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…

Second pruning as a strategy to delay maturation in cv. ‘Touriga nacional’ in the Portuguese Douro region

The advance in maturation of wine grapes is an important climate change risk related effect that could affect warm regions like Portuguese Douro Wine Region. Indeed, the climate analysis over the past years registered a decrease in the precipitation, significant higher average temperatures, and a more frequent occurrence of extreme weather events, including heat waves. In these conditions the length from anthesis until maturation is shortened and the uncoupling of technical and phenolic maturity results in berries with higher sugar concentration (and lower acidity), but lower anthocyanins, tannins, and total phenolic concentration, which produce unbalanced wines.
In this work, an innovative strategy of crop forcing, based on forcing vine regrowth after a second pruning of green shoots, was tested, aimed at delaying ripening until the temperature becomes lower and, therefore, preventing acidity loss and increasing anthocyanin-to-sugar ratio. The experiments were conducted in 2019 and 2020 in a commercial vineyard of ‘Touriga Nacional’ located in the Douro Region. Crop forcing was conducted 15 (CF1) to 30 (CF2) days after fruit set. Vines pruned with conventional methods were used as control (CF0). Results confirmed that fruit ripening was shifted from the hot season (August/September), until a cooler period (October through early-November). At harvest, grapevine berries from CF1 and CF2 presented lower pH and higher acidity, than control, with no significant differences in colour intensity and phenolic levels composition. Sugar content was lower in CF2-treated vines in both seasons. However, in CF-treated vines the number and size of clusters were significantly lower (up to 88% reduction) than in control plants. A metabolomics analysis of mature berries from CF-treated vines and control is underway. Crop forcing was indeed effective in producing a more balance berry composition but severely reduced grapevine yield,

The impact of sustainable management regimes on amino acid profiles in grape juice, grape skin flavonoids, and hydroxycinnamic acids

One of the biggest challenges of agriculture today is maintaining food safety and food quality while providing ecosystem services such as biodiversity conservation, pest and disease control, ensuring water quality and supply, and climate regulation. Organic farming was shown to promote biodiversity and carbon sequestration, and is therefore seen as one possibility of environmentally friendly production. Consumers expect organically grown crops to be free from chemical pesticides and mineral fertilizers and often presume that the quality of organically grown crops is different or higher compared to conventionally grown crops. Integrated, organic, and biodynamic viticulture were compared in a replicated field trial in Geisenheim, Germany (Vitis vinifera L. cv. Riesling). Amino acid profiles in juice, grape skin flavonoids, and hydroxycinnamic acids were monitored over three consecutive seasons beginning 7 years after conversion to organic and biodynamic viticulture, respectively. In addition, parameters such as soil nutrient status, yield, vigor, canopy temperature, and water stress were monitored to draw conclusions on reasons for the observed changes. Results revealed that the different sustainable management regimes highly differed in their amino acid profiles in juice and also in their skin flavonol content, whereas differences in the flavanol and hydroxycinnamic acid content were less pronounced. It is very likely that differences in nutrient status and yield determined amino acid profiles in juice, although all three systems showed similar amounts of mineralized nitrogen in the soil. Canopy structure and temperature in the bunch zone did not differ among treatments and therefore cannot account for the observed differences in favonols. A different light exposure of the bunches in the respective systems due to differences in vigor together with differences in berry size and a different water status of the vines might rather be responsible for the increase in flavonol content under organic and biodynamic viticulture.

Analysis of some environmental factors and cultural practices that affect the production and quality of the Manto Negro, Callet and Prensal Blanc varieties

45 non irrigated vineyards distributed in the DO (Denomination) Pla i Llevant de Mallorca and the DO Binissalem Mallorca were used to investigate the characteristics of production and quality and their relationships certain environmental factors and cultural practices. The grape varieties investigated are autochthonous to the island of Mallorca, Manto Negro and Callet as red and Prensal Blanc as white. All plants were measured for four consecutive years in the main production and quality parameters. Among the environmental factors, the type of soil has been studied, more specifically its water retention capacity, the planting density, the age of the vineyard and the level of viral infection. The presence or absence of virus seems to have no effect on any component studied in the varieties studied. For the white variety Prensal Blanc age is negatively correlated with production and the number of bunches, nevertheless it does not cause any effect on the required quality parameters. However, for the red varieties Callet and Manto Negro, the age of the plantation is the variable that best correlates with the quality parameters, therefore the old vines should be the object of preservation by the viticulturists and winemakers in order to guarantee its contribution to the quality of the wines made with these varieties.

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.

Effect of the commercial inoculum of arbuscular mycorrhiza in the establishment of a commercial vineyard of the cultivar “Manto negro

The favorable effect of symbiosis with arbuscular mycorrhizal fungi (AMF) has been known and studied since the 60s. Nowadays, many companies took the chance to start promoting and selling commercial inoculants of AMF, in order to be used as biofertilizers and encourage sustainable biological agriculture. However, the positive effect of these commercial biofertilizers on plant growth is not always demonstrated, especially under field conditions. In this study, we used a commercial inoculum on newly planted grapevines of a local cultivar grafted on a common rootstock R110. We followed the physiological status of vines, growth and productivity and functional biodiversity of soil bacteria during the first and second years of 20 inoculated with commercial inoculum bases on Rhizophagus irregularis and Funeliformis mosseaeAMF at field planting time and 20 non-inoculated control plants. All the parameters measured showed a neutral to negative effect on plant growth and production. The inoculated plants always presented lower values of photosynthesis, growth and grape production, although in some cases the differences did not reach statistical significance. On the contrary, the inoculation supposed an increase of the bacterial functional diversity, although the differences were not statistically significant either. Several studies show that the effect of inoculation with AMF is context-dependent. The non-favorable effects are probably due to inoculation ineffectiveness under complex field conditions and/or that, under certain conditions, AMF presence may be a parasitic association. This puts into question the effectiveness of its application in the field. Therefore, it is recommended to only resort to this type of biofertilizer when the cultivation conditions require it (e.g., very low previous microbial diversity, foreseeable stress due to drought, salinity, or lack of nutrients) and not as a general fertilization practice.