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…

New tool to evaluate color modifications during oxygen consumption in white and red wines

Measuring the effect of oxygen consumption on the color of wines as the level of dissolved oxygen decreases over time is very useful to know how much oxygen a wine can consume without significantly altering its color. The changes produced in wine after being exposed to high oxygen concentrations have been studied by different authors, but in all cases the wine has been analyzed once the oxygen consumption process has been completed. This work presents the results obtained with the use of an equipment designed and made to measure simultaneously the level of dissolved oxygen and the spectrum of the wine, during the oxygen consumption process from saturation levels with air to very low levels, which indicate the total consumption of the dosed oxygen[1,2].

Volatile composition of Cabernet Sauvignon wines from Argentina, Portugal and Spain

Cabernet Sauvignon is one of the most cultivated grape varieties worldwide being grown in different environmental conditions due to its excellent adaptability. Volatile compounds deeply contribute to the sensory properties of wines therefore to wine quality. The aim of this work was to compare the aroma profile of Cabernet Sauvignon wines from different geographical areas and climatic conditions, namely from Argentina, Portugal and Spain, from the vintage 2022. In addition, the volatile composition of the Cabernet Sauvignon Portuguese wines from three vintages was evaluated.

The use of plasma activated water in barrel disinfection: impact on oak wood composition

The use of barrels is a practice that improves the quality of wines. The porous structure of wood favors the accumulation of microorganisms that can deteriorate the quality of wines so that barrel cleaning and sanitizing treatments are essential. The burning of sulphur discs has been the most common practice in winemaking because ots biocide effect. Nevertheless, its effectiveness is still insufficient and it is harmful for human health.

Time vs drought: leaf age rather than drought drives osmotic adjustment in V. vinifera cv. Pinot Noir

Global warming and increased frequency and/or severity of drought events are among the most threatening consequences of climate change for agricultural crops. In response to drought, grapevine (as many other plants) exhibits osmotic adjustment through active accumulation of osmolytes which in turn shift the leaf turgor loss point (TLP) to more negative values, allowing to maintain stomata opened at lower water potentials1. We investigated the capacity of Pinot noir leaves to modulate their osmotic potential as a function of: (i) time (seasonal osmoregulation), (ii) growing temperatures, and (iii) drought events, to enhance comprehension of the resilience of grapevines in drought conditions. We performed trails under semi-controlled field conditions, and in two different greenhouse chambers (20/15 °C vs 25/20 °C day/night). For two consecutive vegetative seasons, grafted potted grapevines (Pinot noir/SO4) were subjected to two different water regimes for at least 30 days: well-watered (WW) and water deficit (WD).

Advancing grapevine science through genomic research

The seminar will examine the complexities and prospects of genomic research on Vitis species, characterize by exceptionally high heterozygosity and common interspecific gene flow. The seminar will showcase case studies highlighting the critical role of diploid genome references in grape research, specifically in areas such as aroma development, disease resistance, and domestication traits. It will also address the emerging focus on pangenomes within the Vitis genus, particularly in the context of genetic studies on naturally interbreeding populations.