Transcriptomic and Metabolic Analysis of Fruit Development and Identification of Genes Involved in Raffinose and Hydrolysable Tannin Biosynthesis in Walnuts

Arbuscular mycorrhizal symbiosis with Rhizophagus irregularis DAOM197198 modifies the root transcriptome of walnut trees

Walnut trees are cultivated and exploited worldwide for commercial timber and nut production. They are heterografted plants, with the rootstock selected to grow in different soil types and conditions and to provide the best anchorage, vigor, and resistance or tolerance to soil borne pests and diseases. However, no individual rootstock is tolerant of all factors that impact walnut production. In Europe, Juglans regia is mainly used as a rootstock. Like most terrestrial plants, walnut trees form arbuscular mycorrhizal symbioses, improving water and nutrient uptake and providing additional ecosystem services. Effects of arbuscular mycorrhizal symbiosis on root gene regulation, however, has never been assessed. We analyzed the response of one rootstock of J. regia to colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis DAOM197198. Plant growth as well as the nitrogen and phosphorus concentrations in roots and shoots were significantly increased in mycorrhizal plants versus non-colonized plants. In addition, we have shown that 1,549 genes were differentially expressed, with 832 and 717 genes up- and down-regulated, respectively. The analysis also revealed that some rootstock genes involved in plant nutrition through the mycorrhizal pathway, are regulated similarly as in other mycorrhizal woody species: Vitis vinifera and Populus trichocarpa. In addition, an enrichment analysis performed on GO and KEGG pathways revealed some regulation specific to J. regia (i.e., the juglone pathway). This analysis reinforces the role of arbuscular mycorrhizal symbiosis on root gene regulation and on the need to finely study the effects of diverse arbuscular mycorrhizal fungi on root gene regulation, but also of the scion on the functioning of an arbuscular mycorrhizal fungus in heterografted plants such as walnut tree.

Genomic basis of the distinct biosynthesis of β-glucogallin, a biochemical marker for hydrolyzable tannin production, in three oak species

Hydrolyzable tannins (HTs), predominant polyphenols in oaks, are widely used in grape wine aging, feed additives, and human healthcare. However, the limited availability of a high-quality reference genome of oaks greatly hampered the recognition of the mechanism of HT biosynthesis. Here, high-quality reference genomes of three Asian oak species (Quercus variabilis, Quercus aliena, and Quercus dentata) that have different HT contents were generated. Multi-omics studies were carried out to identify key genes regulating HT biosynthesis. In vitro enzyme activity assay was also conducted. Dual-luciferase and yeast one-hybrid assays were used to reveal the transcriptional regulation. Our results revealed that β-glucogallin was a biochemical marker for HT production in the cupules of the three Asian oaks. UGT84A13 was confirmed as the key enzyme for β-glucogallin biosynthesis. The differential expression of UGT84A13, rather than enzyme activity, was the main reason for different β-glucogallin and HT accumulation. Notably, sequence variations in UGT84A13 promoters led to different trans-activating activities of WRKY32/59, explaining the different expression patterns of UGT84A13 among the three species. Our findings provide three high-quality new reference genomes for oak trees and give new insights into different transcriptional regulation for understanding β-glucogallin and HT biosynthesis in closely related oak species.

'Sorrento' and 'Tulare' Walnut Cultivars: Morphological Traits and Phytochemical Enhancement of Their Shell Waste

Walnut processing generates considerable quantities of by-products that could be reprocessed into value-added products that have food and non-food applications. In this context, the aim of this study is to characterize the 'Sorrento' and 'Tulare' walnut cultivars using the UPOV guidelines and analyze the chemical composition and antioxidant activity of their shells. Insight into the chemical composition of the different granulometric fractions of walnut shell, obtained by sieving, was obtained following ultrasound-assisted extraction by Ultra-High-Performance Liquid Chromatography-High-Resolution Mass Spectrometry (UHPLC-HRMS). The total phenolic, flavonoid, and tannin content and antiradical capacity, obtained by DPPH and ABTS assays, and the Fe(III) reducing power of the extracts were also evaluated. The UHPLC-HRMS analysis indicated the presence of thirty-two compounds ascribable to four major classes of specialized metabolites. Furthermore, the extraction efficiency of gallic acid, ellagic acid derivatives, as well as glansreginin A, increased with the decrease in shell matrix particle size in contrast to chlorogenic acids and flavonoid glycosides. This is the first study to highlight new knowledge on the chemical composition of walnut shells. The results obtained demonstrate the feasibility of recovering valuable bioactive components from agro-waste that may be further valorized.

Interactive effects of selenium and arsenic on phenolic constituents and antioxidant activity in rice (Oryza sativa L.)

Arsenic (As) is a heavy toxic metalloid found in air, water and soil that adversely affects the plant growth by inducing oxidative stress in plants. Its contamination of rice is a serious problem throughout the world. Selenium (Se) is a beneficial micronutrient for plants that acts as an antioxidant at low doses and protect the plants against number of environmental stresses either by modulating the primary metabolic pathways or regulating the production of phenolic compounds. In the present investigation, effect of Se on different phenolics, enzymes related to their metabolism and antioxidative potential were studied in As stressed rice leaves. Rice plants were grown in pots containing sodium arsenate (2-10 mg As(V) kg-1 soil) and sodium selenate (0.5-1 mg Se kg-1 soil), both alone and in combination and leaf samples were analyzed for various biochemical parameters. Phenolic constituents increased in rice leaves with As(V) treatment from 2 to 5 mg kg-1 soil and leaves exposed to As(V) @ 5 mg kg-1 soil exhibited 1.7, 1.9 and 2.5 fold increase in total phenolics, o-dihydroxyphenols and flavonols, respectively at grain filling stage. Binary application of Se + As improved various phenolic constituents, FRAP, reducing power and antioxidant activities as compared to control. PAL, TAL and PPO activities increased from 1.3 to 4.6 fold in combined As + Se treatment at both the stages. Anthocyanin contents showed a decline (10.8 fold) with increasing As doses and its content improved at both the stages with maximum increase of 3.76 fold with As5+Se1 combination. Binary application of As + Se improved gallic acid, chlorogenic acid, 3-hydroxy benzoic acid and kaempferol contents than control whereas catechin and coumaric acid showed the reverse trend. Application of Se can modulate phenolic constituents in leaf and grains of rice Cv PR126 due to As stress that helped plants to adapt to excess As and resulted in improved plant growth.

Efficient and effective immobilization of tetracycline and copper from wastewater by zero-valent iron fabricated hydrochar derived from walnut peel

Antibiotics and heavy metals often coexist as non-point-source contaminants in wastewater and their quite contrary physiochemical properties make their co-removal processes challenging. In this work, a bifunctional zero-valent iron-modified hydrochar derived from walnut peel (MWPHC) was synthesized, which was then applied for the simultaneous removal of tetracycline (TC) and Cu(II) from wastewater. Based on the characterizations, Fe0 species were successfully distributed on the surface of the walnut peel substrates. The TC and Cu(II) could be synergistically immobilized, and bridging effects were observed between them, and MWPHC exhibited excellent ability on the simultaneous removal of TC (qmax = 433.59 mg/g) and Cu(II) (qmax = 586.25 mg/g). Furthermore, the engineering feasibility of the MWPHC was evaluated using column and regeneration experiments. These results shed light on the tailored MWPHC as an environmental functional material for pollution control of co-existing antibiotic and heavy metal contaminants in agro-industrial wastewater.

Transcriptomic and metabolomic analyses reveal the flavor of bitterness in the tip shoots of Bambusa oldhamii Munro

The young bamboo shoot of Bambusa oldhamii (green bamboo) has a good taste and is rich in nutrition and widely used in traditional Chinese cuisines. But the shoots flavor of Bambusa oldhamii changed from deliciously sweet to a little bitter when the shoots grew from underground to aboveground. In this paper, we explored the bitterness chemicals of the green bamboo shoot when growing from underground to aboveground using transcriptome and metabolome techniques. Finally, several bitter chemicals were mined out counting for the flavor transformation, such as Solanidine, Amygdalin, Salicin, Arbutin, and others. The transcription factor family of AP2/ERF plays the main role in key bitter chemical regulation via correlation analysis. Moreover, the pathway of Biosynthesis of phenylpropanoids might be the key pathway in the formation of the bitter chemicals in green bamboo shoot development.

Transcriptomic and metabolomic analyses provide new insights into the appropriate harvest period in regenerated bulbs of Fritillaria hupehensis

INTRODUCTION

The bulb of Fritillaria hupehensis, a traditional cough and expectorant medicine, is usually harvested from June to September according to traditional cultivation experience, without practical scientific guidance. Although steroidal alkaloid metabolites have been identified in F. hupehensis, the dynamic changes in their levels during bulb development and their molecular regulatory mechanisms are poorly understood.

METHODS

In this study, integrative analyses of the bulbus phenotype, bioactive chemical investigations, and metabolome and transcriptome profiles were performed to systematically explore the variations in steroidal alkaloid metabolite levels and identify the genes modulating their accumulation and the corresponding regulatory mechanisms.

RESULTS

The results showed that weight, size, and total alkaloid content of the regenerated bulbs reached a maximum at IM03 (post-withering stage, early July), whereas peiminine content reached a maximum at IM02 (withering stage, early June). There were no significant differences between IM02 and IM03, indicating that regenerated bulbs could be harvested appropriately in early June or July. Peiminine, peimine, tortifoline, hupehenine, korseveramine, delafrine, hericenone N-oxide, korseveridine, puqiedinone, pingbeinone, puqienine B, puqienine E, pingbeimine A, jervine, and ussuriedine levels were upregulated in IM02 and IM03, compared with IM01 (vigorous growth stage, early April). The Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that the accumulation of steroidal alkaloid metabolites mainly occurred prior to IM02. HMGR1, DXR, CAS1, CYP 90A1, and DET2 may play a positive role in peiminine, peimine, hupehenine, korseveramine, korseveridine, hericenone N-oxide, puqiedinone, delafrine, tortifoline, pingbeinone, puqienine B, puqienine E, pingbeimine A, jervine, and ussuriedine biosynthesis, whereas the downregulation of FPS1, SQE and 17-DHCR may lead to a reduction in peimisine levels. Weighted gene correlation network analysis showed that CYP 74A2-1, CYP 74A2-2, CYP 71A26-1, CYP 71A26-2, and CYP74A were negatively correlated with peiminine and pingbeimine A, whereas CYP R and CYP707A1 were positively correlated. . CYP 74A2-1 and CYP 74A2-2 may play a negative role in peimine and korseveridine biosynthesis, whereas CYP R plays a positive role. In addition, the highly expressed C2H2, HSF, AP2/ERF, HB, GRAS, C3H, NAC, MYB-related transcription factors (TFs), GARP-G2-like TFs, and WRKY may play positive roles in the accumulation of peiminine, peimine, korseveridine, and pingbeimine A.

DISCUSSION

These results provide new insights into scientific harvesting of F. hupehensis.

The chromosome-scale genome sequence of Triadica sebifera provides insight into fatty acids and anthocyanin biosynthesis

The Chinese tallow tree (Triadica sebifera) can produce oil with high content of unsaturated fatty acids in seeds and shows attractive leaf color in autumn and winter. Here, the 739 Mb chromosome-scale genome sequence of the Chinese tallow tree was assembled and it reveals the Chinese tallow tree is a tetraploid. Numerous genes related to nutrition assimilation, energy utilization, biosynthesis of secondary metabolites and resistance significantly expanded or are specific to the Chinese tallow tree. These genes would enable the Chinese tallow tree to obtain high adaptability. More genes in fatty acids biosynthesis in its genome, especially for unsaturated fatty acids biosynthesis, and higher expression of these genes in seeds would be attributed to its high content of unsaturated fatty acids. Cyanidin 3-O-glucoside was identified as the major component of anthocyanin in red leaves. All structural genes in anthocyanin biosynthesis show significantly higher expression in red leaves than in green leaves. Transcription factors, seven MYB and one bHLH, were predicted to regulate these anthocyanin biosynthesis genes. Collectively, we provided insight into the polyploidization, high adaptability and biosynthesis of the high content of unsaturated fatty acids in seeds and anthocyanin in leaves for the Chinese tallow tree.

A chromosome-level assembly of the economically-important Chinese tallow tree is presented alongside functional analyses into biosynthetic products in the leaves and seeds.

Effects of the Source–Sink Relationship on Walnut Nut Quality at the Scale of the Fruit–Bearing Branch

Fruit quality is known to be regulated by the balance between leaf number/area and fruit number, but less is known about the effects of fruit–bearing branch agronomic traits, particularly for walnuts (Juglans regia L.). We assessed nut quality, physiological and biochemical indexes of leaves, and microstructure of leaves and fruit stalks at various leaf–to–fruit ratios to gain insight into the relationships between branch agronomic traits and nut quality, to identify those traits that made a better contribution to nut quality and to find out the range of the leaf–to–fruit ratio and the object of fruit to be removed for thinning. We found that the top fruit on the fruit stalk had a higher longitudinal diameter and kernel weight than the bottom at the low leaf–to–fruit level, and branches with more pinnate compound leaves had a better capacity for carbohydrate assimilation and transportation to produce better quality fruits. Specifically, with the increasing leaf number, the branch diameter, total leaf area, net photosynthetic rate, chlorophyll content, fruit weight, fruit diameters, and kernel protein content also increased. Moreover, at the microscopic level, the fruit stalk vascular bundle, leaf thickness, palisade mesophyll thickness, and ratios of palisade mesophyll to spongy mesophyll thickness in the leaf also showed the same trend. Therefore, when the ratio of leaf area to the fruit number was less than 181.5 square centimeters per fruit on the branches, reducing the fruit number could improve the size and the crude fat content of fruits. While the ratio was more than 247.8 square centimeters per fruit, the fruit number had no significant effect on fruit quality, but increasing leaf area and branch diameter could improve the fruit size and yield.

Transcriptome analysis of walnut quality formation and color change mechanism of pellicle during walnut development

Walnuts (including those covered with a pellicle) are loved for their rich nutritional value. And the popular varieties of walnut cultivation are Juglans sigillata L. The pellicle (seed coat) of these walnut cultivars has different colors and has an indispensable influence on the walnut quality formation. However, there are few reports on the pellicle color and quality formation in different developmental stages of walnut (Juglans sigillata L.). Therefore, in this study, three walnut cultivars (F, Q, and T) with different pellicle colors were selected for transcriptome sequencing and physiological index analysis of the color and quality formation mechanisms at different development stages. The results showed that with the development of walnut fruit, the starch sucrose metabolism pathway in the pellicle was activated and promoted starch hydrolysis. Meanwhile, the expression levels of genes related to the alpha-linolenic acid metabolism pathway were significantly increased during walnut maturation, especially in F2. Some physiological indicators related to lipid oxidation were also detected and analyzed in this study, such as MDA, CAT, POD and DPPH. These results were similar to the expression patterns of corresponding regulatory genes in the RNA-Seq profile. In addition, lignin synthesis genes were up-regulated in the phenylpropanoid metabolic pathway, while key genes enriched in the flavonoid and anthocyanin synthesis pathways were down-regulated. The results were consistent with the results of total anthocyanins and flavonoid content detection during walnut development. Therefore, this experiment suggested that with the maturation of walnut pellicle, the gene expression in the phenylpropanoid metabolic pathway flowed to the branch of lignin synthesis, especially in the Q variety, resulting in lower flavonoid and anthocyanin content at the maturity stage than immature. This is also the main reason for the pale pellicle of the three walnut varieties after mature. The findings of this study showed that changes in the expression levels of regulating genes for lipid, starch, sugar, and flavonoid synthesis during walnut development influenced the accumulation of the related metabolite for walnut quality formation and pellicle color. The results of this experiment provided the molecular basis and reference for the breeding of high nutritional quality walnut varieties.

Metabolome and Transcriptome Profiling Unveil the Mechanisms of Polyphenol Synthesis in the Developing Endopleura of Walnut (Juglans regia L.)

Walnut (Juglans regia L.) is an important woody nut tree species, and its endopleura (the inner coating of a seed) is rich in many polyphenols. Thus far, the pathways and essential genes involved in polyphenol biosynthesis in developing walnut endopleura remain largely unclear. We compared metabolite differences between endopleura and embryo in mature walnuts, and analyzed the changes of metabolites in endopleura at 35, 63, 91, 119, and 147 days after pollination (DAP). A total of 760 metabolites were detected in the metabolome, and the polyphenol contents in endopleura were higher than those in embryos. A total of 15 types of procyanidins, 10 types of kaempferol glycosides, and 21 types of quercetin glycosides that accumulated during endopleura development were identified. The analysis of the phenylpropane metabolic pathway showed that phenylalanine was gradually transformed into proanthocyanidins and other secondary metabolites with the development of endopleura. A total of 49 unigenes related to polyphenol synthesis were identified by transcriptome analysis of endopleura. The expression patterns of PAL, C4H, 4CL, CHS, CHI, F3H, LDOX, and ANR were similar, and their expression levels were highest in endopleura at maturity. Transcriptome and metabolome analysis showed that endopleura rapidly synthesized and accumulated polyphenols during maturation. Moreover, the transcription factor MYB111 played an important role in synthesizing polyphenols in endopleura, and its expression pattern was positively correlated with the accumulation pattern of quercetin, kaempferol, and proanthocyanidins. MYB111 was co-expressed with NAP, NAC, ATR1, and other genes related to cell senescence and abiotic stress response. Our study analyzed the composition and molecular synthesis mechanism of polyphenols in walnut endopleura, and provided new perspectives and insights regarding the nutritional research of walnut nuts.

Research Progress and Trends in Metabolomics of Fruit Trees

Metabolomics is an indispensable part of modern systems biotechnology, applied in the diseases' diagnosis, pharmacological mechanism, and quality monitoring of crops, vegetables, fruits, etc. Metabolomics of fruit trees has developed rapidly in recent years, and many important research results have been achieved in combination with transcriptomics, genomics, proteomics, quantitative trait locus (QTL), and genome-wide association study (GWAS). These research results mainly focus on the mechanism of fruit quality formation, metabolite markers of special quality or physiological period, the mechanism of fruit tree's response to biotic/abiotic stress and environment, and the genetics mechanism of fruit trait. According to different experimental purposes, different metabolomic strategies could be selected, such as targeted metabolomics, non-targeted metabolomics, pseudo-targeted metabolomics, and widely targeted metabolomics. This article presents metabolomics strategies, key techniques in metabolomics, main applications in fruit trees, and prospects for the future. With the improvement of instruments, analysis platforms, and metabolite databases and decrease in the cost of the experiment, metabolomics will prompt the fruit tree research to achieve more breakthrough results.

Mitochondrial pyruvate carrier blockade results in decreased osteoclastogenesis and bone resorption via regulating mitochondrial energy production

It's widely accepted that increasing mitochondrial respiration plays a pivotal role during osteoclastogenesis. Mitochondrial pyruvate carrier (MPC) is the key transporter that links glycolysis to mitochondrial respiration but little is known about its role during osteoclastogenesis. Our goal was to determine the effects of its blockade on osteoclastogenesis and bone resorption in vivo and in vitro. To address this issue, we performed gene knockdown or pharmacologically inhibited MPC in primary bone marrow-derived monocytes (BMMs) or in an ovariectomized mouse model. We also studied the metabolic changes in RANKL-induced differentiating BMMs with MPC blockade and performed rescue experiments. We found that MPC blockade resulted in decreased osteoclastogenesis both in vivo and in vitro and inhibiting MPC significantly alleviated ovariectomy-induced trabecular bone loss. Further investigations showed that MPC blockade significantly reversed the metabolic profile related to RANK activation, including decreased intermediates involved in citric acid cycle and glutamine metabolism. Moreover, metabolic flux analysis verified that MPC blockade decreased pyruvate flux into TCA cycle with no significant effect on glycolysis. Besides, MPC blockade resulted in suppressed mitochondrial biogenesis in addition to oxidative phosphorylation. Rescue experiments revealed that inhibiting pyruvate dehydrogenase kinase (PDK) via sodium dichloroacetate (DCA), but not targeting glutamine metabolism, could reverse the effects of MPC blockade on osteoclastogenesis. These implied that the effects of MPC blockade were mediated by reduced pyruvate fuel into citric acid cycle in multiple aspects. Taken together, our data demonstrated the inhibitory effects of MPC blockade on osteoclastogenesis, which was mediated by decreased mitochondrial energy production.