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…

The use of δ13C as an indicator of water use efficiency for the selection of drought tolerant grapevine varieties

In the context of climate change with increasing evaporative demand, understanding the water use behavior of different grapevine cultivars is of critical importance. Carbon isotope discrimination (δ13C) measurements in wine provide a precise and integrated assessment of the water status of the vines during the sugar accumulation period in grape berries. When collected over multiple vintages on different cultivars, δ13C measurements can also provide insights into the effects of genotype on water use efficiency.

First results on the chemical composition of red wines from the pressing of marc

In the Bordeaux vineyards, press wine represents approximately 15% of the total volume of wine produced[1]. Valuing this large volume of wine is necessary from an economic point of view, but also because of their organoleptic contribution to the blend, and their contribution to the construction of wines for laying down. Therefore, this study was developed considering the lack of recent scientific knowledge on the composition of red press wines. The aim of this study is to establish an initial assessment of their chemical composition including aromatic compounds and a phenolic part.

The combined use of Lachancea thermotolerans and lactic bacteria in wine technology

The production of most red wines that are sold involves an alcoholic fermentation carried out by yeasts of the Saccharomyces genus, and a subsequent fermentation carried out by lactic bacteria of the Oenococus oeni species after the first one is fully completed. However, the traditional process can face complications, which can be more likely in grape juices with high levels of sugar and pH. Because of climate change, these situations are more frequent in the wine industry. The main hazards in those scenarios are halts or delays in the alcoholic fermentation or the growth of unwanted bacteria while the alcoholic fermentation is not done yet and the wine still has residual sugars.

Application of an in vitro digestion model to study the bioaccessibility and the effect of the intestinal microbiota on the red wine proanthocyanidins 

Proanthocyanidins are important phenolic fraction for wine quality, contributing to astringency, bitterness and color. Their metabolism begins in the mouth and continues throughout the gastrointestinal tract; however, most of them are accumulated in the colon where are metabolized by the intestinal microbiota, giving rise to a whole series of phenolic acids that may have greater activity at physiological level than the precursors[1]. This study aimed to evaluate in vitro the bioaccessibility of proanthocyanidins in a red wine developed by Bodegas Pradorey, as well as to evaluate the potential effect of intestinal microbiota on polyphenols metabolism identifying and quantifying secondary metabolites.

Sugar accumulation disorder Berry Shrivel – from current knowledge towards novel hypothesis

In contrast to fruit and grape berry ripening, the biological processes causing ripening disorders are often much less understood, although shriveling disorders of fruits are manifold and contribute to yield losses and reduced fruit quality worldwide. Shrinking berries are a common feature for all shriveling disorders in grapevine although their timing of appearance during the berry ripening process and their underlying induction processes distinct them from each other. The sugar accumulation disorder Berry Shrivel (BS) is characterized by a suppression of sugar accumulation short after veraison resulting in berries low in sugar content and anthocyanins in berry skins, while the organic acid content is similar. Recent studies analyzed the biochemical, morphological and molecular processes affected in BS berries and linked early changes to the period of ripening onset [1,2].