Novel loci associated with resistance to downy and powdery mildew in grapevine

Among the main challenges in current viticulture, there is the increasing demand for sustainability in the protection from fungal diseases, such as downy mildew (DM) and powdery mildew (PM). Breeding disease-resistant grapevine varieties is a key strategy for better managing fungicide inputs. This study explores the diversity of grapevine germplasm (cultivated and wild) from Caucasus and neighboring areas to identify genotypes resistant to DM and PM, based on 13 Simple Sequence Repeat (SSR) loci and phenotypical (artificial pathogen inoculation) analysis, and to identify loci associated with DM and PM resistance, via Genome-Wide Association Analysis (GWAS) on Single Nucleotide Polymorphism (SNP) profiles. SSR analysis revealed resistant alleles for 16 out of 88 genotypes. Phenotypic data identified seven DM and 31 PM resistant genotypes. GWAS identified two new loci associated with DM resistance, located on chromosome 15 and 16 (designated as Rpv36 and Rpv37), and two with PM resistance, located on chromosome 6 and 17 (designated as Ren14 and Ren15). The four novel loci identified genomic regions rich in genes related to biotic stress response, such as genes involved in pathogen recognition, signal transduction and resistance response. This study highlights potential candidate genes associated with resistance to DM and PM, providing valuable insights for breeding programs for resistant varieties. To optimize their utilization, further functional characterization studies are recommended.

A new digital technology to reduce fungicide use in vineyards

There is a growing demand for technologies able to decrease the environmental impact of agricultural activities without penalizing quali-quantitative characteristics of productions. In the case of viticulture, one of the key problems is represented by the spray drift during fungicide treatments. The diffusion in operational farming contexts of technologies based on variable-rate and recycling tunnel sprayers is often limited by their cost and, for the latter, by their size and lower maneuverability, representing clear disadvantages especially in case of small farms or in hilly and mountain areas. We present a new digital technology implemented in a mobile app that supports the reduction of both the number of treatments and the amount of fungicide distributed per treatment. The technology is based (i) on an alert system that prevents unneeded treatments in case of no risk of infection and (ii) on the quantification of the optimal amounts of active ingredients and dilution water based on the sprayer type/settings and on leaf area index values estimated with a common smartphone. An internal database allows to adjust (in case of need) the active ingredient dose to assure full compliance with product's legal requirements. In case of heterogeneity in leaf area index values inside the vineyard, prescription maps are generated. Results from a 2-year case study in a vineyard in northern Italy are shown, where the system allowed to reduce by 26.4 % and 27.4 % (mean of two years), respectively, the seasonal amounts of fungicides and dilution water, and by 43.8 % the copper content in must. The high usability of the technology proposed (just a common smartphone is needed) and the fact that it does not require updating the farm machine park highlights the suitability of the proposed solution for operational farming conditions, including premium wine production districts often characterized by small farms in hilly areas.

Alpine Viticulture and Climate Change: Environmental Resources and Limitations for Grapevine Ripening in Valtellina, Italy

The effects of the spatial and temporal variability of environmental factors on viticulture are particularly important in mountainous wine regions due to their complex geomorphology. A typical example is Valtellina, an Italian valley in the middle of the Alpine chain known for its wine production. The aim of this work was to assess the effects of the current climatic conditions on Alpine viticultural production by evaluating the relationship between sugar accumulation, acid degradation, and environmental factors. To achieve this objective, a 21-year time series of ripening curves from 15 vineyards (cv Nebbiolo) along the Valtellina wine-growing belt was collected. The ripening curves were then analysed in conjunction with meteorological data to assess the influence of geographical and climatic characteristics, as well as other limiting environmental factors, on grape ripening. Valtellina is currently characterised by a stable warm phase, with yearly precipitation slightly higher than in the past. In this context, the timing of ripening and the level of total acidity are correlated with altitude, temperature, and summer thermal excess. Precipitation shows good correlations with all the maturity indices, so higher precipitation leads to late ripening and higher total acidity. Considering the oenological goal of local wineries, the results suggest that the Alpine area of Valtellina is currently facing favourable environmental conditions, with early development and increased levels of sugar while maintaining good levels of acidity.

Physiological and Transcriptomic Evaluation of Drought Effect on Own-Rooted and Grafted Grapevine Rootstock (1103P and 101-14MGt)

Grapevines worldwide are grafted onto Vitis spp. rootstocks in order to improve their tolerance to biotic and abiotic stresses. Thus, the response of vines to drought is the result of the interaction between the scion variety and the rootstock genotype. In this work, the responses of genotypes to drought were evaluated on 1103P and 101-14MGt plants, own-rooted and grafted with Cabernet Sauvignon, in three different water deficit conditions (80, 50, and 20% soil water content, SWC). Gas exchange parameters, stem water potential, root and leaf ABA content, and root and leaf transcriptomic response were investigated. Under well-watered conditions, gas exchange and stem water potential were mainly affected by the grafting condition, whereas under sever water deficit they were affected by the rootstock genotype. Under severe stress conditions (20% SWC), 1103P showed an "avoidance" behavior. It reduced stomatal conductance, inhibited photosynthesis, increased ABA content in the roots, and closed the stomata. The 101-14MGt maintained a high photosynthetic rate, limiting the reduction of soil water potential. This behavior results in a "tolerance" strategy. An analysis of the transcriptome showed that most of the differentially expressed genes were detected at 20% SWC, and more significantly in roots than in leaves. A core set of genes has been highlighted on the roots as being related to the root response to drought that are not affected by genotype nor grafting. Genes specifically regulated by grafting and genes specifically regulated by genotype under drought conditions have been identified as well. The 1103P, more than the 101-14MGt, regulated a high number of genes in both own-rooted and grafted conditions. This different regulation revealed that 1103P rootstock readily perceived the water scarcity and rapidly faced the stress, in agreement with its avoidance strategy.

A multidisciplinary approach to assess environmental and economic impact of conventional and innovative vineyards management systems in Northern Italy

Viticulture is gradually shifting to more sustainable production systems and a fair number of studies aim at assessing the environmental impacts of different technologies and techniques adopted in the wine production through the Life Cycle Assessment approach. The main environmental issues identified are on water, soil and energy use, management of organic and inorganic solid waste streams, greenhouse gas emissions and use of chemicals. Precision viticulture (PV) techniques can play an important role in the sustainable use of water and fertilizers in grape production, thanks to the site-specific application of these inputs, improving yield and quality of grapes while minimizing negative effects on the environment. However, PV often implies investments and additional management costs. The objective of this study is to compare different strategies for the management of water and fertilizers in vineyards, ranging from the conventional ones to the most technologically advanced, to assess their sustainability both from an economic and an environmental point of view. Six scenarios have been explored, considering different irrigation water supply systems, and irrigation and fertilizer management strategies. A multidisciplinary approach, including Life Cycle Assessment, economic assessment and multivariate analysis was used to assess the sustainability of the different vineyard management approaches. The results show the higher economic and environmental sustainability for the scenario considering irrigation water supplied from an irrigation consortium, a variable rate drip irrigation system for irrigation and fertigation. Finally, also according to PCA results, at least for the scenarios explored in the study, the introduction of PV technologies led to the reduction of environmental impacts and to the increase in economic advantages, which showed to be inversely correlated.

Integrated Bayesian Approaches Shed Light on the Dissemination Routes of the Eurasian Grapevine Germplasm

The domestication and spreading of grapevine as well as the gene flow history had been described in many studies. We used a high-quality 7k SNP dataset of 1,038 Eurasian grape varieties with unique profiles to assess the population genetic diversity, structure, and relatedness, and to infer the most likely migration events. Comparisons of putative scenarios of gene flow throughout Europe from Caucasus helped to fit the more reliable migration routes around the Mediterranean Basin. Approximate Bayesian computation (ABC) approach made possible to provide a response to several questions so far remaining unsolved. Firstly, the assessment of genetic diversity and population structure within a well-covered dataset of ancient Italian varieties suggested the different histories between the Northern and Southern Italian grapevines. Moreover, Italian genotypes were shown to be distinguishable from all the other Eurasian populations for the first time. The entire Eurasian panel confirmed the east-to-west gene flow, highlighting the Greek role as a "bridge" between the Western and Eastern Eurasia. Portuguese germplasm showed a greater proximity to French varieties than the Spanish ones, thus being the main route for gene flow from Iberian Peninsula to Central Europe. Our findings reconciled genetic and archaeological data for one of the most cultivated and fascinating crops in the world.

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.

Correction to: SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination

An amendment to this paper has been published and can be accessed via the original article.

SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination

BACKGROUND

Magna Graecia is the ancient name for the modern geopolitical region of South Italy extensively populated by Greek colonizers, shown by archeological and historical evidence to be the oldest wine growing region of Italy, crucial for the spread of specialized viticulture around Mediterranean shores. Here, the genetic diversity of Magna Graecia grape germplasm was assessed and its role in grapevine propagation around the Mediterranean basin was underlined.

RESULTS

A large collection of grapevines from Magna Graecia was compared with germplasm from Georgia to the Iberian Peninsula using the 18 K SNP array. A high level of genetic diversity of the analyzed germplasm was determined; clustering, structure analysis and DAPC (Discriminant Analysis of Principal Components) highlighted the genetic relationships among genotypes from South Italy and the Eastern Mediterranean (Greece). Gene flow from east (Georgia) to west (Iberian Peninsula) was identified throughout the large number of detected admixed samples. Pedigree analysis showed a complex and well-structured network of first degree relationships, where the cultivars from Magna Graecia were mainly involved.

CONCLUSIONS

This study provided evidence that Magna Graecia germplasm was shaped by historical events that occurred in the area due to the robust link between South Italian and Greek genotypes, as well as, by the availability of different thermal resources for cultivars growing in such different winegrowing areas. The uniqueness of this ampelographic platform was mainly an outcome of complex natural or human-driven crosses involving elite cultivars.

Multi-parameter characterization of water stress tolerance in Vitis hybrids for new rootstock selection

Drought in grapevine could be faced using tolerant rootstocks. The present work aims at the evaluation of 25 new genotypes potentially tolerant to drought by using recent methods of phenotypical screening (thermography and on-solid reaction spectroscopy). Plants were grown in well-watered and stressed field conditions. Proxi for transpiration, wood hydrophobicity and starch content were used to characterize and classify the genotypes. The predominant role of the environment was highlighted, nevertheless genotype and genotype × environment interaction showed significant variations as well. Hybrids were classified based on their steady, susceptible or adaptable behavior. The 14 most promising genotypes were identified, 5 of them showing two tolerance mechanisms. In the future, results from this experiment will support viticulture in water limited areas releasing new drought-tolerant interspecific hybrids to be tested after grafting with different scions.

Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (G×E) on the berry transcriptome

Changes in the performance of genotypes in different environments are defined as genotype × environment (G×E) interactions. In grapevine (Vitis vinifera), complex interactions between different genotypes and climate, soil and farming practices yield unique berry qualities. However, the molecular basis of this phenomenon remains unclear. To dissect the basis of grapevine G×E interactions we characterized berry transcriptome plasticity, the genome methylation landscape and within-genotype allelic diversity in two genotypes cultivated in three different environments over two vintages. We identified, through a novel data-mining pipeline, genes with expression profiles that were: unaffected by genotype or environment, genotype-dependent but unaffected by the environment, environmentally-dependent regardless of genotype, and G×E-related. The G×E-related genes showed different degrees of within-cultivar allelic diversity in the two genotypes and were enriched for stress responses, signal transduction and secondary metabolism categories. Our study unraveled the mutual relationships between genotypic and environmental variables during G×E interaction in a woody perennial species, providing a reference model to explore how cultivated fruit crops respond to diverse environments. Also, the pivotal role of vineyard location in determining the performance of different varieties, by enhancing berry quality traits, was unraveled.

Potential effectiveness of visible and near infrared spectroscopy coupled with wavelength selection for real time grapevine leaf water status measurement

BACKGROUND

Increasing attention is being paid to non-destructive methods for water status real time monitoring as a potential solution to replace the tedious conventional techniques which are time consuming and not easy to perform directly in the field. The objective of this study was to test the potential effectiveness of two portable optical devices (visible/near infrared (vis/NIR) and near infrared (NIR) spectrophotometers) for the rapid and non-destructive evaluation of the water status of grapevine leaves. Moreover, a variable selection methodology was proposed to determine a set of candidate variables for the prediction of water potential (Ψ, MPa) related to leaf water status in view of a simplified optical device.

RESULTS

The statistics of the partial least square (PLS) models showed in validation R² between 0.67 and 0.77 for models arising from vis/NIR spectra, and R² ranged from 0.77 to 0.85 for the NIR region. The overall performance of the multiple linear regression (MLR) models from selected wavelengths was slightly worse than that of the PLS models. Regarding the NIR range, acceptable MLR models were obtained only using 14 effective variables (R² range 0.63-0.69).

CONCLUSION

To address the market demand for portable optical devices and heading towards the trend of miniaturization and low cost of the devices, individual wavelengths could be useful for the design of a simplified and low-cost handheld system providing useful information for better irrigation scheduling. © 2017 Society of Chemical Industry.

Characterization of iron deficiency symptoms in grapevine (Vitis spp.) leaves by reflectance spectroscopy

The work aims at the description of the iron deficiency symptoms in grapevine leaves by reflectance spectroscopy at the plant and leaf levels. 5 genotypes of Vitis spp. were selected and grown in hydroponic conditions with and without iron supply. 450 spectra were collected among basal, young and apical leaves, as well as veins and interveinal areas. Iron deficiency produced significant and characteristic modifications in the pigment accumulation, proportion and distribution in plants. Basal leaves resulted to have higher concentrations of photosynthetic pigments in stressed plants with respect to the control, probably due to compensation effects. Iron deficient plants had lower chlorophyll concentrations in young and apical leaves. In the apical zone, also the relative composition of pigments appeared to be modified, explaining the reddish-yellowish apex appearance of iron deficient vines. Finally, the pigment distribution along the shoot characterized the symptoms, as well as the spectral variations among veins and interveinal areas. These results could support future applications in vineyard management (e.g.: symptom identification and detection; precision fertilization) as well as breeding programs for new rootstock selections (e.g.: fast screenings of seedlings).

Stem Xylem Characterization for Vitis Drought Tolerance

Together with stomatal conductance and root conductivity, the stem water reserve and transport systems could be regulatory mechanisms able to participate in the regulation of the plant water status. Lianas, such as Vitis spp., minimize the trunk support role, and stems have evolved to improve their ability in water transport. In this work, stems of 10 different Vitis species were studied in relation to their expected drought tolerance using reflectance spectroscopy. Spectra were measured before (T0) and after coloration with Sudan IV dye. The T0 spectral signature showed characteristic species features. The partial least squares (PLS) regression and the self-organizing map (SOM) neural network analysis were able to predict the expected drought tolerance score; thus, reflectance spectroscopy was demonstrated to be a useful technique for drought tolerance phenotyping. These methods could be applied for the preliminary selection of new rootstocks/cultivars. Wood composition variation appeared to be correlated with the water stress susceptibility. To clarify this relationship, the attention was focused on the wood hydrophobicity. Sudan IV is a microscopy dye traditionally used to underline suberin, waxes, and, in general, hydrophobic substances. Differences between rough and colored spectra evidenced the absorption band of Sudan IV with a maximum at 539 nm. The coloration intensity was used to develop a hydrophobicity index. The obtained values were correlated with the expected drought tolerance score. Therefore, hydrophobic compounds seem to play an important role in water use efficiency, and an hydrophobic barrier in the xylem tissue appears to be a protective mechanism against water stress.

The Influence of Genotype and Environment on Small RNA Profiles in Grapevine Berry

Understanding the molecular mechanisms involved in the interaction between the genetic composition and the environment is crucial for modern viticulture. We approached this issue by focusing on the small RNA transcriptome in grapevine berries of the two varieties Cabernet Sauvignon and Sangiovese, growing in adjacent vineyards in three different environments. Four different developmental stages were studied and a total of 48 libraries of small RNAs were produced and sequenced. Using a proximity-based pipeline, we determined the general landscape of small RNAs accumulation in grapevine berries. We also investigated the presence of known and novel miRNAs and analyzed their accumulation profile. The results showed that the distribution of small RNA-producing loci is variable between the two cultivars, and that the level of variation depends on the vineyard. Differently, the profile of miRNA accumulation mainly depends on the developmental stage. The vineyard in Riccione maximizes the differences between the varieties, promoting the production of more than 1000 specific small RNA loci and modulating their expression depending on the cultivar and the maturation stage. In total, 89 known vvi-miRNAs and 33 novel vvi-miRNA candidates were identified in our samples, many of them showing the accumulation profile modulated by at least one of the factors studied. The in silico prediction of miRNA targets suggests their involvement in berry development and in secondary metabolites accumulation such as anthocyanins and polyphenols.