Grafting with rootstocks promotes phenolic compound accumulation in grape berry skin during development based on integrative multi-omics analysis

Widely Targeted Metabolomic Analysis Provides New Insights into the Effect of Rootstocks on Citrus Fruit Quality

The use of different rootstocks has a significant effect on the content of flavor components and overall fruit quality. However, little information is available about the metabolic basis of the nutritional value of citrus plants. In this study, UPLC-MS/MS (ultra-performance liquid chromatography-tandem mass spectrometry) was performed to analyze the metabolites of three late-maturing hybrid mandarin varieties ('Gold Nugget', 'Tango' and 'Orah') grafted on four rootstocks ('Trifoliate orange', 'Carrizo citrange', 'Red tangerine' and 'Ziyang Xiangcheng'). A total of 1006 metabolites were identified through OPLS-DA (Orthogonal Partial Least Squares-Discriminant Analysis) analysis. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis revealed the most critical pathways among the different pathways associated with genes grafted on the four rootstocks that were differentially activated, including tryptophan metabolism and sphingolipid metabolism in 'Gold Nugget'; tryptophan metabolism, phenylpropanoid biosynthesis and sphingolipid metabolism in 'Tango'; and pantothenate and CoA biosynthesis- and photosynthesis-related biosynthesis in 'Orah'. A considerable difference between the different rootstocks was also observed in the accumulation of lipids, phenolic acids and flavonoids; further analysis revealed that the rootstocks regulated specific metabolites, including deacetylnomylinic acid, sudachinoid A, amoenin evodol, rutaevin, cyclo (phenylalanine-glutamic acid), cyclo (proline-phenylalanine), 2-hydroxyisocaproic acid, and 2-hydroxy-3-phenylpropanoic acid. The results of this study provide a useful foundation for further investigation of rootstock selection for late-maturation hybrid mandarin varieties.

Transcriptome and metabolome profiling reveal the effects of hormones on current-year shoot growth in Chinese 'Cuiguan' pear grafted onto vigorous rootstock 'Duli' and dwarf rootstock 'Quince A'

BACKGROUND

Dwarf rootstocks have important practical significance for high-density planting in pear orchards. The shoots of 'Cuiguan' grafted onto the dwarf rootstock were shorter than those grafted onto the vigorous rootstock. However, the mechanism of shorter shoot formation is not clear.

RESULTS

In this study, the current-year shoot transcriptomes and phytohormone contents of 'CG‒QA' ('Cuiguan' was grafted onto 'Quince A', and 'Hardy' was used as interstock) and 'CG‒DL' ('Cuiguan' was grafted onto 'Duli', and 'Hardy' was used as interstock) were compared. The transcriptome results showed that a total of 452 differentially expressed genes (DEGs) were identified, including 248 downregulated genes and 204 upregulated genes; the plant hormone signal transduction and zeatin biosynthesis pathways were significantly enriched in the top 20 KEGG enrichment terms. Abscisic acid (ABA) was the most abundant hormone in 'CG‒QA' and 'CG‒DL'; auxin and cytokinin (CTK) were the most diverse hormones; additionally, the contents of ABA, auxin, and CTK in 'CG‒DL' were higher than those in 'CG‒QA', while the fresh shoot of 'CG‒QA' accumulated more gibberellin (GA) and salicylic acid (SA). Metabolome and transcriptome co-analysis identified three key hormone-related DEGs, of which two (Aldehyde dehydrogenase gene ALDH3F1 and YUCCA2) were upregulated and one (Cytokinin oxidase/dehydrogenase gene CKX3) was downregulated.

CONCLUSIONS

Based on the results of transcriptomic and metabolomic analysis, we found that auxin and CTK mainly regulated the shoot differences of 'CG-QA' and 'CG-DL', and other hormones such as ABA, GA, and SA synergistically regulated this process. Three hormone-related genes ALDH3F1, YUCCA2, and CKX3 were the key genes contributing to the difference in shoot growth between 'CG-QA' and 'CG-DL' pear. This research provides new insight into the molecular mechanism underlying shoot shortening after grafted onto dwarf rootstocks.

Integrated Transcriptomic and Proteomic Analysis Identifies Novel Regulatory Genes Associated with Plant Growth Regulator-Induced Astringency in Grape Berries

Astringency influences the sensory characteristics and flavor quality of table grapes. We tested the astringency sensory attributes of berries and investigated the concentration of flavan-3-ols/proanthocyanidins (PAs) in skins after the application of the plant growth regulators CPPU and GA3 to the flowers and young berries of the "Summer Black" grape. Our results showed that CPPU and GA3 applications increase sensory astringency perception scores and flavan-3-ol/proanthocyanidin concentrations. Using integrated transcriptomic and proteomic analysis, differentially expressed transcripts and proteins associated with growth regulator treatment were identified, including those for flavonoid biosynthesis that contribute to the changes in sensory astringency levels. Transient overexpression of candidate astringency-related regulatory genes in grape leaves revealed that VvWRKY71, in combination with VvMYBPA1 and VvMYC1, could promote the biosynthesis of proanthocyanidins, while overexpression of VvNAC83 reduced the accumulation of proanthocyanidins. However, in transient promoter studies in Nicotiana benthamiana, VvWRKY71 repressed the promoter of VvMYBPA2, while VvNAC83 had no significant effect on the promoter activity of four PA-related genes, and VvMYBPA1 was shown to activate its own promoter. This study provides new insights into the molecular mechanisms of sensory astringency formation induced by plant growth regulators in grape berries.

Effects of Vine Water Status on Malate Metabolism and γ-Aminobutyric Acid (GABA) Pathway-Related Amino Acids in Marselan (Vitis vinifera L.) Grape Berries

Malic acid is the predominant organic acid in grape berries, and its content is affected by abiotic factors such as temperature (fruit zone microclimate) and water (vine water status). The objectives of this study were to explore the potential mechanisms behind the effects of vine water status on the biosynthesis and degradation of berry malic acid and the potential downstream effects on berry metabolism. This study was conducted over two growing seasons in 2021 and 2022, comprising three watering regimes: no water stress (CK), light water stress (LWS), and moderate water stress (MWS). Compared to CK, a significantly higher level of malic acid was found in berries from the MWS treatment when the berry was still hard and green (E-L 33) in both years. However, water stress reduced the malic acid content at the ripe berry harvest (E-L 38) stage. The activities of NAD-malate dehydrogenase (NAD-MDH) and pyruvate kinase (PK) were enhanced by water stress. Except for the E-L 33 stage, the activity of phosphoenolpyruvate carboxylase (PEPC) was reduced by water stress. The highest phosphoenolpyruvate carboxykinase (PEPCK) activity was observed at the berry veraison (E-L 35) stage and coincided with the onset of a decrease in the malate content. Meanwhile, the expression of VvPEPCK was consistent with its enzyme activity. This study showed that water stress changed the content of some free amino acids (GABA, proline, leucine, aspartate, and glutamate), two of which (glutamate and GABA) are primary metabolites of the GABA pathway.

Transcriptome and UPLC-MS/MS reveal mechanisms of amino acid biosynthesis in sweet orange 'Newhall' after different rootstocks grafting

Sweet orange 'Newhall' (C. sinensis) is a popular fruit in high demand all over the world. Its peel and pulp are rich in a variety of nutrients and are widely used in catering, medicine, food and other industries. Grafting is commonly practiced in citrus production. Different rootstock types directly affect the fruit quality and nutritional flavor of citrus. However, the studies on citrus metabolites by grafting with different rootstocks are very limited, especially for amino acids (AAs). The preliminary test showed that there were significant differences in total amino acid content of two rootstocks (Poncirus trifoliata (CT) and C. junos Siebold ex Tanaka (CJ)) after grafting, and total amino acid content in the peel was higher than flesh. However, the molecular mechanism affecting amino acid differential accumulation remains unclear. Therefore, this study selected peel as the experimental material to reveal the amino acid components and differential accumulation mechanism of sweet orange 'Newhall' grafted with different rootstocks through combined transcriptome and metabolome analysis. Metabolome analysis identified 110 amino acids (AAs) and their derivatives in sweet orange 'Newhall' peels, with L-valine being the most abundant. L-asparagine was observed to be affected by both developmental periods and rootstock grafting. Weighted gene co-expression network analysis (WGCNA) combined with Redundancy Analysis (RDA) revealed eight hub structural genes and 41 transcription factors (TFs) that significantly influenced amino acid biosynthesis in sweet orange 'Newhall' peels. Our findings further highlight the significance of rootstock selection in enhancing the nutritional value of citrus fruits and might contribute to the development of functional citrus foods and nutritional amino acid supplements.

Hetero-grafting affects flavonoid biosynthesis in sweet orange 'Newhall' (Citrus sinensis) peels: a metabolomics and transcriptomics analysis

Citrus cultivation involves the widespread practice of grafting, which has a significant impact on citrus development and fruit quality and yield. However, understanding the effect of flavonoid compounds after different rootstock grafting have been limited. Flavonoid compounds, found at the highest levels in citrus peels, contribute to improving fruit quality and nutritional value. In this study, scion-rootstock interaction was investigated at various developmental stages when sweet orange 'Newhall' was hetero-grafted with two commonly used rootstocks (Poncirus trifoliate population, C. junos Siebold ex Tanaka). Physiological index detection showed a higher concentration of total flavonoid content in peels of sweet orange 'Newhall' grafted on Poncirus trifoliate population (ct) than C. junos Siebold ex Tanaka (cj). Further metabolomic analysis identified 703 flavonoid compounds, including flavones, flavonols, and flavanones. Out of the 25 flavonoids affected by different rootstock grafting and developmental stages, most were flavones. Transcriptomic analysis identified 8,562 differentially expressed genes (DEGs). Co-expression and Pearson's correlation analysis discovered six hub structure genes and 19 transcription factors (TFs) that affected flavonoid biosynthesis. In addition to increasing the transcript levels of genes that synthesize flavones, flavonols, and flavanones, the scion-rootstock interaction also affected the expression of many TFs. Taken together, our findings suggested that hetero-grafting could promote the accumulation of flavonoid compounds in citrus peels during the development stages. These results offered fresh perspectives on grafting's application usefulness and the enhancement of the accumulation of nutritive flavonoid components by grafting in citrus.

Comprehensive metabolomics-based analysis of sugar composition and content in berries of 18 grape varieties

Xinjiang is the largest grape-producing region in China and the main grape cultivation area in the world. The Eurasian grape resources grown in Xinjiang are very rich in diversity. The sugar composition and content are the main factors that determine the quality of berries. However, there are currently no systematic reports on the types and contents of sugars in grapes grown in Xinjiang region. In this research, we evaluated the appearance and fruit maturity indicators of 18 grape varieties during fruit ripening and determined their sugar content using GC-MS. All cultivars primarily contained glucose, D-fructose, and sucrose. The glucose content in varieties varied from 42.13% to 46.80% of the total sugar, whereas the fructose and sucrose contents varied from 42.68% to 50.95% and 6.17% to 12.69%, respectively. The content of trace sugar identified in grape varieties varied from 0.6 to 2.3 mg/g. The comprehensive assessment by principal component analysis revealed strong positive correlations between some sugar components. A comprehensive study on the content and types of sugar will provide the foundation to determine the quality of grape cultivars and effective ways to utilize resources to improve sugar content through breeding.

Oligomeric Proanthocyanidins: An Updated Review of Their Natural Sources, Synthesis, and Potentials

Oligomeric Proanthocyanidins (OPCs), as a class of compounds widely found in plants, are particularly abundant in grapes and blueberries. It is a polymer comprising many different monomers, such as catechins and epicatechins. The monomers are usually linked to each other by two types of links, A-linkages (C-O-C) and B-linkages (C-C), to form the polymers. Numerous studies have shown that compared to high polymeric procyanidins, OPCs exhibit antioxidant properties due to the presence of multiple hydroxyl groups. This review describes the molecular structure and natural source of OPCs, their general synthesis pathway in plants, their antioxidant capacity, and potential applications, especially the anti-inflammatory, anti-aging, cardiovascular disease prevention, and antineoplastic functions. Currently, OPCs have attracted much attention, being non-toxic and natural antioxidants of plant origin that scavenge free radicals from the human body. This review would provide some references for further research on the biological functions of OPCs and their application in various fields.

Advances in understanding cold tolerance in grapevine

Grapevine (Vitis ssp.) is a deciduous perennial fruit crop, and the canes and buds of grapevine should withstand low temperatures annually during winter. However, the widely cultivated Vitis vinifera is cold-sensitive and cannot survive the severe winter in regions with extremely low temperatures, such as viticulture regions in northern China. By contrast, a few wild Vitis species like V. amurensis and V. riparia exhibit excellent freezing tolerance. However, the mechanisms underlying grapevine cold tolerance remain largely unknown. In recent years, much progress has been made in elucidating the mechanisms, owing to the advances in sequencing and molecular biotechnology. Assembly of grapevine genomes together with resequencing and transcriptome data enable researchers to conduct genomic and transcriptomic analyses in various grapevine genotypes and populations to explore genetic variations involved in cold tolerance. In addition, a number of pivotal genes have been identified and functionally characterized. In this review, we summarize recent major advances in physiological and molecular analyses of cold tolerance in grapevine and put forward questions in this field. We also discuss the strategies for improving the tolerance of grapevine to cold stress. Understanding grapevine cold tolerance will facilitate the development of grapevines for adaption to global climate change.

Comparison of rockwool and coir for greenhouse cucumber production: chemical element, plant growth, and fruit quality

Replacing rockwool with more sustainable materials, such as coir, is an effective measure to improve the sustainability of soilless cultivation in the greenhouse. To comprehensively assess the feasibility of coir before using it widely, coir was compared to rockwool as a cucumber cultivation substrate to evaluate its performance on mineral elements in the substrates, drainage, and in the plants. Plant growth, amino acids, and flavor substances of cucumber fruits were also compared between the two substrates. Compared to rockwool, coir significantly increased the LAI and yield of cucumber crops as well as contents of Ca, Mg, S, Cl and Zn in leaves and fruits. Contents of P, K, Ca, Mg, Cl, Zn, and B in the substrate were higher for coir while those of Fe, Cu, and Mn in the drainage lower. Moreover, coir also significantly increased contents of amino acids (His, Leu, Ile, Phe, Lys, Asp, Glu and Pro) and flavor substance (TC, PS, TP, CLL, CuB, and LA) in cucumber fruits. Our results demonstrated the potential of coir as a replacement of rockwool to improve sustainability of soilless cultivation in the greenhouse.

The combined influence of rootstock and vintage climate on the grape and wine flavonoids of Vitis vinifera L. cv. Cabernet Sauvignon in eastern China

Rootstocks are commonly utilized owing to their resistance to abiotic and biotic stress in viticulture. This study evaluated the effects of three rootstocks (1103P, SO4, and 5A) on the Cabernet Sauvignon (CS) vine growth, and their berries and wines flavonoids profiles in four consecutive vintages. The results showed that 1103P increased the pruning weight of CS and decreased the anthocyanin concentration in berries and wines, especially in the vintages with more rainy and cloudy days. 5A tended to decrease the pruning weight of CS and increase the anthocyanin concentration in berries and wines. Orthogonal partial least squares discriminant analysis (OPLS-DA) showed that the concentrations of total anthocyanins, F3'H-anthocyanins, malvidin-3-O-glucoside (Mv-glu), and malvidin-3-O-acetylglucoside (Mv-acglu) were the key substances affected by the rootstocks in CS berries and were significantly decreased by 1103P. Total anthocyanins, pinotins, Mv-glu, epicatechin, and vitisins were the rootstock-sensitive compounds that commonly differed in wines among the three comparison groups in the two vintages. Furthermore, 1103P brought more brightness to the wine and 5A gave the wine more red tones. In conclusion, rootstock 5A was recommended in the rainy and cloudy climate regions with regard to the berry flavonoids accumulation and the wine color.