GiESCO 2019 banner
IVES 9 IVES Conference Series 9 GiESCO 9 GiESCO 2019 9 Towards the definition of a detailed transcriptomic map of grape berry development

Towards the definition of a detailed transcriptomic map of grape berry development

Abstract

Context and purpose of the study ‐ In the last years the application of genomic tools to the analysis of gene expression during grape berry development generated a huge amount of transcriptomic data from different varieties and growing conditions. This information set the stage to understand the molecular basis of crucial developmental and metabolic rearrangements occurring during grape berry formation and ripening. It is now clear that the variation of a portion of berry transcriptome is conserved across cultivars and growing conditions, and thus may be used universally to describe the stage of berry development. In this work we explore the possibility of using the transcriptomic data generated from two cultivars to define a very detailed developmental map of the grape berry.

Material and methods ‐ To map the molecular events associated with berry development at very high temporal resolution, we performed RNA‐seq analysis of berry samples collected every week from fruit‐ set to maturity from Pinot noir and Cabernet Sauvignon vines grown in the same location. The experiment was replicated across three consecutive years (2012, 2013, 2014) resulting in 219 samples overall. Applying multivariate analyses to the most variable portion of the transcriptome, we built a transcriptomic model of berry development based on the molecular information obtained from samples of both cultivars.

Results ‐ The Pinot noir and Cabernet Sauvignon samples mostly aligned in a 3D transcriptomic map (~80% of the variance described by Principal Component Analysis), allowing to define a general model of berry development based on gene expression. The performance of the model in describing the development of other grape varieties was accessed projecting RNA‐seq samples of fruit development of ten Italian cultivars onto the model. Both red and white‐skin berry samples mapped on the transcriptomic map and revealed alignment by standard ripening parameters (e.g. total soluble solids) as well as unrelated to any of these. Moreover, we validated that berry maturation of the same cultivar cultivated in different International growing regions can be well represented and aligned by means of our transcriptomic map. These results showed that the transcriptomic information can be accessed to precisely define a model of “molecular phenology” that can be used to map the ontogenetic development of the fruit with high precision and to align the stage of berry development of different grapes. 

DOI:

Publication date: June 19, 2020

Issue: GiESCO 2019

Type: Article

Authors

Marianna FASOLI (1), Chandra L. RICHTER (1), Sara ZENONI (2), Marco SANDRI (2), Paola ZUCCOLOTTO (3), Mario PEZZOTTI (2), Nick DOKOOZLIAN (1), and Giovanni Battista TORNIELLI(2)

(1) E&J Gallo Winery, Modesto, CA 95353, USA
(2) Department of Biotechnology, University of Verona, 37134 Verona, Italy
(3) Big & Open Data Innovation Laboratory, University of Brescia, 25123 Brescia, Italy

Contact the author

Keywords

Grapevine, Berry development, Ripening, Molecular Phenology, Transcriptomics

Tags

GiESCO 2019 | IVES Conference Series

Citation

Related articles…

Impact of climate change on the viticultural climate of the Protected Designation of Origin “Jumilla” (SE Spain)

Protected Designation of Origin “Jumilla” (PDO Jumilla) is located in the Spanish provinces of Albacete and Murcia, in the South-eastern part of the Iberian Peninsula, where most of the models predict a severe impact of climate change in next decades. PDO Jumilla covers an area of 247,054 hectares, of which more than 22,000 hectares

Effect of vigour and number of clusters on eonological parameters and metabolic profile of Cabernet Sauvignon red wines

Vegetative growth and yield are reported to affect grape and wine quality. They can be controlled through different techniques linked to vine management. The objective of this research was to determine the effect of vine vigour and number of clusters per vine on physicochemical composition and phenolic profile of red wines. The experiment was carried out during two vegetative cycles, with cv. Cabernet Sauvignon grafted onto Paulsen 1103. Three vine vigour were defined, according to shoot weight at previous harvests, being low, medium and high. Five treatments of number of clusters were used for each vigour, with 15, 22, 29, 36, and 45 clusters per vine. Grapes from all treatments were harvested in the same day from Brix and total acidity criteria. Thirty days after bottling, classical analyzes and phenolic compounds were performed. As results, different responses were obtained from each vintage. In 2020, a dry season from veraison to harvest, grapes and wines obtained from low vigour treatment and 45 clusters per vine was the highest in sugar and alcohol content respectively, while grapes and wines from high vigour and 15 clusters presented the lowest sugar and alcohol content. Total anthocyanins were higher in treatment with low vigour and 15 clusters, while the lowest amounts were found in low vigour with 45 clusters, as well as medium and high vigour with 36 clusters per vine. Total tannins were higher in high vigour with 22 clusters and medium vigour with 29 clusters, while were lower in low vigour with 36 clusters. In 2021, a wet season at harvest, responses were different, and great variations were observed between treatments. As conclusions, yield and vine vigour had strong influence on grape and wine quality, promoting different enological potentials on which can be indicated/used for aging strategies of red and even rosé wines.

Soil quality in Beaujolais vineyard. Importance of pedology and cultural practices

A pedological study was carried out from 2009 to 2017 in Beaujolais vineyard, to improve physical and chemical knowledge of soils. It was completed in 2016 and 2017 by the current study, dealing with microbial aspects, in order to build a reference frame for improved advice in soil management. Microbial biomass was measured on representative plots of the six most common soil types identified in Beaujolais and, for each soil type, on plots with different levels of the main impacting parameters: total organic carbon, pH, cation exchange capacity, extractable copper. A total of 59 soil samples were collected. Confirming the results of various trials carried out in Beaujolais over the past 20 years, the results of the present study showed that the soils were still alive, but exhibited a large variability of biological parameters, which appeared dependant on both pedological and anthropic factors. Therefore, a good interpretation of biological parameters and advice for vine growers must rely on a pedologically-based referential with differentiated main driving factors. For example, the control of pH is of primary importance in granitic soils and in no way organic matter addition can improve soil quality if pH is too low. Conversely, in calcareous soils, biological parameters are more directly affected by direct or indirect (cover crops for example) inputs of organic matter. The use of biological parameters, such as microbial biomass, is of great potential value to improve advice on agro-viticultural practices (soil management, fertilization, liming, etc.), basis of a sustainable wine production on fragile soils.

Updating the Winkler index: An analysis of Cabernet sauvignon in Napa Valley’s varied and changing climate

This study aims to create an updated, agile viticultural climate index (similar to the Winkler Index) by performing in-depth analyses of current and historical data from industry partners in several major winegrowing regions. The Winkler Index was developed in the early twentieth century based on analysis of various grape-growing regions in California. The index uses heat accumulation (i.e. Growing Degree Days) throughout the growing season to determine which grape varieties are best suited to each region. As viticultural regions are increasingly subject to the complexity and uncertainty of a changing climate, a more rigorous, agile model is needed to aid grape growers in determining which cultivars to plant where. For the first phase of this study, 21 industry partners throughout Napa Valley shared historical phenology, harvest, viticultural practice, and weather data related to their Cabernet sauvignon vineyard blocks. To complement this data, berry samples were collected throughout the 2021 growing season from 50 vineyard blocks located throughout 16 American Viticultural Areas that were then analyzed for basic berry chemistry and phenolics. These blocks have been mapped using a Geographic Information System (GIS), enabling analysis of altitude, vineyard row orientation, slope, and remotely sensed climate data. Sampling sites were also chosen based on their proximity to a weather station. By analyzing historical data from industry partners and data specifically collected for this study, it is possible to identify key parameters for further analysis. Initial results indicate extreme variability at a high spatial resolution not currently accounted for in modern viticultural climate indices and suggest that viticultural practices play a major role. Using the structure of data collection and analyses developed for the first phase, this project will soon be expanded to other wine regions globally, while continuing data collection in Napa Valley.

Spatial variability of temperature is linked to grape composition variability in the Saint-Emilion winegrowing area

Elevated temperature during the grape maturation period is a major threat for grape quality and thus wine quality. Therefore, characterizing the grape composition response to temperature at a larger scale would represent a crucial step towards adaptation to climate change. In response to changes in temperature, various physiological mechanisms regulate grape composition. Primary and secondary metabolisms are both involved in this response, with well-known effects, for example on anthocyanins, and lesser known effects, for example on aromas or aroma precursors. At the field scale or at the regional scale, however, numerous environmental or plant-specific factors intervene to make the effects of temperature difficult to distinguish from overall variability. In this study, it was attempted to overcome this difficulty by selecting well-characterized situations with differing temperatures.
A long-term study of air temperature variability across several Merlot vineyards in the Saint-Emilion and Pomerol wine producing area found significant temperature differences and gradients at various time scales linked to environmental factors. From this study area, a few sites were selected with similar age, soil and training system conditions, and with repeated and contrasted temperature differences during the maturation period. The average temperature difference during the maturation period was about 2°C between cooler and warmer sites, a difference similar to that expected under future climate change scenarios. In close vicinity to the temperature sensors at each site, grape berries were sampled at different times until full maturity during 2019 and 2020. Also, berries from bunches on either side of the row were analyzed separately, allowing an investigation of bunch exposure effect associated with the coupling of berry temperature and solar radiation. Four replicates of pooled berries for each time – site – bunch exposure combination were obtained and analyzed for biochemical composition. Analyses of variance of the biochemical composition data collected at different sampling times reveal significant effects associated with temperature, site, and bunch azimuth. For instance, anthocyanins in grape skins are clearly influenced by temperature and solar radiation exposure, with up to 30% reduction in warmer conditions.