Terroir 2010 banner
IVES 9 IVES Conference Series 9 Différenciation de parcelles de Chenin du Val de Loire, a l’aide de l’etude des flores fongiques des raisins, en utilisant l’outil DGGE

Différenciation de parcelles de Chenin du Val de Loire, a l’aide de l’etude des flores fongiques des raisins, en utilisant l’outil DGGE

Abstract

Depuis le millésime 2002, une étude est menée sur la diversité de la flore fongique de parcelles du cépage chenin, situées essentiellement sur les appellations de Vouvray et Montlouis ; deux appellations séparées par le fleuve nommé la Loire. Les parcelles se situent dans des conditions pédoclimatiques différentes, qui se retrouvent au travers des suivis de maturité et l’état sanitaire.

L’objectif est d’utiliser la flore fongique comme facteur de différenciation entre les parcelles, et d’évolution au cours de la maturité. C’est dans ce cadre qu’un outil d’écologie microbienne a été utilisé : Denaturating Gradient Gel Electrophoresis (DGGE). Après une étude spécifique sur les moisissures des raisins, qui ont permis d’établir le référentiel, les échantillons complexes constitués de l’eau de lavage des baies de raisins, ont été analysés. Ainsi, nous avons pu analyser et différencier plusieurs parcelles de cépage chenin, situées dans des conditions pédoclimatiques différentes.

English version: Since the vintage wine 2002, a study is led on the variety of the fungal flora of parcels of the Chenin vine, situated essentially on the controlled origin label of Vouvray and Montlouis; two controlled origin label separated by the river named the Loire. The parcels are situated in conditions different of soils and of climate, which meet through the follow-ups of maturity and the sanitary state.

The objective is to use the fungal flora as factor of differentiation between the parcels, and evolution during the maturity. It is in this frame that a tool of microbial ecology was used: Denaturing Gradient Gel Electrophoresis (DGGE). PCR-DGGE is a molecular method which allows the direct analysis of DNA in complex samples without any culture step. This method is based on the separation in a denaturing gradient of double-strand DNA fragments which have the same length but different nucleotide sequences. After a specific study on fungus of grapes, which allowed establishing the reference table, the complex samples constituted by some water of wash of the berries of grapes, were analyzed. This tool will allow us to draw a parallel between the dynamic of fungal populations present in different conditions of soil and of climate. PCR-DGGE showed its potentialities for a fast characterization of fungi in complex mixes.

DOI:

Publication date: October 8, 2020

Issue: Terroir 2010

Type: Article

Authors

L. Guérin (1), M.Bouix (2), P. Poupault (1), R. Laforgue (1), P. Mallier (3), A. Mallet (3), J. Dupont (4)

(1) IFV Tours, 46 avenue Gustave Eiffel, 37100 Tours, France
(2) AgroParistech, Département de microbiologie industrielle, 1 avenue des Olympiades, 91744 Massy Cedex, France
(3) Chambre d’Agriculture d’Indre et Loire, 38 rue Augustin Fresnel, 37170 Chambray les Tours, France
(4) Muséum National d’Histoire Naturelle, Département Systématique et Evolution – Mycologie, 75005 Paris Cedex 05, France

Contact the author

Tags

IVES Conference Series | Terroir 2010

Citation

Related articles…

Exploring resilience and competitiveness of wine estates in Languedoc-Roussillon in the recent past: a multi-level perspective

The Languedoc-Roussillon wineries are facing a decline in wine yields particularly PGI yields due to many factors. Climate change is just ones, but is expected to increase in the future. There is also structurally a large heterogeneity of yield profiles among terroirs, varieties and strategies. This work investigates the link between yield, competitiveness and resilience to explore how resilient winegrowers have been in the recent past. To this end two approaches have been combined; (i) an accountancy database analysis at estate scale and (ii) municipality level competitiveness analysis. A new resilience indicator that characterizes the capacity of an estate to absorb yield variation is also defined. The FADN database between 2000 and 2018 of ex-Languedoc-Roussillon (France) and other data are used to analyse the current situation and the past evolution of competitiveness and resilience by type of estate (type of farm: PGI and/or PDO & type of commercialization: bulk and/or bottles). The net margin, which defines competitiveness, is not correlated to yield for all types but depends on the type of commercialization and the level of specialisation. The resilience indicator shows that the net margin of estates specialized in PGI is particularly sensitive to yield declines. We also show that price evolutions seem to compensate the effect of yield losses for the majority of types. Municipality scale analysis shows the links between local pedoclimate, yield, commercialization strategies and price. Overlapping a PDO with a PGI does not always increase a municipality’s PGI competitiveness. It is difficult to make links between causes and effects due to the complexity of the wine production system. Production diversification may be a solution. Resorting to the two level of analysis helps resolving the data gap that is necessary to explore the links between yield and economic performance of the wine estates in the long term.

Comparison of imputation methods in long and varied phenological series. Application to the Conegliano dataset, including observations from 1964 over 400 grape varieties

A large varietal collection including over 1700 varieties was maintained in Conegliano, ITA, since the 1950s. Phenological data on a subset of 400 grape varieties including wine grapes, table grapes, and raisins were acquired at bud break, flowering, veraison, and ripening since 1964. Despite the efforts in maintaining and acquiring data over such an extensive collection, the data set has varying degrees of missing cases depending on the variety and the year. This is ubiquitous in phenology datasets with significant size and length. In this work, we evaluated four state-of-the-art methods to estimate missing values in this phenological series: k-Nearest Neighbour (kNN), Multivariate Imputation by Chained Equations (mice), MissForest, and Bidirectional Recurrent Imputation for Time Series (BRITS). For each phenological stage, we evaluated the performance of the methods in two ways. 1) On the full dataset, we randomly hold-out 10% of the true values for use as a test set and repeated the process 1000 times (Monte Carlo cross-validation). 2) On a reduced and almost complete subset of varieties, we varied the percentage of missing values from 10% to 70% by random deletion. In all cases, we evaluated the performance on the original values using normalized root mean squared error. For the full dataset we also obtained performance statistics by variety and by year. MissForest provided average errors of 17% (3 days) at budbreak, 14% (4 days) at flowering, 14.5% (7 days) at veraison, and 17% (3 days) at maturity. We completed the imputations of the Conegliano dataset, one of the world’s most extensive and varied phenological time series and a steppingstone for future climate change studies in grapes. The dataset is now ready for further analysis, and a rigorous evaluation of imputation errors is included.

Effect of multi-level and multi-scale spectral data source on vineyard state assessment

Currently, the main goal of agriculture is to promote the resilience of agricultural systems in a sustainable way through the improvement of use efficiency of farm resources, increasing crop yield and quality under climate change conditions. This last is expected to drastically modify plant growth, with possible negative effects, especially in arid and semi-arid regions of Europe on the viticultural sector. In this context, the monitoring of spatial behavior of grapevine during the growing season represents an opportunity to improve the plant management, winegrowers’ incomes, and to preserve the environmental health, but it has additional costs for the farmer. Nowadays, UAS equipped with a VIS-NIR multispectral camera (blue, green, red, red-edge, and NIR) represents a good and relatively cheap solution to assess plant status spatial information (by means of a limited set of spectral vegetation indices), representing important support in precision agriculture management during the growing season. While differences between UAS-based multispectral imagery and point-based spectroscopy are well discussed in the literature, their impact on plant status estimation by vegetation indices is not completely investigated in depth. The aim of this study was to assess the performance level of UAS-based multispectral (5 bands across 450-800nm spectral region with a spatial resolution of 5cm) imagery, reconstructed high-resolution satellite (Sentinel-2A) multispectral imagery (13 bands across 400-2500 nm with spatial resolution of <2 m) through Convolutional Neural Network (CNN) approach, and point-based field spectroscopy (collecting 600 wavelengths across 400-1000 nm spectral region with a surface footprint of 1-2 cm) in a plant status estimation application, and then, using Bayesian regularization artificial neural network for leaf chlorophyll content (LCC) and plant water status (LWP) prediction. The test site is a Greco vineyard of southern Italy, where detailed and precise records on soil and atmosphere systems, in-vivo plant monitoring of eco-physiological parameters have been conducted.

Measurement of redox potential as a new analytical winegrowing tool

Excell laboratory has initiated the development of an analytical method based on electrochemistry to evaluate the ability of wines to undergo or resist to oxidative phenomena. Electrochemistry is a powerful tool to probe reactions involving electron transfers and offers possibility of real-time measurements. In that context, the laboratory has implemented electrochemical analysis to assess oxidation state of different wine matrices but also in order to evaluate oxidative or reduced character of leaf and soil. Initially, our laboratory focused on dosage of compounds involved in responses of plant stresses and we were also interested in microbiological activity of soils. These analyses were compared with the measurement of redox potential (Eh) and pH which are two fundamental variables involved in the modulation of plant metabolism. Indeed, the variation of redox states of the plant reflects its biological activity but also its capacity to absorb nutriments. The Eh-pH conditions mainly determine metabolic processes involved in soil and leaf and our goal is to determine if this combined analytical approach will be sufficiently precise to detect biological evolutions (plant health, parasitic attack…).

Assessment of the impact of actions in the vineyard and its surrounding environment on biodiversity in Rioja Alavesa (Spain)

Traditional viticulture areas have experienced in the last decades an intensification of field practices, linked to an increased use of fertilisers and phytosanitary products, and to a more intensive mechanization and uniformization of the landscape. This change in management has sometimes led to higher rates of soil erosion andloss of soil structure, fertility decline, groundwater contamination, and to an increased pressure of pests and diseases. Additionally, intensification usually leads to a simplification of landscapes, of particular concern in prestigious wine grape regions where the economical revenue encourages the conversion of land use from natural habitats to high value wine grape production. To revert this trend, it is necessary that growers implement actions that promote biodiversity in their vineyards. The aim of this study is to assess the impact of the implementation of cover crops, vegetational corridors, dry stone walls and vineyard biodiversity hotspots estimated through the study of arthropods. The work has been carried out in four vineyards in Rioja Alavesa belonging to Ostatu winery, where these infrastructures were implemented in 2020. The presence and diversity of arthropods was studied by capturing them at different times in the season and at different distances from the infrastructure using pit-fall traps in the soil and yellow, white and blue chromatic traps at the canopy level. This is a preliminary study in which all adult insects were sorted to the taxonomic level of order and Coleoptera were classified to morphospecies. The results obtained show that there is a relationship between the basic characteristics of the vineyard and the arthropods captured, with a positive effect, although also dependent on the vineyard, of the presence of infrastructure.