Comparative transcriptome analysis of genes involved in anthocyanin synthesis in blueberry

Seasonal variation of antioxidant bioactive compounds in southern highbush blueberry leaves and non-destructive quality prediction in situ by a portable near-infrared spectrometer

Blueberry leaves (BBL) are a natural source with strong antioxidant activity, but bioactive compounds and their seasonal variation remain vague. Here, two major classes of compounds including four caffeoylquinic acids and eight flavonoids were identified in two southern highbush cultivars ("Lanmei" #1 and "Jewel") grown in China. Major bioactive compounds were discovered using an online HPLC post-column derivatization system and determined as neochlorogenic acid (NeoCA), chlorogenic acid (CA), rutin, hyperoside, and isoquercitrin. CA contributed the most to the BBL antioxidant activity. "Lanmei" showed significant advantages in terms of rutin content and antioxidant activity over "Jewel" (P < 0.05). The highest CA content (CAC) of juvenile "Jewel" leaves reached 17.9%. July was the optimum harvest time for both cultivars after fruiting stage. Total phenolic content (TPC) and Trolox equivalent antioxidant capacity (TEAC) of fresh BBL were accurately predicted by a portable near-infrared (NIR) device in a rapid, low-cost, and non-destructive way in situ.

Carrageenan-based functional films hybridized with carbon dots and anthocyanins from rose petals for smart food packaging applications

Multifunctional smart biopolymeric films were fabricated using rose petal anthocyanin (RPA) and carrageenan (CAR) doped with rose petal-derived carbon dots (RP-CDs). Response surface-optimized RPA showed the highest total anthocyanins and radical scavenging ability. Produced RP-CD exhibited UV absorption and high fluorescence with antibacterial/antioxidant abilities. Enrichment with 2 % RP-CD and 5 % RPA in the CAR matrix results in improved physicochemical, i.e., water contact angle, water vapor permeability, and UV-blocking properties of the fabricated material. Results showed that nanocomposite films scavenged radicals better than the neat CAR films. Zeta potential, FTIR, SEM, and XPS suggested improved compatibility/stability and enhanced elemental configuration of RP-CDs/RPA additives in the CAR polymer matrix. Perishable food packaging (minced pork and shrimp) demonstrated that nanocomposite films work efficiently and non-destructively and are promising tools for monitoring real-time freshness through interpretable visual changes from red to yellow. The CAR/RP-CDs/RPA-based nanocomposite indicator films are expected to be applied as various smart packaging materials. These films possess the ability to promptly detect changes in quality, preserve the quality, and prolong the shelf life of packaged foods.

Integrated Untargeted Metabolome, Full-Length Sequencing and Transcriptome Analyses Reveal the Mechanism of Flavonoid Biosynthesis in Blueberry (Vaccinium spp.) Fruit

As a highly economic berry fruit crop, blueberry is enjoyed by most people and has various potential health benefits, many of which are attributed to the relatively high concentrations of flavonoids. To obtain more accurate and comprehensive transcripts, the full-length transcriptome of half-highbush blueberry (Vaccinium corymbosum/angustifolium cultivar Northland) obtained using single molecule real-time and next-generation sequencing technologies was reported for the first time. Overall, 147,569 consensus transcripts (average length, 2738 bp; N50, 3176 bp) were obtained. After quality control steps, 63,425 high-quality isoforms were obtained and 5030 novel genes, 3002 long non-coding RNAs, 3946 transcription factor genes (TFs), 30,540 alternative splicing events, and 2285 fusion gene pairs were identified. To better explore the molecular mechanism of flavonoid biosynthesis in mature blueberry fruit, an integrative analysis of the metabolome and transcriptome was performed on the exocarp, sarcocarp, and seed. A relatively complete biosynthesis pathway map of phenylpropanoids, flavonoids, and proanthocyanins in blueberry was constructed. The results of the joint analysis showed that the 228 functional genes and 42 TFs regulated 78 differentially expressed metabolites within the biosynthesis pathway of phenylpropanoids/flavonoids. O2PLS analysis results showed that the key metabolites differentially accumulated in blueberry fruit tissues were albireodelphin, delphinidin 3,5-diglucoside, delphinidin 3-O-rutinoside, and delphinidin 3-O-sophoroside, and 10 structural genes (4 Vc4CLs, 3 VcBZ1s, 1 VcUGT75C1, 1 VcAT, and 1 VcUGAT), 4 transporter genes (1 VcGSTF and 3 VcMATEs), and 10 TFs (1 VcMYB, 2 VcbHLHs, 4 VcWD40s, and 3 VcNACs) exhibited strong correlations with 4 delphinidin glycosides. These findings provide insights into the molecular mechanisms of flavonoid biosynthesis and accumulation in blueberry fruit.

Unveiling the evolutionary history of lingonberry (Vaccinium vitis-idaea L.) through genome sequencing and assembly of European and North American subspecies

Lingonberry (Vaccinium vitis-idaea L.) produces tiny red berries that are tart and nutty in flavor. It grows widely in the circumpolar region, including Scandinavia, northern parts of Eurasia, Alaska, and Canada. Although cultivation is currently limited, the plant has a long history of cultural use among indigenous communities. Given its potential as a food source, genomic resources for lingonberry are significantly lacking. To advance genomic knowledge, the genomes for 2 subspecies of lingonberry (V. vitis-idaea ssp. minus and ssp. vitis-idaea var. 'Red Candy') were sequenced and de novo assembled into contig-level assemblies. The assemblies were scaffolded using the bilberry genome (Vaccinium myrtillus) to generate a chromosome-anchored reference genome consisting of 12 chromosomes each with a total length of 548.07 Mb [contig N50 = 1.17 Mb, BUSCO (C%) = 96.5%] for ssp. vitis-idaea and 518.70 Mb [contig N50 = 1.40 Mb, BUSCO (C%) = 96.9%] for ssp. minus. RNA-seq-based gene annotation identified 27,243 and 25,718 genes on the respective assembly, and transposable element detection methods found that 45.82 and 44.58% of the genome were repeats. Phylogenetic analysis confirmed that lingonberry was most closely related to bilberry and was more closely related to blueberries than cranberries. Estimates of past effective population size suggested a continuous decline over the past 1-3 MYA, possibly due to the impacts of repeated glacial cycles during the Pleistocene leading to frequent population fragmentation. The genomic resource created in this study can be used to identify industry-relevant genes (e.g. anthocyanin production), infer phylogeny, and call sequence-level variants (e.g. SNPs) in future research.

Assessment of the Fruit Chemical Characteristics and Antioxidant Activity of Different Mulberry Cultivars (Morus spp.) in Semi-Arid, Sandy Regions of China

As a traditional cash crop with ecological and nutritional values, mulberry is gradually expanding its consumption worldwide due to its great regional adaptability and superior health functions. The widespread interest in nutrients has led to a growing need to explore in depth the health benefits of mulberries. Many studies are actively being conducted to investigate the adaptability of the diversity of mulberries in different applications. This study systematically investigated the physicochemical properties and antioxidant activity of four mulberry genotypes cultivated in China's semi-arid sandy regions to better understand the composition and health-promoting potential of this super crop. Chemical composition identification was identified via HPLC and antioxidant activity was further determined via DPPH and FRAP. The moisture, crude protein, ash, soluble solids, phenolics, anthocyanins, and flavonoids contents of mulberry were comparatively analyzed. The study revealed that the four mulberry genotypes showed significant differences in quality and content of the analyzed characteristics. The greatest antioxidant activity was found in Shensang 1, which had the most soluble solids (17%) and the highest amounts of free sugar (fructose: 5.14% and glucose: 5.46%). Ji'an had the most minerals (K: 2.35 mg/g, Ca: 2.27 mg/g, and Fe: 467.32 mg/kg) and it also contained chlorogenic acid, which has the potential to be turned into a natural hypoglycemic agent. PCA and Pearson correlation analysis indicated that the antioxidant activity was closely related to the chemical contents of total phenols, flavonoids, anthocyanins, and soluble sugars. If the antioxidant activity and nutrient content of the developed plants are considered, Shen Sang 1 is the most favorable variety. This finding can be used to support the widespread cultivation of mulberries to prevent desertification as well as to promote the development of the mulberry industry.

Characterization and Functional Analysis of Chalcone Synthase Genes in Highbush Blueberry (Vaccinium corymbosum)

Chalcone synthase (CHS) is the first key enzyme-catalyzing plant flavonoid biosynthesis. Until now, however, the blueberry CHS gene family has not been systematically characterized and studied. In this study, we identified 22 CHS genes that could be further classified into four subfamilies from the highbush blueberry (Vaccinium corymbosum) genome. This classification was well supported by the high nucleotide and protein sequence similarities and similar gene structure and conserved motifs among VcCHS members from the same subfamily. Gene duplication analysis revealed that the expansion of the blueberry CHS gene family was mainly caused by segmental duplications. Promoter analysis revealed that the promoter regions of VcCHSs contained numerous cis-acting elements responsive to light, phytohormone and stress, along with binding sites for 36 different types of transcription factors. Gene expression analysis revealed that Subfamily I VcCHSs highly expressed in fruits at late ripening stages. Through transient overexpression, we found that three VcCHSs (VcCHS13 from subfamily II; VcCHS8 and VcCHS21 from subfamily I) could significantly enhance the anthocyanin accumulation and up-regulate the expression of flavonoid biosynthetic structural genes in blueberry leaves and apple fruits. Notably, the promoting effect of the Subfamily I member VcCHS21 was the best. The promoter of VcCHS21 contains a G-box (CACGTG) and an E-box sequence, as well as a bHLH binding site. A yeast one hybridization (Y1H) assay revealed that three anthocyanin biosynthesis regulatory bHLHs (VcAN1, VcbHLH1-1 and VcbHLH1-2) could specifically bind to the G-box sequence (CACGTG) in the VcCHS21 promoter, indicating that the expression of VcCHS21 was regulated by bHLHs. Our study will be helpful for understanding the characteristics and functions of blueberry CHSs.

Genome-Wide Identification of Bilberry WRKY Transcription Factors: Go Wild and Duplicate

WRKY transcription factor genes compose an important family of transcriptional regulators that are present in several plant species. According to previous studies, these genes can also perform important roles in bilberry (Vaccinium myrtillus L.) metabolism, making it essential to deepen our understanding of fruit ripening regulation and anthocyanin biosynthesis. In this context, the detailed characterization of these proteins will provide a comprehensive view of the functional features of VmWRKY genes in different plant organs and in response to different intensities of light. In this study, the investigation of the complete genome of the bilberry identified 76 VmWRKY genes that were evaluated and distributed in all twelve chromosomes. The proteins encoded by these genes were classified into four groups (I, II, III, and IV) based on their conserved domains and zinc finger domain types. Fifteen pairs of VmWRKY genes in segmental duplication and four pairs in tandem duplication were detected. A cis element analysis showed that all promoters of the VmWRKY genes contain at least one potential cis stress-response element. Differential expression analysis of RNA-seq data revealed that VmWRKY genes from bilberry show preferential or specific expression in samples. These findings provide an overview of the functional characterization of these proteins in bilberry.

The Characteristics of Whey Protein and Blueberry Juice Mixed Fermentation Gels Formed by Lactic Acid Bacteria

The properties of blueberry juice and whey protein gels formed by the mixed fermentation of L. plantarum 67 and L. paracasei W125 were investigated. The state of the gels, including the colour and surface morphology of the microspheres, showed significant changes with different fermentation times. The polyphenolic, flavonoid, and protein release of whey protein or combined blueberry juice fermented gels under in vitro digestion were investigated. The whey protein and blueberry juice fermented gels had more small pores, with a honeycomb structure, compared to whey protein fermented gels. The hardness of the gels was increased after fermentation for 7 h for the whey protein gels and whey protein mixture blueberry juice gels. The storage modulus and water-holding capacity of the gels were increased between fermentation times of 6 h and 8 h. The swelling rates of the whey protein gels fermented for 7 h and whey protein mixed blueberry juice gels fermented for 8 h and kept in pepsin-free simulated gastric fluid for 1 h had higher values. The release of polyphenols, flavonoids, and protein for the fermented gels was higher at fermentation of 7 h in the in vitro digestion experiment. We found that the chewiness of the whey protein gels, or whey protein mixed fermentation gels, was higher at a fermentation time of 7.5 h and 8 h. However, the cohesiveness values were not significantly different. Therefore, whey protein fermented gels and whey protein mixed blueberry juice fermented gels should be fermented for more than 7 h. This facilitates the release of polyphenols, flavonoids, and protein in the gastric juices.

Comparative transcriptome analysis of Veratrum maackii and Veratrum nigrum reveals multiple candidate genes involved in steroidal alkaloid biosynthesis

Veratrum (Melanthiaceae; Liliales) is a genus of perennial herbs known for the production of unique bioactive steroidal alkaloids. However, the biosynthesis of these compounds is incompletely understood because many of the downstream enzymatic steps have yet to be resolved. RNA-Seq is a powerful method that can be used to identify candidate genes involved in metabolic pathways by comparing the transcriptomes of metabolically active tissues to controls lacking the pathway of interest. The root and leaf transcriptomes of wild Veratrum maackii and Veratrum nigrum plants were sequenced and 437,820 clean reads were assembled into 203,912 unigenes, 47.67% of which were annotated. We identified 235 differentially expressed unigenes potentially involved in the synthesis of steroidal alkaloids. Twenty unigenes, including new candidate cytochrome P450 monooxygenases and transcription factors, were selected for validation by quantitative real-time PCR. Most candidate genes were expressed at higher levels in roots than leaves but showed a consistent profile across both species. Among the 20 unigenes putatively involved in the synthesis of steroidal alkaloids, 14 were already known. We identified three new CYP450 candidates (CYP76A2, CYP76B6 and CYP76AH1) and three new transcription factor candidates (ERF1A, bHLH13 and bHLH66). We propose that ERF1A, CYP90G1-1 and CYP76AH1 are specifically involved in the key steps of steroidal alkaloid biosynthesis in V. maackii roots. Our data represent the first cross-species analysis of steroidal alkaloid biosynthesis in the genus Veratrum and indicate that the metabolic properties of V. maackii and V. nigrum are broadly conserved despite their distinct alkaloid profiles.

Metabolomic and transcriptomic analyses of the flavonoid biosynthetic pathway in blueberry (Vaccinium spp.)

As a highly economic small fruit crop, blueberry is enjoyed by most people in terms of color, taste, and rich nutrition. To better understand its coloring mechanism on the process of ripening, an integrative analysis of the metabolome and transcriptome profiles was performed in three blueberry varieties at three developmental stages. In this study, 41 flavonoid metabolites closely related to the coloring in blueberry samples were analyzed. It turned out that the most differential metabolites in the ripening processes were delphinidin-3-O-arabinoside (dpara), peonidin-3-O-glucoside (pnglu), and delphinidin-3-O-galactoside (dpgal), while the most differential metabolites among different varieties were flavonols. Furthermore, to obtain more accurate and comprehensive transcripts of blueberry during the developmental stages, PacBio and Illumina sequencing technology were combined to obtain the transcriptome of the blueberry variety Misty, for the very first time. Finally, by applying the gene coexpression network analysis, the darkviolet and bisque4 modules related to flavonoid synthesis were determined, and the key genes related to two flavonoid 3', 5'-hydroxylase (F3'5'H) genes in the darkviolet module and one bHLH transcription factor in the bisque4 module were predicted. It is believed that our findings could provide valuable information for the future study on the molecular mechanism of flavonoid metabolites and flavonoid synthesis pathways in blueberries.

Influence of Storage Conditions on Stability of Phenolic Compounds and Antioxidant Activity Values in Nutraceutical Mixtures with Edible Flowers as New Dietary Supplements

This paper investigates the effects of storage conditions on the stability of phenolics and their antioxidant activities in unique nutraceutical supplements containing non-traditional cereal flakes, edible flowers, fruits, nuts, and seeds. Significant total phenolic content (TPC) of 1170-2430 mg GAE/kg and total anthocyanin content (TAC) with the values of 322-663 mg C3G/kg were determined with the highest TPC content established in free phenolic fractions. The most notable declines in TPC (by 53%), TAC (by 62%), phenolics (e.g., glycosylated anthocyanins by 35-67%), and antioxidant activity (by 25% using DPPH) were established in the presence of sunlight at 23 °C followed by the storage at 40 °C. Quercetin, rutin, peonidin, pelargonidin, p-coumaric, ellagic, and p-hydroxybenzoic acids were identified as the least stable phenolics when exposed to sunlight. Furthermore, glycosylated forms of anthocyanins demonstrated a greater stability when compared with anthocyanidins. The mixtures considerably eliminated ABTS and DPPH radicals. In all samples, water-soluble substances showed a higher antioxidant activity than lipid-soluble substances with the main contributors in the following order: delphinidin-3-glucoside (r = +0.9839) > p-coumaric > gallic > sinapic > p-hydroxybenzoic acids > delphinidin > peonidin and malvidin (r = +0.6538). Gluten-free nutraceutical mixtures M3 (containing red rice and black quinoa flakes, red and blue cornflowers, blueberries, and barberries) and M4 (containing red and black rice flakes, rose, blue cornflower, blueberries, raspberries, and barberries) were evaluated as the least stable under all storage conditions although they showed considerable phenolic concentrations. Phenolic contents and antioxidant activity of the nutraceutical mixtures were the highest at 23 °C without the presence of sunlight with the most stable M1 nutraceutical mixture (containing oat and red wheat flakes, hibiscus, lavender, blueberries, raspberries, and barberries).

The Antioxidant Activity and Protection of Probiotic Bacteria in the In Vitro Gastrointestinal Digestion of a Blueberry Juice and Whey Protein Fermentation System

Blueberries have received great attention due to the health effects of their bioactive compounds, such as antioxidant, antitumor, and anti-obesity properties. Probiotics also have these health-promoting benefits. However, these biological activities may be affected by the processs of gastrointestinal digestion, which decreases their functionality. This study aimed to use a more convenient method to improve the blueberries’ antioxidant activity and protective effects on probiotic cells by fermentation with whey protein, and to explore the possible mechanisms underlying these effects. This result showed that the total phenolic content, anthocyanin content, reducing power, DPPH radical scavenging capacity, and probiotic cells’ survival in a blueberry juice and whey protein fermentation system were enhanced in a model of in vitro gastrointestinal digestion. The bioactive compounds in blueberry juice interacted with whey protein, as shown through FTIR. The stability of phenolic compounds was enhanced, and the release of functional compounds in the mixture fermentation system was delayed through CLSM. Interactions between bioactive compounds in blueberries, whey protein, and bacterial surface proteins, glycoproteins or polysaccharides during fermentation were studied by SDS-PAGE. Thus, the stability of bioactive activities in the mixed system after fermentation was strengthened by the interaction. The mixed fermentation system has promising potential for improving antioxidant activity and protecting probiotic cells.

Genome-Wide Analysis of MYB Transcription Factors and Screening of MYBs Involved in the Red Color Formation in Rhododendron delavayi

Flower color is one of the crucial traits of ornamental plants. Rhododendron delavayi Franch. is a famous ornamental plant species distributed in the mountain areas of Southwest China. This plant has red inflorescence and young branchlets. However, the molecular basis of the color formation of R. delavayi is unclear. In this study, 184 MYB genes were identified based on the released genome of R. delavayi. These genes included 78 1R-MYB, 101 R2R3-MYB, 4 3R-MYB, and 1 4R-MYB. The MYBs were divided into 35 subgroups using phylogenetic analysis of the MYBs of Arabidopsis thaliana. The members of the same subgroup in R. delavayi had similar conserved domains and motifs, gene structures, and promoter cis-acting elements, which indicate their relatively conserved function. In addition, transcriptome based on unique molecular identifier strategy and color difference of the spotted petals, unspotted petals, spotted throat, unspotted throat, and branchlet cortex were detected. Results showed significant differences in the expression levels of R2R3-MYB genes. Weighted co-expression network analysis between transcriptome and chromatic aberration values of five types of red samples showed that the MYBs were the most important TFs involved in the color formation, of which seven were R2R3-MYB, and three were 1R-MYB. Two R2R3-MYB (DUH019226.1 and DUH019400.1) had the highest connectivity in the whole regulation network, and they were identified as hub genes for red color formation. These two MYB hub genes provide references for the study of transcriptional regulation of the red color formation of R. delavayi.

The mechanism leading to color differences between purple-red and green partridge tea leaves

BACKGROUND

Partridge tea (Mallotus oblongifolius) is used as an important beverage and medical plant in Hainan province of China. Although some information about the morphology, cytology, and genetics of partridge tea has been reported in the literature, knowledge about this plant is still very limited. The leaves are the most important part for every tea plant, with a major role in nutrition and other functions. The leaves of different cultivars of partridge tea are different in colors and functions. The molecular mechanism of color formation of partridge tea leaf is still unclear. We reveal the molecular mechanism of the color difference between purple-red and green partridge tea leaves through metabolome and transcriptome analysis.

RESULTS

We identified 665 compounds in the two partridge tea cultivars through metabolome analysis. Among these compounds, the content of 324 differed between the two cultivars. We also annotated 50 042 unigenes in the two cultivars by transcriptome analysis; 9665 unigenes were expressed differently between the two cultivars. Using an integrated analysis of the metabolome and transcriptome data, we found that the compounds and genes involved in anthocyanin biosynthesis were up-regulated in the purple-red leaves, compared with the green leaves.

CONCLUSION

Our results showed that the anthocyanin biosynthesis pathway genes were up-regulated, which resulted in the up-regulation of the anthocyanin, making the leaf color purple-red. Our study reveals the molecular mechanism of the color difference between purple-red and green partridge tea, and lays a foundation for the genetic breeding of partridge tea genetic and the utilization of its volatile components. © 2022 Society of Chemical Industry.

Transcriptional networks orchestrating red and pink testa color in peanut

BACKGROUND

Testa color is an important trait of peanut (Arachis hypogaea L.) which is closely related with the nutritional and commercial value. Pink and red are main color of peanut testa. However, the genetic mechanism of testa color regulation in peanut is not fully understood. To elucidate a clear picture of peanut testa regulatory model, samples of pink cultivar (Y9102), red cultivar (ZH12), and two RNA pools (bulk red and bulk pink) constructed from F₄ lines of Y9102 x ZH12 were compared through a bulk RNA-seq approach.

RESULTS

A total of 2992 differential expressed genes (DEGs) were identified among which 317 and 1334 were up-regulated and 225 and 1116 were down-regulated in the bulk red-vs-bulk pink RNA pools and Y9102-vs-ZH12, respectively. KEGG analysis indicates that these genes were divided into significantly enriched metabolic pathways including phenylpropanoid, flavonoid/anthocyanin, isoflavonoid and lignin biosynthetic pathways. Notably, the expression of the anthocyanin upstream regulatory genes PAL, CHS, and CHI was upregulated in pink and red testa peanuts, indicating that their regulation may occur before to the advent of testa pigmentation. However, the differential expression of down-stream regulatory genes including F3H, DFR, and ANS revealed that deepening of testa color not only depends on their gene expression bias, but also linked with FLS inhibition. In addition, the down-regulation of HCT, IFS, HID, 7-IOMT, and I2'H genes provided an alternative mechanism for promoting anthocyanin accumulation via perturbation of lignin and isoflavone pathways. Furthermore, the co-expression module of MYB, bHLH, and WRKY transcription factors also suggested a fascinating transcriptional activation complex, where MYB-bHLH could utilize WRKY as a co-option during the testa color regulation by augmenting anthocyanin biosynthesis in peanut.

CONCLUSIONS

These findings reveal candidate functional genes and potential strategies for the manipulation of anthocyanin biosynthesis to improve peanut varieties with desirable testa color.

Integrated transcriptome and metabolome analysis reveals the anthocyanin biosynthesis mechanisms in blueberry (Vaccinium corymbosum L.) leaves under different light qualities

INTRODUCTION

Blueberry (Vaccinium corymbosum L.) is a popular fruit with an abundance of anthocyanins in its leaves and fruits. Light is one of the pivotal environmental elements that affects plant growth and development, but the regulatory mechanism between light quality and anthocyanin formation is poorly understood.

METHODS

An integrated transcriptome and metabolome analysis was performed to investigate the effects of white (control), blue (B), red (R), and red/blue (60R/40B) light on blueberry growth and reveal the potential pathway controlling anthocyanin biosynthesis in blueberry leaves.

RESULTS

The anthocyanin content was significantly improved by the blue and red/blue light when compared with white light, whereas there was a significant reduction in the photosynthesis under the blue light, showing an inverse trend to that of anthocyanin accumulation. Transcriptomic analysis resulted in the assembly of 134,709 unigenes. Of these, 22 were differentially expressed genes (DEGs) that participate in the anthocyanin biosynthesis pathway, with the majority being significantly up-regulated under the blue light. Most of the photosynthesis-related genes that were down-regulated were expressed during anthocyanin accumulation. Targeted metabolome profiling identified 44 metabolites associated with anthocyanin biosynthesis. The contents of most of these metabolites were higher under blue light than the other light conditions, which was consistent with the transcriptome results. The integrated transcriptome and metabolome analysis suggested that, under blue light, leucoanthocyanidin dioxygenase (LDOX), O-methyltransferase (OMT), and UDP-glucose flavonoid glucosyltransferase (UFGT) were the most significantly expressed, and they promoted the synthesis of cyanidin (Cy), malvidin (Mv), and pelargonidin (Pg) anthocyanidins, respectively. The expression levels of dihydroflavonol 4-reductase (DFR) and OMT, as well as the accumulation of delphinidin (Dp), peonidin (Pn), and petunidin (Pt), were significantly increased by the red/blue light.

DISCUSSION

The blue and red/blue lights promoted anthocyanin biosynthesis via inducing the expression of key structural genes and accumulation of metabolites involved in anthocyanin synthesis pathway. Moreover, there was a possible feedback regulating correlation between anthocyanin biosynthesis and photosynthesis under different light qualities in blueberry leaves. This study would provide a theoretical basis for elucidating the underlying regulatory mechanism of anthocyanin biosynthesis of V. corymbosum.

Comparative transcriptome analysis reveals key candidate genes mediating ovarian development in Spodoptera frugiperda fed on two host plants

The fall armyworm (FAW), Spodoptera frugiperda, is a highly polyphagous lepidopteran pest, with its growth and adaptation affected by different host plants. However, little is known about the effects of host plants on ovarian development in this species. Thus, we evaluated the effects of feeding on corn (Zea mays L.) and goosegrass (Eleusine indica), on the ovarian development of S. frugiperda. Using various stages of S. frugiperda, we also evaluated the larval and pupal weights, number of eggs, and differentiation of ovarioles over time. Results showed that females fed on goosegrass had shorter ovarioles and laid less eggs than those fed on corn. Transcriptome analysis identified 3,213 genes involved in ovarian development in the fall armyworm. Of these, 881 genes were differentially expressed when fed on corn and goosegrass. The analysis also indicated that the hormone biosynthetic pathways may be involved in the reproductive system. In relation to the reproductive function, nine juvenile hormone (JH) biosynthetic genes, four 20-hydroxyecdysone (20E) biosynthetic genes, and four ovary-relevant functional genes were identified. The time course of the expression profiles of these hormone- and ovary development-related genes was measured by quantitative real-time PCR (qRT-PCR). In total, six of them showed a decreasing trend in the ovary of the FAW fed on goosegrass, while two genes showed an increasing trend. Our results showed that significant changes in the reproductive activity/ovary development in the FAW occurred in response to different diets. These results serve as bases for evaluating how optimal host plants and feeding preference affect ovarian development in the FAW.

Composition and antioxidant activity of anthocyanins from Aronia melanocarpa extracted using an ultrasonic-microwave-assisted natural deep eutectic solvent extraction method

A time-saving, efficient, and environmentally friendly ultrasonic-microwave-assisted natural deep eutectic solvent (UMAE-NADES) extraction method was developed for the extraction of anthocyanins from Aronia melanocarpa. Eight different natural eutectic solvents were screened initially, and choline chloride-glycerol was selected as the extraction solvent. The extraction conditions were optimized using the response surface methodology, and the extraction rate of anthocyanins was higher than those achieved using the traditional ethanol method, natural deep eutectic solvent extraction method, and ultrasonic-microwave-assisted ethanol method. Six anthocyanins, including cyanidin-3-O-galactoside, cyanidin-3-O-glucoside, cyanidin-3-O-arabinoside, cyanidin-3-O-xyloside, cyanidin-3,5-O-dihexoside, and the dimer of cyanidin-hexoside were identified and extracted at a purity of 448.873 mg/g using high performance liquid chromatography-mass spectrometry (HPLC-MS). The compounds extracted using UMAE-NADES had higher antioxidant capacities than those extracted by the other three methods. The UMAE-NADES demonstrated significant efficiency toward the extraction of bioactive substances and has potential utility in the food and pharmaceutical industries.

Melatonin Enhances the Postharvest Disease Resistance of Blueberries Fruit by Modulating the Jasmonic Acid Signaling Pathway and Phenylpropanoid Metabolites

In this study, to investigate the physiological and molecular mechanisms of melatonin inhibiting the postharvest rot of blueberry fruits, blueberry fruits were dipped in 0.3 mmol L⁻¹ melatonin solution for 3 min and stored at 0°C for 80 days. The results indicated that melatonin did not significantly (p > 0.05) inhibit the mycelial growth or spore germination of Alternaria alternata, Botrytis cinerea, and Colletotrichum gloeosporioides. In addition, an in vivo study revealed that melatonin treatment increased the enzymatic activities of phenylalanine ammonia lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate-CoA ligase (4CL), cinnamyl alcohol dehydrogenase (CAD), polyphenol oxidase (PPO), and peroxidase (POD) in fruits. Furthermore, genes related to jasmonic acid synthesis were upregulated (VaLOX, VaAOS, and VaAOC), as were those related to pathogenesis-related proteins (VaGLU and VaCHT) and phenylpropane metabolism (VaPAL, VaC4H, Va4CL, VaCAD, VaPPO, and VaPOD), which promoted the accumulation of total phenols, flavonoids, anthocyanins, and lignin in the fruits. These results suggest that melatonin enhances the postharvest disease resistance of blueberry fruits by mediating the jasmonic acid signaling pathway and the phenylpropane pathway.

There and back again; historical perspective and future directions for Vaccinium breeding and research studies

The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have increased worldwide over the crops' relatively short domestication history (~100 years). Other species, including bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and ohelo berry (Vaccinium reticulatum) are largely still harvested from the wild but with crop improvement efforts underway. Here, we present a review article on these Vaccinium berry crops on topics that span taxonomy to genetics and genomics to breeding. We highlight the accomplishments made thus far for each of these crops, along their journey from the wild, and propose research areas and questions that will require investments by the community over the coming decades to guide future crop improvement efforts. New tools and resources are needed to underpin the development of superior cultivars that are not only more resilient to various environmental stresses and higher yielding, but also produce fruit that continue to meet a variety of consumer preferences, including fruit quality and health related traits.

Comparative Transcriptome Analysis Reveals Differential Regulation of Flavonoids Biosynthesis Between Kernels of Two Pecan Cultivars

Flavonoids influence the flavor and nutritional value of pecan nuts. However, limited information is available regarding the molecular mechanisms underlying pecan flavonoid biosynthesis. Here, we used a high ("YLC28") and a low ("Oconee") flavonoid content cultivar as the research objects. The changes in flavonoid content and the gene transcription patterns during kernel development were identified. Different accumulation patterns of total flavonoids (TF) and condensed tannins (CT) were observed between the two cultivars. The contents of TF and CT in "YLC28" were 1.76- and 2.67-fold higher levels than that of "Oconee" on 150 days after full bloom of female flowers, respectively. In total, 30 RNA-Seq libraries were constructed and sequenced. The upregulated genes in "YLC28" were highly enriched in flavonoid-related pathways. Thirty-three structural genes were identified, and the expression of two phenylalanine ammonia lyases, one chalcone synthase, one flavonoid 3',5'-hydroxylase, and one flavonol synthase exhibited high correlation (r ≥ 0.7, p < 0.01) with the condensed tannin content in "YLC28." A putative MYB transcription factor, CIL1093S0100, might act as a flavonoid biosynthesis repressor during kernel development. Altogether, these results will be useful for uncovering the molecular mechanisms of flavonoid biosynthesis and subsequently accelerating quality pecan breeding.

Transcriptomic and Physiological Analysis Reveals the Responses to Auxin and Abscisic Acid Accumulation During Vaccinium corymbosum Flower Bud and Fruit Development

Blueberry (Vaccinium corymbosum) is reputed as a rich source of health-promoting phytonutrients, which contributes to its burgeoning consumer demand and production. However, blueberries are much smaller and have lower yields than most domesticated berries, and the inherent regulatory mechanisms remain elusive. In this study, the cytological and physiological changes, as well as comparative transcriptomic analysis throughout flower and fruit development in the southern highbush blueberry cultivar 'O'Neal' were performed. 'O'Neal' hypanthium and fruit exhibited a distinctive cell proliferation pattern, and auxin accumulation was unusual throughout development, while abscisic acid (ABA) levels rapidly increased in association with anthocyanin accumulation, total phenolic reduction and fruit maturation. Transcriptomic data showed that many differentially expressed genes (DEGs) were specifically expressed at each flower bud and fruit developmental stage. Further weighted gene co-expression network analysis (WGCNA) revealed numerous DEGs that correlated with the cell numbers of outer mesocarp and columella, showed two distinctive expression patterns. Most of the DEGs involved in auxin biosynthesis, transportation and signal transduction were upregulated, and this upregulation was accompanied by cell expansion, and flower bud and fruit development. However, individual members of VcSAUR50 and VcIAA9 families might be insensitive to auxin, suggesting that these genes play a distinctive role in the growth and development of blueberry fruits. These results will support future research to better understand the flower and fruit development of southern highbush blueberry.

Combined Transcriptome and Metabolome Analysis of Alfalfa Response to Thrips Infection

Thrips (Thysanoptera: Thripidae) is a major insect pest for alfalfa which can result in decreased plant nutrients, low yields, and even plant death. To identify the differentially expressed genes and metabolites in response to thrips in alfalfa, a combination of metabolomics and transcriptomics was employed using alfalfa (Caoyuan No. 2) with and without thrips infestation. The results showed that the flavonoid biosynthesis and isoflavonoid biosynthesis pathways were the most significantly enriched pathways in response to thrips infection, as shown by the combined transcriptome and metabolome analysis. The transcriptome results showed that SA and JA signal transduction and PAPM-triggered immunity and the MAPK signaling pathway–plant pathways played a crucial role in thrips-induced plant resistance in alfalfa. In addition, we found that thrips infestation could also induce numerous changes in plant primary metabolism, such as carbohydrate and amino acid metabolism as compared to the control. Overall, our results described here should improve fundamental knowledge of molecular responses to herbivore-inducible plant defenses and contribute to the design of strategies against thrips in alfalfa.

Transcriptome analysis reveals important candidate gene families related to oligosaccharides biosynthesis in Morindaofficinalis

Morinda officinalis How (MO) is one of the best-known traditional herbs and is widely cultivated in subtropical and tropical areas for many years, especially in southern China. Oligosaccharides are the major constituents in the roots of MO, which is well known for its therapeutic effects with anti-depression, anti-osteoporosis, memory-enhancing, ect. To date, the main gene families that regulate the biosynthetic pathway of MO oligosaccharides metabolism yet have been published. In our study, six cDNA libraries generated from six plants of MO were sequenced utilizing an Illumina HiSeq 4000 platform. Corresponding totals of more than 132.60 million clean reads were obtained from the six libraries and assembled into 25,812 unigenes with an average length of 1288 bp. Moreover, 6036 unigenes were found to be allocated to 26 pathways maps using several public databases, and 2538 differential expression genes (DEGs) were screened. Among them, 25 genes from three families were selected as the mainly candidate genes related to MO oligosaccharides biosynthesis. Then, the expression patterns of six DEGs closely related to MO oligosaccharides biosynthesis were verified by quantitative real-time PCR (qRT-PCR). Besides, the MO was clustered more closely to Coffea arabica of Rubiaceae. In summary, the transcriptomic analysis was used to investigate the differences in expression genes of oligosaccharides biosynthesis, with the notable outcome that several key gene families were closely linked to oligosaccharides biosynthesis.

Transcriptome and Metabolome Analysis Unveil Anthocyanin Metabolism in Pink and Red Testa of Peanut (Arachis hypogaea L.)

Peanut (Arachis hypogaea L.) is an important source of oil and food around the world, and the testa color affects its appearance and commercial value. However, few studies focused on the mechanism of pigment formation in peanut testa. In this study, cultivars Shanhua 15 with pink testa and Zhonghua 12 with red testa were used as materials to perform the combined analysis of transcriptome and metabolome. A total of 198 flavonoid metabolites were detected, among which petunidin 3-O-glucoside and cyanidin O-acetylhexoside in Zhonghua12 were 15.23 and 14.72 times higher than those of Shanhua 15 at the R7 stage, revealing the anthocyanins underlying the red testa. Transcriptome analysis showed that there were 6059 and 3153 differentially expressed genes between Shanhua 15 and Zhonghua 12 in different growth periods, respectively. These differentially expressed genes were significantly enriched in the flavonoid biosynthesis, biosynthesis of secondary metabolites, and metabolic pathways. Integrated analysis of transcriptome and metabolome indicated CHS gene (arahy.CM90T6), F3'H genes (arahy. 8F7PE4 and arahy. K8H9R8), and DFR genes (arahy. LDV9QN and arahy. X8EVF3) may be the key functional genes controlling the formation of pink and red testa in peanut. Transcription factors MYB (arahy.A2IWKV, arahy.US2SKM, arahy.SJGE27, arahy.H8DJRL, and arahy.PR7AYB), bHLH (arahy.26781N, arahy.HM1IVV, and arahy.MP3D3D), and WD40 (arahy.L6JJW9) in the biosynthetic pathway of anthocyanin were significantly upregulated in Zhonghua 12 which may be the key regulatory genes in testa pigment formation. This is a comprehensive analysis on flavonoid metabolites and related genes expression in peanut testa, providing reference for revealing the regulatory mechanism of pigment accumulation in peanut testa.

Exploring the genes involved in biosynthesis of dihydroquercetin and dihydromyricetin in Ampelopsis grossedentata

Dihydroquercetin (DHQ), an extremely low content compound (less than 3%) in plants, is an important component of dietary supplements and used as functional food for its antioxidant activity. Moreover, as downstream metabolites of DHQ, an extremely high content of dihydromyricetin (DHM) is up to 38.5% in Ampelopsis grossedentata. However, the mechanisms involved in the biosynthesis and regulation from DHQ to DHM in A. grossedentata remain unclear. In this study, a comparative transcriptome analysis of A. grossedentata containing extreme amounts of DHM was performed on the Illumina HiSeq 2000 sequencing platform. A total of 167,415,597 high-quality clean reads were obtained and assembled into 100,584 unigenes having an N50 value of 1489. Among these contigs, 57,016 (56.68%) were successfully annotated in seven public protein databases. From the differentially expressed gene (DEG) analysis, 926 DEGs were identified between the B group (low DHM: 210.31 mg/g) and D group (high DHM: 359.12 mg/g) libraries, including 446 up-regulated genes and 480 down-regulated genes (B vs. D). Flavonoids (DHQ, DHM)-related DEGs of ten structural enzyme genes, three myeloblastosis transcription factors (MYB TFs), one basic helix-loop-helix (bHLH) TF, and one WD40 domain-containing protein were obtained. The enzyme genes comprised three PALs, two CLs, two CHSs, one F3'H, one F3'5'H (directly converts DHQ to DHM), and one ANS. The expression profiles of randomly selected genes were consistent with the RNA-seq results. Our findings thus provide comprehensive gene expression resources for revealing the molecular mechanism from DHQ to DHM in A. grossedentata. Importantly, this work will spur further genetic studies about A. grossedentata and may eventually lead to genetic improvements of the DHQ content in this plant.

Structural and compositional changes of whey protein and blueberry juice fermented using Lactobacillus plantarum or Lactobacillus casei during fermentation

This study aimed to improve the stability of the anthocyanins and phenolic acids of blueberry by forming hydrogen bonds or hydrophobic interactions with whey protein using lactic acid fermentation. The effects of the initial pH on the characteristics of the whey protein and blueberry juice system fermented using Lactobacillus plantarum and Lactobacillus casei were investigated. The color and total phenol and anthocyanin contents of the blueberry juice and whey protein system became stable after fermentation using Lactobacillus plantarum and Lactobacillus casei. Fluorescence measurements and Fourier transform infrared spectroscopy (FTIR) analysis reveal that the characteristics of whey protein and blueberry juice changed significantly after fermentation using Lactobacillus plantarum and Lactobacillus casei indicating the binding of anthocyanins or phenolic hydroxyl groups of blueberry to N-H, C-N and C[double bond, length as m-dash]O groups of whey protein. The α-helix content of whey protein and blueberry fermented using Lactobacillus plantarum alone decreased by 18% and β-sheet content increased by approximately 27% compared to whey protein fermented using Lactobacillus plantarum.

Comparative anatomical and transcriptomic insights into Vaccinium corymbosum flower bud and fruit throughout development

BACKGROUND

Blueberry (Vaccinium spp.) is characterized by the production of berries that are smaller than most common fruits, and the underlying mechanisms of fruit size in blueberry remain elusive. V. corymbosum 'O'Neal' and 'Bluerain' are commercial southern highbush blueberry cultivars with large- and small-size fruits, respectively, which mature 'O'Neal' fruits are 1 ~ 2-fold heavier than those of 'Bluerain'. In this study, the ontogenetical patterns of 'O'Neal' and 'Bluerain' hypanthia and fruits were compared, and comparative transcriptomic analysis was performed during early fruit development.

RESULTS

V. corymbosum 'O'Neal' and 'Bluerain' hypanthia and fruits exhibited intricate temporal and spatial cell proliferation and expansion patterns. Cell division before anthesis and cell expansion after fertilization were the major restricting factors, and outer mesocarp was the key tissue affecting fruit size variation among blueberry genotypes. Comparative transcriptomic and annotation analysis of differentially expressed genes revealed that the plant hormone signal transduction pathway was enriched, and that jasmonate-related TIFYs genes might be the key components orchestrating other phytohormones and influencing fruit size during early blueberry fruit development.

CONCLUSIONS

These results provided detailed ontogenetic evidence for determining blueberry fruit size, and revealed the important roles of phytohormone signal transductions involving in early fruit development. The TIFY genes could be useful as markers for large-size fruit selection in the current breeding programs of blueberry.

Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species

Blueberries (Vaccinium spp.) are highly vulnerable to changing climatic conditions, especially increasing temperatures. To gain insight into mechanisms underpinning the response to heat stress, two blueberry species were subjected to heat stress for 6 and 9 h at 45 °C, and leaf samples were used to study the morpho-physiological and transcriptomic changes. As compared with Vaccinium corymbosum, Vaccinium darrowii exhibited thermal stress adaptation features such as small leaf size, parallel leaf orientation, waxy leaf coating, increased stomatal surface area, and stomatal closure. RNAseq analysis yielded ~135 million reads and identified 8305 differentially expressed genes (DEGs) during heat stress against the control samples. In V. corymbosum, 2861 and 4565 genes were differentially expressed at 6 and 9 h of heat stress, whereas in V. darrowii, 2516 and 3072 DEGs were differentially expressed at 6 and 9 h, respectively. Among the pathways, the protein processing in the endoplasmic reticulum (ER) was the highly enriched pathway in both the species: however, certain metabolic, fatty acid, photosynthesis-related, peroxisomal, and circadian rhythm pathways were enriched differently among the species. KEGG enrichment analysis of the DEGs revealed important biosynthesis and metabolic pathways crucial in response to heat stress. The GO terms enriched in both the species under heat stress were similar, but more DEGs were enriched for GO terms in V. darrowii than the V. corymbosum. Together, these results elucidate the differential response of morpho-physiological and molecular mechanisms used by both the blueberry species under heat stress, and help in understanding the complex mechanisms involved in heat stress tolerance.

Nitric Oxide and Hydrogen Peroxide Are Involved in Methyl Jasmonate-Regulated Response against Botrytis cinerea in Postharvest Blueberries

The involvement and the relationship between nitric oxide (NO) and hydrogen peroxide (H₂O₂) in methyl jasmonate (MeJA)-induced immune responses in blueberries against Botrytis cinerea was explored using diphenylene iodonium (DPI, NADPH oxidase inhibitor) and 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO, NO scavenger). MeJA induced NO and H₂O₂ burst and enhanced the resistance of blueberries by elevating defense-related enzymes and the phenylpropanoid pathway. However, the above impacts stimulated by MeJA were weakened by DPI and destroyed by cPTIO. Furthermore, cPTIO abolished the increment in H₂O₂ by regulating the activities of NADPH oxidase, superoxide dismutase, catalase, and ascorbate peroxidase, whereas DPI weakened the increase in H₂O₂ but barely affected the generation of NO and the activity of nitric oxide synthase elevated by MeJA. These results indicated that NO and H₂O₂ were involved in the MeJA-induced resistance in blueberries, and NO worked upstream of H₂O₂ in this process.

Characterization and Analysis of Anthocyanin-Related Genes in Wild-Type Blueberry and the Pink-Fruited Mutant Cultivar ‘Pink Lemonade’: New Insights into Anthocyanin Biosynthesis

Blueberries are one of the richest sources of antioxidants, such as anthocyanins, among fruits and vegetables. Anthocyanin mutants, like the pink-fruited cultivar ‘Pink Lemonade’, are valuable resources for investigating anthocyanin biosynthesis in blueberries. In this study, we examined expression of flavonoid pathway genes during fruit development in wild-type, blue-fruited blueberries using quantitative real-time PCR. Expression was also compared between wild-type and the pink-fruited ‘Pink Lemonade’. This revealed significantly lower expression in ‘Pink Lemonade’ than in wild-type of nearly all the structural genes examined suggesting that a transcriptional regulator of the pathway was affected. Hence, we compared expression of three known regulatory genes and found that the gene encoding the transcription factor MYB1 was expressed at a significantly lower level in ‘Pink Lemonade’ than in the wild-type. To validate the capacity of this MYB1 to regulate the transcription of anthocyanin genes in blueberries, a transient expression assay was conducted. Results indicated MYB1 overexpression enhanced anthocyanin production. Comparative sequence analysis between wild-type and mutant MYB1 variants found differences in highly conserved features suggesting a mechanistic explanation for the mutant phenotype. Collectively, the results presented here contribute to a better understanding of mechanisms regulating anthocyanin biosynthesis in Vaccinium.

Transcriptome Analysis of Ophraella communa Male Reproductive Tract in Indirect Response to Elevated CO2 and Heat Wave

Increase in atmospheric CO₂ directly affects the insect physiology and behavior, and indirectly affects the herbivorous insects by affecting their hosts. The increase in atmospheric CO₂ is accompanied by an increase in temperature and heat waves. Ophraella communa LeSage is a natural enemy of Ambrosia artemisiifolia (common ragweed). The development and reproduction of this beetle is weakened upon eating common ragweed grown under stress conditions. As female behavior and physiology alter after mating, the reproductive tract of males is likely to modulate reproduction and development in this species. Herein, the transcriptional profiles of testes and accessory glands from male O. communa individuals feeding on common ragweed under conditions of high CO₂ concentration and heat waves and that grown under ambient CO₂ concentration were compared. Differentially expressed genes (DEGs) were identified between the same tissues from beetles fed on common ragweed grown under different stress conditions. There were 3, 2, 3, 1and 5 genes related to decomposition and transport of macromolecular substances, host location, stress response, reproduction, and poisonous food-utilization. No expected response was observed in the male reproductive tract, but some of the identified DEGs might control the development of the population. The results presented here should be helpful in guiding future studies on deciphering the indirect response of other organs to high CO₂ concentration and heat waves, as well as the functions of seminal fluid proteins in O. communa.

Transcriptomic profiling and discovery of key genes involved in adventitious root formation from green cuttings of highbush blueberry (Vaccinium corymbosum L.)

BACKGROUND

Propagation of cuttings is frequently used in various plant species, including blueberry, which shows special root characteristics that may hinder adventitious root (AR) formation. AR formation is influenced by various factors, and auxin is considered to play a central role; however, little is known of the related regulatory mechanisms. In this study, a comparative transcriptome analysis of green cuttings treated with or without indole-butyric acid (IBA) was performed via RNA_seq to identify candidate genes associated with IBA-induced AR formation.

RESULTS

Rooting phenotypes, especially the rooting rate, were significantly promoted by exogenous auxin in the IBA application. Blueberry AR formation was an auxin-induced process, during which adventitious root primordium initiation (rpi) began at 14 days after cutting (DAC), root primordium (rp) was developed at 21 DAC, mature AR was observed at 28 DAC and finally outgrowth from the stem occurred at 35 DAC. Higher IAA levels and lower ABA and zeatin contents might facilitate AR formation and development. A time series transcriptome analysis identified 14,970 differentially expressed genes (DEGs) during AR formation, of which there were 7467 upregulated and 7503 downregulated genes. Of these, approximately 35 candidate DEGs involved in the auxin-induced pathway and AR formation were further identified, including 10 auxin respective genes (ARFs and SAURs), 13 transcription factors (LOB domain-containing protein (LBDs)), 6 auxin transporters (AUX22, LAX3/5 and PIN-like 6 (PIL6s)) and 6 rooting-associated genes (root meristem growth factor 9 (RGF9), lateral root primordium 1 (LRP1s), and dormancy-associated protein homologue 3 (DRMH3)). All these identified DEGs were highly upregulated in certain stages during AR formation, indicating their potential roles in blueberry AR formation.

CONCLUSIONS

The transcriptome profiling results indicated candidate genes or major regulatory factors that influence adventitious root formation in blueberry and provided a comprehensive understanding of the rooting mechanism underlying the auxin-induced AR formation from blueberry green cuttings.

Diversity in Metabolites and Fruit Quality Traits in Blueberry Enables Ploidy and Species Differentiation and Establishes a Strategy for Future Genetic Studies

Blueberry is well recognized as a rich source of health promoting phytochemicals such as flavonoids and phenolic acids. Multiple studies in blueberry and other crops indicated that flavonoids and phenolic acids function as bioactive compounds in the human body promoting multiple health effects. Despite their importance, information is limited about the levels of variation in bioactive compounds within and between ploidy level and species, and their association with fruit quality traits. Such information is crucial to define a strategy to study the genetic mechanisms controlling these traits and to select for these traits in blueberry breeding programs. Here we evaluated 33 health related phytochemicals belonging to four major groups of flavonoids and phenolic acids across 128 blueberry accessions over two years together with fruit quality traits, including fruit weight, titratable acidity, total soluble acids and pH. Highly significant variation between accessions, years, and accession by year interaction were identified for most of the traits. Cluster analysis grouped phytochemicals by their functional structure (e.g., anthocyanins, flavanols, flavonols, and phenolic acids). Multivariate analysis of the traits resulted in separation of diploid, tetraploid and hexaploid accessions. Broad sense heritability of the traits estimated in 100 tetraploid accessions, ranged from 20 to 90%, with most traits revealing moderate to high broad sense heritability (H² > 40%), suggesting that strong genetic factors control these traits. Fruit size can be estimated as a proxy of fruit weight or volume and vice versa, and it was negatively correlated with content of most of phytochemicals evaluated here. However, size-independent variation for anthocyanin content and profile (e.g., acylated vs. non-acylated anthocyanin) exists in the tetraploid accessions and can be explored to identify other factors such as genes related to the biosynthetic pathway that control this trait. This result also suggests that metabolite concentrations and fruit size, to a certain degree can be improved simultaneously in breeding programs. Overall, the results of this study provide a framework to uncover the genetic basis of bioactive compounds and fruit quality traits and will be useful to advance blueberry-breeding programs focusing on integrating these traits.

Differential Regulation of Anthocyanin Synthesis in Apple Peel under Different Sunlight Intensities

Sunlight radiation is a main environmental factor which affects anthocyanin synthesis. To clarify the regulatory mechanism of sunlight on the synthesis of anthocyanin in apple peel, bagged apples were exposed to diverse intensities of sunlight through different shading treatments. Under an increased solar ultraviolet-B (UV-B) light intensity, the concentration of anthocyanin in apple peels was consistent with the Michaelis-Menten equation. Under lower sunlight intensities, diphenyleneiodonium chloride (DPI, an inhibitor of plasma membrane NAD(P)H oxidase) treatment increased both the concentration of cyanidin-3-glycoside and the activity of dihydroflavonol 4-reductase (DFR). However, under higher sunlight intensities, DPI treatment decreased the concentrations of cyanidin-3-glycoside and quercetin-3-glycoside, as well as the activities of DFR and UDP-glycose: flavonoid 3-O-glycosyltransferase (UFGT). These results indicate that, under low sunlight intensity, anthocyanin synthesis in apple peel was limited by the supply of the substrate cyanidin, which was regulated by the DFR activity. Nevertheless, after exposure to high sunlight intensity, the anthocyanin produced in the apple peel was dependent on UFGT activity.

Identification and Expression of NAC Transcription Factors of Vaccinium corymbosum L. in Response to Drought Stress

Research Highlights: Phenotypic changes and expression profiles, phylogeny, conserved motifs, and expression correlations of NAC (NAM, ATAF1, ATAF2 and CUC2) transcription factors (TFs) in blueberry genome were detected under drought stress, and the expression patterns and functions of 12 NACs were analyzed. Background and Objectives: Blueberry is an important shrub species with a high level of flavonoids in fruit, which are implicated in a broad range of health benefits. However, the molecular mechanism of this shrub species in response to drought stress still remains elusive. NAC TFs widely participate in stress tolerance in many plant species. The characterization and expression profiles of NAC TFs were analyzed on the basis of genome data in blueberry when subjected to drought stress. Materials and Methods: Combined with the analysis of chlorophyll a fluorescence and endogenous phytohormones, the phenotypic changes of blueberry under drought stress were observed. The phylogenetic tree, conserved motifs, differently expressed genes, and expression correlation were determined by means of multiple bioinformatics analysis. The expression profiles of NACs in different organs were examined and compared through RNA-seq and qRT-PCR assay. Results: The chlorophyll a fluorescence parameters φPo, φEo, φRo, and PIabs of leaves were significantly inhibited under drought stress. ABA (abscisic acid) content noticeably increased over the duration of drought, whereas GA3 (gibberellic acid) and IAA (indole acetic acid) content decreased continuously. A total of 158 NACs were identified in blueberry genome and 62 NACs were differently expressed in leaf and root of blueberry under drought stress. Among them, 14 NACs were significantly correlated with the expression of other NAC genes. Conclusions: Our results revealed the phenotypic changes of this shrub under drought stress and linked them with NAC TFs, which are potentially involved in the process of response to drought stress.

Transcriptional regulation of abscisic acid biosynthesis and signal transduction, and anthocyanin biosynthesis in 'Bluecrop' highbush blueberry fruit during ripening

Highbush blueberry (Vaccinium corymbosum) fruit accumulate high levels of anthocyanins during ripening, which might be controlled by abscisic acid (ABA), a signal molecule in non-climacteric fruits. For an integrated view of the ripening process from ABA to anthocyanin biosynthesis, we analyzed the transcriptomes of ‘Bluecrop’ highbush blueberry fruit using RNA-Seq at three ripening stages, categorized based on fruit skin coloration: pale green at ca. 30 days after full bloom (DAFB), reddish purple at ca. 40 DAFB, and dark purple at ca. 50 DAFB. Mapping the trimmed reads against the reference sequences yielded 25,766 transcripts. Of these, 143 transcripts were annotated to encode five ABA biosynthesis enzymes, four ABA signal transduction regulators, four ABA-responsive transcription factors, and 12 anthocyanin biosynthesis enzymes. The analysis of differentially expressed genes between the ripening stages revealed that 11 transcripts, including those encoding nine-cis-epoxycarotenoid dioxygenase, SQUAMOSA-class MADS box transcription factor, and flavonoid 3′,5′-hydroxylase, were significantly up-regulated throughout the entire ripening stages. In fruit treated with 1 g L⁻¹ ABA, at least nine transcripts of these 11 transcripts as well as one transcript encoding flavonoid 3′-hydroxylase were up-regulated, presumably promoting anthocyanin accumulation and fruit skin coloration. These results will provide fundamental information demonstrating that ABA biosynthesis and signal transduction, and anthocyanin biosynthesis are closely associated with anthocyanin accumulation and skin coloration in highbush blueberry fruit during ripening.

MYBA From Blueberry (Vaccinium Section Cyanococcus) Is a Subgroup 6 Type R2R3MYB Transcription Factor That Activates Anthocyanin Production

The Vaccinium genus in the family Ericaceae comprises many species, including the fruit-bearing blueberry, bilberry, cranberry, huckleberry, and lingonberry. Commercially, the most important are the blueberries (Vaccinium section Cyanococcus), such as Vaccinium corymbosum (northern highbush blueberry), Vaccinium virgatum (rabbiteye blueberry), and Vaccinium angustifolium (lowbush blueberry). The rising popularity of blueberries can partly be attributed to their "superfood" status, with an increasing body of evidence around human health benefits resulting from the fruit metabolites, particularly products of the phenylpropanoid pathway such as anthocyanins. Activation of anthocyanin production by R2R3-MYB transcription factors (TFs) has been characterized in many species, but despite recent studies on blueberry, cranberry, and bilberry, no MYB anthocyanin regulators have been reported for Vaccinium. Indeed, there has been conjecture that at least in bilberry, MYB TFs divergent to the usual type are involved. We report identification of MYBA from blueberry, and show through sequence analysis and functional studies that it is homologous to known anthocyanin-promoting R2R3-MYBs of subgroup 6 of the MYB superfamily. In transient assays, MYBA complemented an anthocyanin MYB mutant of Antirrhinum majus and, together with a heterologous bHLH anthocyanin regulator, activated anthocyanin production in Nicotiana benthamiana. Furthermore anthocyanin accumulation and anthocyanin structural gene expression (assayed by qPCR and RNA-seq analyses) correlated with MYBA expression, and MYBA was able to transactivate the DFR promoter from blueberry and other species. The RNA-seq data also revealed a range of other candidate genes involved in the regulation of anthocyanin production in blueberry fruit. The identification of MYBA will help to resolve the regulatory mechanism for anthocyanin pigmentation in the Vaccinium genus. The sequence information should also prove useful in developing tools for the accelerated breeding of new Vaccinium cultivars.