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…

Drought tolerance assessment and differentiation of grapevine cultivars using physiological metrics: insights from field studies

This study aimed to validate a protocol and compare metrics for evaluating drought tolerance in two Vitis vinifera grapevine cultivars under field conditions. Various metrics were calculated to represent the physiological responses of plants to progressive water deficit. Data were collected from Sauvignon Blanc and Chardonnay plants subjected to three irrigation levels during the 2022-2023 season, along with data from three previous seasons. Hydro-escape areas were used to assess the plant’s ability to reduce water potential with decreasing soil water availability.

Vineyard management practices to reduce sugar content on ‘Monastrell’ grapes

Climate change is resulting in more dry and hot summers, accelerating grape ripening and increasing berry sugars concentration. This results in wines with a higher alcohol content, which has a negative impact on wine quality, as well as, on consumer health. Agronomic practices that minimize these effects on berry composition and, consequently, on wine quality must be defined. In this work, different management practices have been assessed on rainfed ‘Monastrell’ grapevines in Jumilla (Murcia, Spain) from 2021 to 2023 vintages. Mulching, shading, application of kaolin and different types of pruning were evaluated, among others field adaptation practices.

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).

Evaluation of interception traps for capture of Xylotrechus arvicola (Coleoptera: Cerambycidae) in vineyards varieties from Protected Denomination of Origin León

Xylotrechus arvicola (Coleoptera: Cerambycidae) is a pest in vineyards (Vitis vinifera) in the main Spain wine-producing regions with Protected Denomination of Origin (PDO). The action of the larvae, associated to the spreading of wood fungi, causes damage especially in important varieties of V. vinifera. X. arvicola females lay eggs concentrated in cracks or under the rhytidome in the wood vines, which allows the emerging larvae to get into the wood and make galleries inside the plant being then necessary to prune intensively or to pull up the bored plants (1). The objective of the study was to evaluate captures of X. arvicola insects in five varieties of V. vinifera in PDO León.

Exploring the prevalence of esca-induced leaf symptoms in French vineyards and the role of climate: a national scale analysis

Esca, a severe trunk disease affecting vineyards, is caused by fungal pathogens that induce wood necrosis and decay, leaf symptoms, yield losses, and potentially a rapid death of the vine. The prevalence of this disease varies across years, regions, cultivars, and plot ages. Despite its significance in understanding and predicting dieback risk in different vineyards, the role of climate in trunk diseases remains a relatively unexplored research area. While some studies have demonstrated the impact of certain climatic conditions on the prevalence of the disease, they often focus on a limited number of plots and yield conflicting results.We conducted a statistical analysis, using a Bayesian approach on a national database comprising prevalence data of esca from over 500 different plots in France, spanning the years 2003 to 2022 and encompassing various cultivars.