Transcriptome analysis reveals the effects of grafting on sugar and α-linolenic acid metabolisms in fruits of cucumber with two different rootstocks

Root exudation under maize/soybean intercropping system mediates the arbuscular mycorrhizal fungi diversity and improves the plant growth

Introduction

Maize/soybean intercropping is a common cropping practice in Chinese agriculture, known to boost crop yield and enhance soil fertility. However, the role of below-ground interactions, particularly root exudates, in maintaining intercropping advantages in soybean/maize intercropping systems remains unclear.

Methods

This study aimed to investigate the differences in root exudates between intercropping and monocropping systems through two pot experiments using metabolomics methods. Multiple omics analyses were conducted to explore correlations between differential metabolites and the community of Arbuscular Mycorrhizal Fungi (AMF), shedding light on the mechanisms underlying the dominance of intercropping from the perspective of root exudates-soil microorganism interactions.

Results and discussion

The study revealed that intercropping significantly increased the types and contents of root exudates, lowered soil pH, increased the availability of nutrients like available nitrogen (AN) and available phosphorus (AP), and enhanced AMF colonization, resulting in improving the community composition of AMF. Besides, root exudates in intercropping systems differed significantly from those in monocropping, with 41 and 39 differential metabolites identified in the root exudates of soybean/maize, predominantly amino acids and organic acids. The total amount of amino acids in the root exudates of soybean intercropping was 3.61 times higher than in monocropping. Additionally, the addition of root exudates significantly improved the growth of soybean/maize and AMF colonization, with the mycorrhizal colonization rate in intercropping increased by 105.99% and 111.18% compared to monocropping, respectively. The identified metabolic pathways associated with root exudates were closely linked to plant growth, soil fertility improvement, and the formation of AMF. Correlation analysis revealed a significant relationship (P < 0.05) between certain metabolites such as tartaric acid, oxalic acid, malic acid, aspartic acid, alanine, and the AMF community. Notably, the photosynthetic carbon fixation pathway involving aspartic acid showed a strong association with the function of Glomus_f_Glomerace, the dominant genus of AMF. A combined analysis of metabolomics and high throughput sequencing revealed that the root exudates of soybean/maize intercropping have direct or indirect connections with AMF and soil nutrients.

Conclusion

This suggests that the increased root exudates of the soybean/maize intercropping system mediate an improvement in AMF community composition, thereby influencing soil fertility and maintaining the advantage of intercropping.

The effect of environmental factors on the genetic differentiation of Cucurbita ficifolia populations based on whole-genome resequencing

BACKGROUND

Cucurbita ficifolia is one of the squash species most resistant to fungal pathogens, and has especially high resistance to melon Fusarium wilt. This species is therefore an important germplasm resource for the breeding of squash and melon cultivars.

RESULTS

Whole-genome resequencing of 223 individuals from 32 populations in Yunnan Province, the main cucurbit production area in China, was performed and 3,855,120 single-nucleotide polymorphisms (SNPs) and 1,361,000 InDels were obtained. SNP analysis suggested that levels of genetic diversity in C. ficifolia were high, but that different populations showed no significant genetic differentiation or geographical structure, and that individual C. ficifolia plants with fruit rinds of a similar color did not form independent clusters. A Mantel test conducted in combination with geographical distance and environmental factors suggested that genetic distance was not correlated with geographical distance, but had a significant correlation with environmental distance. Further associations between the genetic data and five environmental factors were analyzed using whole-genome association analysis. SNPs associated with each environmental factor were investigated and genes 250 kb upstream and downstream from associated SNPs were annotated. Overall, 15 marker-trait-associated SNPs (MTAs) and 293 genes under environmental selection were identified. The identified genes were involved in cell membrane lipid metabolism, macromolecular complexes, catalytic activity and other related aspects. Ecological niche modeling was used to simulate the distribution of C. ficifolia across time, from the present and into the future. We found that the area suitable for C. ficifolia changed with the changing climate in different periods.

CONCLUSIONS

Resequencing of the C. ficifolia accessions has allowed identification of genetic markers, such as SNPs and InDels. The SNPs identified in this study suggest that environmental factors mediated the formation of the population structure of C. ficifolia in China. These SNPs and Indels might also contribute to the variation in important pathways of genes for important agronomic traits such as yield, disease resistance and stress tolerance. Moreover, the genome resequencing data and the genetic markers identified from 223 accessions provide insight into the genetic variation of the C. ficifolia germplasm and will facilitate a broad range of genetic studies.

Study on the Applications and Regulatory Mechanisms of Grafting on Vegetables

Grafting can overcome problems with soil sensitivity, enhance plant stress tolerance, improve product quality, and increase crop yield and value. This paper reviews the various mechanisms of vegetable grafting, the graft survival process and its influencing factors, the practical applications of grafting, and the molecular regulation of grafting in vegetables. The importance of germplasm and rootstock interactions, the mechanization of vegetable grafting, and future aspects, including intelligence and digitalization, are discussed.

Transcriptomic and metabolomic perspectives for the growth of alfalfa (Medicago sativa L.) seedlings with the effect of vanadium exposure

Hitherto, the effect of vanadium on higher plant growth remains an open topic. Therefore, nontargeted metabolomic and RNA-Seq profiling were implemented to unravel the possible alteration in alfalfa seedlings subjected to 0.1 mg L^-1 (B group) and 0.5 mg L^-1 (C group) pentavalent vanadium [(V(V)] versus control (A group) in this study. Results revealed that vanadium exposure significantly altered some pivotal transcripts and metabolites. The number of differentially expressed genes (DEGs) markedly up- and down-regulated was 21 and 23 in B_vs_A, 27 and 33 in C_vs_A, and 24 and 43 in C_vs_B, respectively. The number for significantly up- and down-regulated differential metabolites was 17 and 15 in B_vs_A, 43 and 20 in C_vs_A, and 24 and 16 in C_vs_B, respectively. Metabolomics and transcriptomics co-analysis characterized three significantly enriched metabolic pathways in C_vs_A comparing group, viz., α-linolenic acid metabolism, flavonoid biosynthesis, and phenylpropanoid biosynthesis, from which some differentially expressed genes and differential metabolites participated. The metabolite of traumatic acid in α-linolenic acid metabolism and apigenin in flavonoid biosynthesis were markedly upregulated, while phenylalanine in phenylpropanoid biosynthesis was remarkably downregulated. The genes of allene oxide cyclase (AOC) and acetyl-CoA acyltransferase (fadA) in α-linolenic acid metabolism, and chalcone synthase (CHS), flavonoid 3'-monooxygenase (CYP75B1), and flavonol synthase (FLS) in flavonoid biosynthesis, and caffeoyl-CoA O-methyltransferase (CCoAOMT) in phenylpropanoid biosynthesis were significantly downregulated. While shikimate O-hydroxycinnamoyltransferase (HCT) in flavanoid and phenylpropanoid biosynthesis were conspicuously upregulated. Briefly, vanadium exposure induces a readjustment yielding in metabolite and the correlative synthetic precursors (transcripts/unigenes) in some branched metabolic pathways. This study provides a practical and in-depth perspective from transcriptomics and metabolomics in investigating the effects conferred by vanadium on plant growth and development.

Luffa rootstock enhances salt tolerance and improves yield and quality of grafted cucumber plants by reducing sodium transport to the shoot

Soil salinity severely limits crop yield and quality. Grafting onto tolerant rootstocks is known as an effective means to alleviate salt stress. The present study was planned to find out the potential roles, mechanisms and applications of luffa rootstock to improve salt tolerance of grafted cucumber plants. Here, we screened a highly salt-tolerant luffa rootstock by evaluating the growth, photosynthetic performance, antioxidant defense and the accumulation of Na⁺ and K⁺ under salt stress. Reciprocal grafting between cucumber and luffa showed that luffa rootstock significantly improved the salt tolerance of cucumber plants, as evidenced by higher fresh weight, photochemical efficiency (Fv/Fm), and lower relative electrical conductivity (REC), which was closely associated with the decreased accumulation of Na⁺ and increased the accumulation of K⁺ in shoots of luffa grafted cucumber seedlings, leading to a lower Na⁺:K⁺ ratio in shoot when compared with self-grafted cucumber. Furthermore, grafting with intermediate stock of luffa also sufficiently alleviated cucumber salt stress by reducing Na⁺ accumulation in shoot and the whole plant but increasing Na⁺ accumulation in interstock and root under salt stress, fully proving the salt tolerance depending on the capacity of luffa interstock to limit the transport of Na⁺ from the root to the shoot. More importantly, luffa rootstock improved the growth, yield and quality of grafted cucumber plants grown in pots in solar greenhouse as revealed by increased net photosynthetic rate, plant height, leaf number, yield, Vitamin C and soluble sugar but decreased titratable acid under both salinity and normal conditions. Together, these results, for the first time, clearly demonstrated that luffa,a new highly salt-tolerant rootstock, enhances salt tolerance and improves yield and quality of grafted cucumber plants by reducing sodium transport to the shoot.

Modification of the Sensory Profile and Volatile Aroma Compounds of Tomato Fruits by the Scion × Rootstock Interactive Effect

Sensory quality is of increasing importance to consumer decisions in choosing a product, and it is certainly an important factor in repurchasing in terms of meeting the necessary aroma quality and taste properties. To better understand the effects of rootstocks and scions on fruit quality, the sensory profile and volatile aroma composition of the fruits of hydroponically grown tomato plants were evaluated. Experiments were established using the tomato cultivars Clarabella and Estatio as scions during two spring-summer seasons. In both experiments, the scion plants were self-grafted or grafted onto rootstocks of cultivars Arnold, Buffon, Emperador, and Maxifort, with the exception that in experiment 1, the Estatio scion was not grafted onto Buffon. The scions and rootstocks caused differences in observed sensory properties in both experiments. For most of the sensory traits, interaction effects between scion and rootstock were observed. Compared to those obtained from self-grafted Clarabella, the fruits obtained from Clarabella grafted onto Buffon in the first experiment and Clarabella grafted onto Arnold in the second experiment were sweeter by one measurement unit. The contents of seven aldehydes, six alcohols, five terpenes and two ketones were determined. A lower accumulation of total aldehydes, 22-45%, due to lower amounts of pentanal, (E)-2-heptanal and (E,E)-2,4-decadienal, was found in the fruits from plants where Estatio was rootstock compared with the other rootstocks treatments. Clarabella as a rootstock increased (Z)-3-hexenal + (E)-2-hexenal accumulation from 35 to 65%. Grafting Clarabella onto the tested rootstocks led to a change in the composition of volatile compounds, while differences between the combinations with Estatio as a scion were generally not recorded. Fruits from self-grafted Clarabella had higher (Z)-3-hexenal + (E)-2-hexenal concentrations than did fruits from Clarabella grafted onto Arnold (for 54%) and Emperador (for 68%), and in the second experiment, grafting onto all commercial rootstocks reduced (Z)-3-hexenal + (E)-2-hexenal concentrations, from 25 to 74%, compared to those from self-grafted Clarabella. Higher (+)-2-carene and (-)-caryophyllene oxide concentrations were attained in plants in which Clarabella was grafted onto Maxifort (by 56%) and plants in which Estatio was grafted onto Arnold (by 36%) compared to self-grafted plants. This study showed the possibility of altering the composition of volatile aroma compounds and sensory properties of tomato fruits by the use of grafting techniques.

Vegetable Grafting From a Molecular Point of View: The Involvement of Epigenetics in Rootstock-Scion Interactions

Vegetable grafting is extensively used today in agricultural production to control soil-borne pathogens, abiotic and biotic stresses and to improve phenotypic characteristics of the scion. Commercial vegetable grafting is currently practiced in tomato, watermelon, melon, eggplant, cucumber, and pepper. It is also regarded as a rapid alternative to the relatively slow approach of breeding for increased environmental-stress tolerance of fruit vegetables. However, even though grafting has been used for centuries, until today, there are still many issues that have not been elucidated. This review will emphasize on the important mechanisms taking place during grafting, especially the genomic interactions between grafting partners and the impact of rootstocks in scion's performance. Special emphasis will be drawn on the relation between vegetable grafting, epigenetics, and the changes in morphology and quality of the products. Recent advances in plant science such as next-generation sequencing provide new information regarding the molecular interactions between rootstock and scion. It is now evidenced that genetic exchange is happening across grafting junctions between rootstock and scion, potentially affecting grafting-mediated effects already recorded in grafted plants. Furthermore, significant changes in DNA methylation are recorded in grafted scions, suggesting that these epigenetic mechanisms could be implicated in grafting effects. In this aspect, we also discuss the process and the molecular aspects of rootstock scion communication. Finally, we provide with an extensive overview of gene expression changes recorded in grafted plants and how these are related to the phenotypic changes observed. Τhis review finally seeks to elucidate the dynamics of rootstock-scion interactions and thus stimulate more research on grafting in the future. In a future where sustainable agricultural production is the way forward, grafting could play an important role to develop products of higher yield and quality in a safe and "green" way.

The Formation of Fruit Quality in Cucumis sativus L

Cucumber is one of the most widely grown vegetables in China and an indispensable fresh fruit in the diet. With the development of society, the demand of people for cucumber quality is higher and higher. Therefore, cultivating high-quality cucumber varieties is one of the main goals of cucumber breeding. With the rapid development of biotechnology such as molecular marker, cucumber quality control network is becoming clear. In this review, we describe the formation mechanism of cucumber fruit quality from three aspects: (1) the commercial quality of cucumber fruit, (2) nutritional quality formation, and (3) flavor quality of cucumber fruit. In addition, the determinants of cucumber fruit quality were summarized from two aspects of genetic regulation and cultivation methods in order to provide ideas for cucumber researchers and cultivators to improve fruit quality.

Investigation of Differentially Expressed Proteins Induced by Alteration of Natural Se Uptake with Ultrahigh-Performance Liquid Chromatography Quadrupole Orbitrap Uncovers the Potential Nutritional Value in Se-Enriched Green Tea

Se-enriched green tea, with an increasing consumption, is the shoot of tea plants grown naturally in a seleniferous region. A label-free proteomic strategy based on ultrahigh-performance liquid chromatography quadrupole Orbitrap was applied to characterize and distinguish the difference between the Se-enriched and normal green tea with a total of 283 proteins identified and 264 proteins quantified, in which 96 proteins were observed different. The expressions of 10 proteins were upregulated and 40 proteins were downregulated (p < 0.05) in Se-enriched samples. Gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway, and protein-protein interaction (PPI) network analysis results indicated that these differentially expressed proteins significantly interacted and were involved in secondary metabolites and inflammatory response biological processes. Furthermore, the expression of methyl-jasmonate- and ethylene-related genes changed significantly in Se-enriched green tea, and catalase proteins were employed as the center of the pathway that changed significantly in the PPI network. These results associating with the current knowledge of selenium in soil-plant cycling revealed that organic selenium was synthesized in green tea, which provided novel information on Se assimilation in Camellia sinensis and improved the understanding of Se-enriched green tea as a possible ideal selenium supplement in daily life.

Systemic Long-Distance Signaling and Communication Between Rootstock and Scion in Grafted Vegetables

Grafting is widely used in fruit, vegetable, and flower propagation to improve biotic and abiotic stress resistance, yield, and quality. At present, the systemic changes caused by grafting, as well as the mechanisms and effects of long-distance signal transport between rootstock and scion have mainly been investigated in model plants (Arabidopsis thaliana and Nicotiana benthamiana). However, these aspects of grafting vary when different plant materials are grafted, so the study of model plants provides only a theoretical basis and reference for the related research of grafted vegetables. The dearth of knowledge about the transport of signaling molecules in grafted vegetables is inconsistent with the rapid development of large-scale vegetable production, highlighting the need to study the mechanisms regulating the rootstock-scion interaction and long-distance transport. The rapid development of molecular biotechnology and "omics" approaches will allow researchers to unravel the physiological and molecular mechanisms involved in the rootstock-scion interaction in vegetables. We summarize recent progress in the study of the physiological aspects (e.g., hormones and nutrients) of the response in grafted vegetables and focus in particular on long-distance molecular signaling (e.g., RNA and proteins). This review provides a theoretical basis for studies of the rootstock-scion interaction in grafted vegetables, as well as provide guidance for rootstock breeding and selection to meet specific demands for efficient vegetable production.

Comparative analysis of primary metabolites and transcriptome changes between ungrafted and pumpkin-grafted watermelon during fruit development

Grafting has been reported as a factor that influences fruit quality. However, a comprehensive study of the metabolic profile related to fruit quality and the underlying molecular mechanism in grafted watermelon has not been carried out. Metabolomics and transcriptome analysis were performed on both pumpkin-grafted watermelon and ungrafted watermelon at different developmental stages. In total, 56 primary metabolites were identified with either high or low abundance between ungrafted and pumpkin-grafted watermelon. The results indicated that ornithine, arginine, lysine (amino acids), glucose, sucrose, glucosamine (sugars), malic acid, fumaric acid and succinic acid (organic acids) were among the dominant metabolites influencing fruit quality. Additionally, comparative RNA sequence analysis on grafted and ungrafted watermelon yielded 729, 174, 128 and 356 differentially expressed genes at 10, 18, 26 and 34 days after pollination (DAP), respectively. Functional annotations of these genes indicated that grafting significantly altered the biological and metabolic processes related to fruit quality. Our comparative metabolomics and transcriptome analysis revealed that FBA2, FK, SuSy, SPS, IAI, AI and sugar transporter gene (SWT3b) might play a central role in the accumulation of glucose and sucrose, whereas higher malic acid content was attributed to high down regulation of ALMT13 and ALMT8 in pumpkin-grafted watermelon. Changes in the ornithine, glutamine, alanine, tyrosine, valine, asparagine, phenylalanine, arginine and tryptophan contents were consistent with the transcript level of their metabolic genes such as NAOD, GS, AGT, TaT, aDH1, OGDH, aDC, 4CL 1, PaL, CaT and two nitrate transporter genes (NRT1) in pumpkin-grafted watermelon. This study provides the basis for understanding the graft-responsive changes in the metabolic profile and regulatory mechanism related to fruit quality.

Transcriptome changes in reciprocal grafts involving watermelon and bottle gourd reveal molecular mechanisms involved in increase of the fruit size, rind toughness and soluble solids

Transcriptome landscape reveals the molecular mechanisms involved in the improvement of fruit traits by the grafting of watermelon and bottle gourd. Grafting has been used as a sustainable alternative for watermelon breeding to control soil-borne pathogens and to increase tolerance to various abiotic stresses. However, some reports have shown that grafting can negatively affect the quality of fruits. Despite several field studies on the effects of grafting on fruit quality, the regulation of this process at the molecular level has not been revealed. The aim of this study was to elucidate various molecular mechanisms involved in different tissues of heterografted watermelon and bottle gourd plants. Grafting with bottle gourd rootstock increased the size and rind thickness of watermelon fruits, whereas that with watermelon rootstock produced bottle gourd fruits with higher total soluble solid content and thinner rinds. Correspondingly, genes related to ripening, softening, cell wall strengthening, stress response and disease resistance were differentially expressed in watermelon fruits. Moreover, genes associated mainly with sugar metabolism were differentially expressed in bottle gourd fruits. RNA-seq revealed more than 400 mobile transcripts across the heterografted sets. More than half of these were validated from PlaMoM, a database for plant mobile macromolecules. In addition, some of these mobile transcripts contained a transfer RNA-like structure. Other RNA motifs were also enriched in these transcripts, most with a biological role based on GO analysis. This transcriptome study provided a comprehensive understanding of various molecular mechanisms underlying grafted tissues in watermelon.

Integrated Metabolome and Transcriptome Analysis Provide Insights into the Effects of Grafting on Fruit Flavor of Cucumber with Different Rootstocks

Rootstocks frequently exert detrimental effects on the fruit quality of grafted cucumber (Cucumis sativus L.) plants. To understand and ultimately correct this deficiency, a transcriptomic and metabolomic comparative analysis was performed among cucumber fruits from non-grafted plants (NG), and fruits from plants grafted onto different rootstocks of No.96 and No.45 (Cucurbita moschata. Duch), known to confer a different aroma and taste. We found remarkable changes in the primary metabolites of sugars, organic acids, amino acids, and alcohols in the fruit of the grafted cucumber plants with different rootstocks, compared to the non-grafted ones, especially No.45. We identified 140, 131, and 244 differentially expressed genes (DEGs) in the comparisons of GNo.96 vs. NG, GNo.45 vs. NG, and GNo.45 vs. GNo.96. The identified DEGs have functions involved in many metabolic processes, such as starch and sucrose metabolism; the biosynthesis of diterpenoid, carotenoid, and zeatin compounds; and plant hormone signal transduction. Members of the HSF, AP2/ERF-ERF, HB-HD-ZIP, and MYB transcription factor families were triggered in the grafted cucumbers, especially in the cucumber grafted on No.96. Based on a correlation analysis of the relationships between the metabolites and genes, we screened 10 candidate genes likely to be involved in sugar metabolism (Fructose-6-phosphate and trehalose), linoleic acid, and amino-acid (isoleucine, proline, and valine) biosynthesis in grafted cucumbers, and then confirmed the gene expression patterns of these genes by qRT-PCR. The levels of TPS15 (Csa3G040850) were remarkably increased in cucumber fruit with No.96 rootstock compared with No.45, suggesting changes in the volatile chemical production. Together, the results of this study improve our understanding of flavor changes in grafted cucumbers, and identify the candidate genes involved in this process.