Transcriptional Characterization of a Widely-Used Grapevine Rootstock Genotype under Different Iron-Limited Conditions

The activation of iron deficiency responses of grapevine rootstocks is dependent to the availability of the nitrogen forms

BACKGROUND

In viticulture, iron (Fe) chlorosis is a common abiotic stress that impairs plant development and leads to yield and quality losses. Under low availability of the metal, the applied N form (nitrate and ammonium) can play a role in promoting or mitigating Fe deficiency stresses. However, the processes involved are not clear in grapevine. Therefore, the aim of this study was to investigate the response of two grapevine rootstocks to the interaction between N forms and Fe uptake. This process was evaluated in a hydroponic experiment using two ungrafted grapevine rootstocks Fercal (Vitis berlandieri x V. vinifera) tolerant to deficiency induced Fe chlorosis and Couderc 3309 (V. riparia x V. rupestris) susceptible to deficiency induced Fe chlorosis.

RESULTS

The results could differentiate Fe deficiency effects, N-forms effects, and rootstock effects. Interveinal chlorosis of young leaves appeared earlier on 3309 C from the second week of treatment with NO3-/NH4+ (1:0)/-Fe, while Fercal leaves showed less severe symptoms after four weeks of treatment, corresponding to decreased chlorophyll concentrations lowered by 75% in 3309 C and 57% in Fercal. Ferric chelate reductase (FCR) activity was by trend enhanced under Fe deficiency in Fercal with both N combinations, whereas 3309 C showed an increase in FCR activity under Fe deficiency only with NO3-/NH4+ (1:1) treatment. With the transcriptome analysis, Gene Ontology (GO) revealed multiple biological processes and molecular functions that were significantly regulated in grapevine rootstocks under Fe-deficient conditions, with more genes regulated in Fercal responses, especially when both forms of N were supplied. Furthermore, the expression of genes involved in the auxin and abscisic acid metabolic pathways was markedly increased by the equal supply of both forms of N under Fe deficiency conditions. In addition, changes in the expression of genes related to Fe uptake, regulation, and transport reflected the different responses of the two grapevine rootstocks to different N forms.

CONCLUSIONS

Results show a clear contribution of N forms to the response of the two grapevine rootstocks under Fe deficiency, highlighting the importance of providing both N forms (nitrate and ammonium) in an appropriate ratio in order to ease the rootstock responses to Fe deficiency.

Physiological and Transcriptional Responses to Saline Irrigation of Young 'Tempranillo' Vines Grafted Onto Different Rootstocks

The use of more salt stress-tolerant vine rootstocks can be a sustainable strategy for adapting traditional grapevine cultivars to future conditions. However, how the new M1 and M4 rootstocks perform against salinity compared to conventional ones, such as the 1103-Paulsen, had not been previously assessed under real field conditions. Therefore, a field trial was carried out in a young 'Tempranillo' (Vitis vinifera L.) vineyard grafted onto all three rootstocks under a semi-arid and hot-summer Mediterranean climate. The vines were irrigated with two kinds of water: a non-saline Control with EC of 0.8 dS m-1 and a Saline treatment with 3.5 dS m-1. Then, various physiological parameters were assessed in the scion, and, additionally, gene expression was studied by high throughput sequencing in leaf and berry tissues. Plant water relations evidenced the osmotic effect of water quality, but not that of the rootstock. Accordingly, leaf-level gas exchange rates were also reduced in all three rootstocks, with M1 inducing significantly lower net photosynthesis rates than 1103-Paulsen. Nevertheless, the expression of groups of genes involved in photosynthesis and amino acid metabolism pathways were not significantly and differentially expressed. The irrigation with saline water significantly increased leaf chloride contents in the scion onto the M-rootstocks, but not onto the 1103P. The limitation for leaf Cl- and Na+ accumulation on the scion was conferred by rootstock. Few processes were differentially regulated in the scion in response to the saline treatment, mainly, in the groups of genes involved in the flavonoids and phenylpropanoids metabolic pathways. However, these transcriptomic effects were not fully reflected in grape phenolic ripeness, with M4 being the only one that did not cause reductions in these compounds in response to salinity, and 1103-Paulsen having the highest overall concentrations. These results suggest that all three rootstocks confer short-term salinity tolerance to the scion. The lower transcriptomic changes and the lower accumulation of potentially phytotoxic ions in the scion grafted onto 1103-Paulsen compared to M-rootstocks point to the former being able to maintain this physiological response in the longer term. Further agronomic trials should be conducted to confirm these effects on vine physiology and transcriptomics in mature vineyards.

Volatile composition and sensory properties of wines from vineyards affected by iron chlorosis

Recent studies have shown that mild to moderate iron chlorosis can have positive effects on grape quality potential, including volatile profile. The main objective of this work was to investigate, for the first time, how moderate iron stress in grapevines affects the presence of volatile organic compounds (VOCs) in wines. The study was carried out during 2018-2019 seasons, in 20 Tempranillo vineyard subzones with different degree of iron deficiency, located in Ribera del Duero (North-Central Spain). The results showed that moderate iron stress increased in wines the concentrations of VOCs associated with floral notes, such as 2-phenylacetaldehyde, 2-phenylethanol and 2-phenylethyl acetate, while reducing the presence of C6-alcohols, responsible for green-herbaceous aroma. A favourable reduction of pH and a betterment of parameters related to colour were detected in wines from iron deficient subzones. Chlorosis incidence was associated to improvements in wine sensory attributes as layer intensity, black fruit and aroma intensity.

Transcriptome Analysis Revealed the Molecular Response Mechanism of Non-heading Chinese Cabbage to Iron Deficiency Stress

Iron is a trace metal that is found in animals, plants, and the human body. Human iron absorption is hampered by plant iron shortage, which leads to anemia. Leafy vegetables are one of the most direct and efficient sources of iron for humans. Despite the fact that ferrotrophic disorder is common in calcareous soil, however, non-heading Chinese cabbage performs a series of reactions in response to iron deficiency stress that help to preserve iron homeostasis in vivo. In this study, we discovered that iron deficiency stress caused leaf yellowing and impeded plant development in both iron-deficient and control treatments by viewing or measuring phenotypic, chlorophyll content, and Fe²⁺ content in both iron-deficient and control treatments. We found a total of 9213 differentially expressed genes (DEGs) in non-heading Chinese cabbage by comparing root and leaf transcriptome data with iron deficiency and control treatments. For instance, 1927 DEGs co-expressed in root and leaf, including 897 up-regulated and 1030 down-regulated genes, respectively. We selected some key antioxidant genes, hormone signal transduction, iron absorption and transport, chlorophyll metabolism, and transcription factors involved in the regulation of iron deficiency stress utilizing GO enrichment, KEGG enrichment, multiple types of functional annotation, and Weighted Gene Co-expression Network Analysis (WGCNA). This study identifies prospective genes for maintaining iron homeostasis under iron-deficient stress, offering a theoretical foundation for further research into the molecular mechanisms of greater adaptation to iron-deficient stress, and perhaps guiding the development of iron-tolerant varieties.

How Do Novel M-Rootstock (Vitis Spp.) Genotypes Cope with Drought?

Most of the vineyards around the world are in areas characterized by seasonal drought, where water deficits and high temperatures represent severe constraints on the regular grapevine growth cycle. Although grapevines are well adapted to arid and semi-arid environments, water stress can cause physiological changes, from mild to irreversible. Screening of available Vitis spp. genetic diversity for new rootstock breeding programs has been proposed as a way for which new viticulture challenges may be faced. In 2014, novel genotypes (M-rootstocks) were released from the University of Milan. In this work, the behavior of M1, M3 and M4 in response to decreasing water availabilities (80%, 50% and 20% soil water content, SWC) was investigated at the physiological and gene expression levels, evaluating gas exchange, stem water potential and transcript abundances of key genes related to ABA (abscisic acid) biosynthesis (VvZEP, VvNCED1 and VvNCED2) and signaling (VvPP2C4, VvSnRK2.6 and VvABF2), and comparing them to those of cuttings of nine commercial rootstocks widely used in viticulture. M-rootstocks showed a change at physiological levels in severe water-stressed conditions (20% soil water content, SWC), reducing the stomatal conductance and stem water potential, but maintaining high photosynthetic activity. Water use efficiency was high in water-limiting conditions. The transcriptional changes were observed at 50% SWC, with an increment of transcripts of VvNCED1 and VvNCED2 genes. M-rootstocks showed similar behavior to 1103P and 110R rootstocks, two highly tolerant commercial genotypes. These rootstocks adopted a tolerant strategy to face water-stressed conditions.

Scion genotypes exert long distance control over rootstock transcriptome responses to low phosphate in grafted grapevine

BACKGROUND

Grafting is widely used in horticulture and rootstocks are known to modify scion growth and adaptation to soil conditions. However, the role of scion genotype in regulating rootstock development and functioning has remained largely unexplored. In this study, reciprocal grafts of two grapevine genotypes were produced as well as the corresponding homo-graft controls. These plants were subjected to a low phosphate (LP) treatment and transcriptome profiling by RNA sequencing was done on root samples collected 27 h after the onset of the LP treatment.

RESULTS

A set of transcripts responsive to the LP treatment in all scion/rootstock combinations was identified. Gene expression patterns associated with genetic variation in response to LP were identified by comparing the response of the two homo-grafts. In addition, the scion was shown to modify root transcriptome responses to LP in a rootstock dependent manner. A weighted gene co-expression network analysis identified modules of correlated genes; the analysis of the association of these modules with the phosphate treatment, and the scion and rootstock genotype identified potential hub genes.

CONCLUSIONS

This study provides insights into the response of grafted grapevine to phosphate supply and identifies potential shoot-to-root signals that could vary between different grapevine genotypes.

Novel Aspects on The Interaction Between Grapevine and Plasmopara viticola: Dual-RNA-Seq Analysis Highlights Gene Expression Dynamics in The Pathogen and The Plant During The Battle For Infection

Mgaloblishvili, a Vitis vinifera cultivar, exhibits unique resistance traits against Plasmopara viticola, the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pinot noir (a V. vinifera susceptible cultivar), and Bianca (a resistant hybrid) leaves, inoculated and non-inoculated with the pathogen, were used to identify P. viticola effector-encoding genes and plant susceptibility/resistance genes. Multiple effector-encoding genes were identified in P. viticola transcriptome, with remarkable expression differences in relation to the inoculated grapevine cultivar. Intriguingly, five apoplastic effectors specifically associated with resistance in V. vinifera. Gene coexpression network analysis identified specific modules and metabolic changes occurring during infection in the three grapevine cultivars. Analysis of these data allowed, for the first time, the detection in V. vinifera of a putative P. viticola susceptibility gene, encoding a LOB domain-containing protein. Finally, the de novo assembly of Mgaloblishvili, Pinot noir, and Bianca transcriptomes and their comparison highlighted novel candidate genes that might be at the basis of the resistant phenotype. These results open the way to functional analysis studies and to new perspectives in molecular breeding of grapevine for resistance to P. viticola.

Morphological Root Responses and Molecular Regulation of Cation Transporters Are Differently Affected by Copper Toxicity and Cropping System Depending on the Grapevine Rootstock Genotype

The high copper (Cu) concentration in vineyard soils causes the increase of Cu toxicity symptoms in young grapevines. Recently, intercropping of grapevine and oat was shown to reduce Cu toxicity effects, modulating the root ionome. On these bases, the focus of the work was to investigate the impact of Cu toxicity of either monocropped or oat-intercropped grapevine rootstocks plants (196.17 and Fercal), at both phenotypic (i.e., root architecture), and molecular (i.e., expression of transporters) levels. The results showed a different response in terms of root morphology that are both rootstock- and cropping system dependent. Moreover, the expression pattern of transporter genes (i.e., VvCTr, VvNRAMP, and VvIRT1) in monocropped grapevine might resemble a Mn deficiency response induced by the excess of Cu, especially in Fercal plants. The gene expression in intercropped grapevines suggested rootstock-specific response mechanisms, depending on Cu levels. In fact, at low Cu concentrations, Fercal enhanced both root system growth and transporter genes expression; contrarily, 196.17 increased apoplast divalent cations accumulation and transporters expression. At high Cu concentrations, Fercal increased the expression of all bivalent cation transporters and, as previously observed, enhanced the release of root exudates, whereas the 196.17 only modulated transporters. In conclusion, our results might suggest that the different adaptation strategies of the two rootstocks to Cu toxicity could be mainly ascribable to a fine-tuning of bivalent cations transporters expression at root level.

Drought Exacerbates Botryosphaeria Dieback Symptoms in Grapevines and Confounds Host-based Molecular Markers of Infection by Neofusicoccum parvum

Neofusicoccum parvum, causal fungus of the grapevine trunk disease Botryosphaeria dieback, attacks the wood of Vitis vinifera. Because lesions are internal, using putative host-based markers of infection from leaves for diagnosis is a nondestructive option. However, their specificity under drought stress is unknown. Potted 'Cabernet-Sauvignon' were inoculated with N. parvum in the greenhouse after wounding (IW), and with wounded and nonwounded noninoculated controls. At 2 weeks postinoculation (WPI), half of the plants were severely stressed (SS), receiving 30% water volume of the well-watered (WW) plants. Larger lesions at 12 WPI among IW-SS plants, compared with all other treatments, revealed an interactive effect of inoculation and drought on lesion length. Expression of eight putative marker genes was analyzed in leaves by qPCR at the onset of drought stress, and at 8 and 12 WPI. One marker showed consistent over-expression at 8 WPI in IW plants, regardless of water treatment, suggesting specificity to infection. By 12 WPI, higher expression of seven genes in all SS plants (across inoculation treatments) revealed specificity to drought. Cross-reactivity of markers to drought, therefore, limits their utility for disease diagnosis in the field, where drought induced by climate and deficit irrigation is common.

Rootstock effects on scion phenotypes in a 'Chambourcin' experimental vineyard

Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops. Grafting is a common horticultural practice that joins the roots (rootstock) of one plant to the shoot (scion) of another, providing an excellent method for investigating how these two organ systems affect each other. In this study, we used the French-American hybrid grapevine 'Chambourcin' (Vitis L.) as a model to explore the rootstock-scion relationship. We examined leaf shape, ion concentrations, and gene expression in 'Chambourcin' grown ungrafted as well as grafted to three different rootstocks ('SO4', '1103P' and '3309C') across 2 years and three different irrigation treatments. We found that a significant amount of the variation in leaf shape could be explained by the interaction between rootstock and irrigation. For ion concentrations, the primary source of variation identified was the position of a leaf in a shoot, although rootstock and rootstock by irrigation interaction also explained a significant amount of variation for most ions. Lastly, we found rootstock-specific patterns of gene expression in grafted plants when compared to ungrafted vines. Thus, our work reveals the subtle and complex effect of grafting on 'Chambourcin' leaf morphology, ionomics, and gene expression.

Unique resistance traits against downy mildew from the center of origin of grapevine (Vitis vinifera)

The Eurasian grapevine (Vitis vinifera), an Old World species now cultivated worldwide for high-quality wine production, is extremely susceptible to the agent of downy mildew, Plasmopara viticola. The cultivation of resistant V. vinifera varieties would be a sustainable way to reduce the damage caused by the pathogen and the impact of disease management, which involves the economic, health and environmental costs of frequent fungicide application. We report the finding of unique downy mildew resistance traits in a winemaking cultivar from the domestication center of V. vinifera, and characterize the expression of a range of genes associated with the resistance mechanism. Based on comparative experimental inoculations, confocal microscopy and transcriptomics analyses, our study shows that V. vinifera cv. Mgaloblishvili, native to Georgia (South Caucasus), exhibits unique resistance traits against P. viticola. Its defense response, leading to a limitation of P. viticola growth and sporulation, is determined by the overexpression of genes related to pathogen recognition, the ethylene signaling pathway, synthesis of antimicrobial compounds and enzymes, and the development of structural barriers. The unique resistant traits found in Mgaloblishvili highlight the presence of a rare defense system in V. vinifera against P. viticola which promises fresh opportunities for grapevine genetic improvement.