terclim by ICS banner
IVES 9 IVES Conference Series 9 International Congress on Grapevine and Wine Sciences 9 2ICGWS-2023 9 Predicting provenance and grapevine cultivar implementing machine learning on vineyard soil microbiome data: implications in grapevine breeding

Predicting provenance and grapevine cultivar implementing machine learning on vineyard soil microbiome data: implications in grapevine breeding

Abstract

The plant rhizosphere microbial communities are an essential component of plant microbiota, which is crucial for sustaining the production of healthy crops. The main drivers of the composition of such communities are the growing environment and the planted genotype. Recent viticulture studies focus on understanding the effects of these factors on soil microbial composition since microbial biodiversity is an important determinant of plant phenotype, and of wine’s organoleptic properties. Microbial biodiversity of different wine regions, for instance, is an important determinant of wine terroir. While conventional methods for microbiome analysis are extensively used, application of modern Artificial Intelligence (AI) based methods could unravel non-linear associations between microbial taxa and environmental/plant genetic factors. Here we compare the performance of shallow and Deep Machine Learning methods to predict the geographical provenance and the planted grape cultivar solely based on the soil microbiota. We used 885 previously published microbial amplicon-sequencing datasets (16S) collected from vineyards located in 13 countries across 4 continents and planted with 34 Vitis vinifera cultivars representing the largest collection of vineyard microbiomes analyzed to date. This research also aimed at addressing some common challenges associated with most ML-based studies such as easy availability of models to non-technical researchers which is necessary for research reproducibility. To facilitate this, the models built in this study will be available through a GUI-based containerized web platform. Also, to provide compatibility of processed data from other 16S studies, a computational step will be included that merge the features either by taxonomy or sequence identity. This study will be beneficial in several ways such as inferring lost/mislabeled samples, identifying important location-specific and cultivar-specific taxa. Ultimately, this approach could be implemented for the identification of the genes regulating host/microbe interactions, which will provide valuable targets for breeding programs aimed at producing more sustainable crops.  

Acknowledgements: This study was supported by the National Institute of Food and Agriculture, AFRI Competitive Grant Program Accession number 1018617, and the National Institute of Food and Agriculture, United States Department of Agriculture, Hatch Program accession number 1020852.

DOI:

Publication date: October 5, 2023

Issue: ICGWS 2023

Type: Article

Authors

Carlos M. Rodríguez López1*, Lakshay Anand1

1Environmental Epigenomics and Genomics Group, Department of Horticulture, College of Agriculture, Food and environment, University of Kentucky, Lexington, Kentucky, USA

Contact the author*

Keywords

rhizosphere microbiome, provenance, plant-microbiome interactions, breeding, machine learning

Tags

2ICGWS | ICGWS | ICGWS 2023 | IVES Conference Series

Citation

Related articles…

Wine without added SO2: Oxygen impact and color evolution during red wine aging

SO2 play a major role in wine stability and evolution during its aging and storage. Winemaking without SO2 is a big challenge for the winemakers since the lack of SO2 affects directly the wine chemical evolution such as the aromas compounds as well as the phenolic compounds. During the red wine aging, phenolic compounds such as anthocyanin, responsible of the red wine colour, and tannins, responsible of the mouthfeel organoleptic properties of wine, evolved quickly from the winemaking process to aging [1]. A lot of new interaction and molecules occurred lead by oxygen[2] thus the lack of SO2 will induce wine properties changes. Nowadays, the phenolic composition of the wine without added SO2 have not been clearly reported.

Read More

Sensory profile of wines obtained from disease-resistant varieties in La Rioja

The European wine industry is facing multiple challenges derived from climate change and the pressure of different fungal diseases that are compromising the production of traditional varieties. A sustainable alternative maybe the adoption of resistant varieties.
In this study, we have evaluated the enological potential of 9 resistant varieties (5 white and 4 red varieties) in La Rioja. Microvinifications were carried out with three biological replications. Oenological parameters were very diverse with acid content varying from 2.6 g/L to 6.6 g/L.

Read More

Phenolic composition and chromatic characteristics of blends of cv. Tempranillo wines from vines grown with different viticultural techniques in a semi-arid area

The quality and color stability of red wines are directly related to content and distribution of phenolic compounds. However, the climate change produces the asynchrony between the dates of technological and maturity of grapes. The crop-forcing technique (CF) restores the coupling between phenolic and technological ripeness while limits vineyard yields. Blending of wines is frequently used to equilibriate composition of wines and to increase their stability, color and quality. The aim of the present work is to study the phenolic composition and color of wine blends made with FW (wines from vines subjected to CF) and CW (wines for vines under the usual cultivation practices).

Read More

Symbiotic microorganisms application in vineyards: impacts on grapevine performance and microbiome

Microorganism-based inoculants have been suggested as a viable solution to mitigate the adverse effects of climate change on viticulture. However, the actual effectiveness of these inoculants when applied under field conditions remains a challenge, and their effects on the existing soil microbiota are still uncertain. This study investigates the impact of arbuscular mycorrhizal fungi inoculation on grapevine performance and microbiome. The study was conducted in a vineyard of Callet cultivar in Binissalem, Mallorca, Spain. Two different treatments were applied: control and inoculation with commercial mycorrhizae complex of Rhizoglomus irregulare applied to plants through irrigation.

Read More

Indicators of Sustainable Vineyard Soil Management: Metrics for Assessing Environmental Impacts

The vital role of soils in supporting life on our planet cannot be overstated. Soils provide numerous ecosystem services and functions, including biomass production, carbon sequestration, physical support, biological habitat, and genetic reserve, among others. Understanding the characteristics and sensitivity of soils in a specific terroir, along with effective soil management practices, is crucial for the sustainable management of natural resources.

Read More