formation in peach fruit for future research.