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…

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).

Combined use of leaf removal and natural shading to delay grape ripening in Manto negro (Vitis vinifera L.) under deficit irrigation 

The increasingly frequent heat waves during grape ripening pose challenges for premium wine grape production. This makes the development of irrigation and canopy management techniques of great importance to maximize yield and grape quality. A field experiment was carried out during 2021 and 2022 using Manto negro wine grapes to study the effect of two irrigation strategies and different light exposure levels on grape quality.

Metabolomic profiling of heat-stressed grape berries 

The projected rise in mean air temperatures together with the frequency, intensity, and length of heat waves in many wine-growing regions worldwide will deeply impact grape berry development and quality. Several studies have been conducted and a large set of molecular data was produced to better understand the impact of high temperatures on grape berry development and metabolism[1]. According to these data, it is highly likely that the metabolomic dynamics could be strongly modulated by heat stress (HS).

Possible methods of adaptation to the effects of climate change in the Tokaj Wine Region 

Viticulture’s adaptation to the harmful effects of climate change is globally the biggest challenge of the near future. Short, extremely intensive rainfalls and longer periods of drought are getting more frequent in the Tokaj Wine Region, where the majority of the vineyards are cultivated on steep slopes. Hence, erosion has high risk, especially when combined with the loess-based soils on about ten percent of the region. The environmentally beneficial cover crop and mulch usage can effectively reduce the risk of erosion, according to research done by the Tokaj Wine Region Research Institute of Viticulture and Oenology.

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.