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…

Impact of toasting and botanical origin on oak wood (Q. sp.) volatilome using untargeted GCxGC-ToFMS analysis

Many works have been carried out to identify the key aroma volatile compounds of oak wood (e.g., whisky-lactone, furfural, maltol, eugenol, guaiacol, vanillin) using conventional gas chromatography coupled with olfactometry and mass spectrometry (GC-O-MS). Inspired by recent untargeted approaches in the field of food “omics”, this work aims to extend our knowledge on the impact of cooperage process on the volatile composition of oak wood using two-dimensional comprehensive gas chromatography coupled with time of flight mass spectrometry (GCxGC-ToFMS).

Read More

Preliminary results of water status and metabolite content of three new crossbreed winegrape genotypes

This study presents the preliminary results obtained in 2022, of the evaluation of three new crossbreed winegrape genotypes and their parental varieties, grown under controlled irrigation (60% ETc) and rainfed conditions in a wine-growing area with scarcity of water and high temperatures (Murcia, southeast Spain). The genotypes MC16 and MC80 were obtained from crosses between the varieties ‘Monastrell’ and ‘Cabernet Sauvignon’, and MS104 from crosses between ‘Monastrell’ and ‘Syrah’ [1]. The objective of this study was to analyse the physiological response and vegetative development of the 6 genotypes under the two irrigation conditions, and to study their effect on the content of soluble sugars and chlorophyll in the leaf.

Read More

Early defoliation positively enhances bioactive composition of berries with no effect on cuticle characteristics

Leaf removal in the fruit-zone has been employed to improve cluster light exposure and ventilation and therefore increase metabolite accumulation and reduce botrytis incidence in berries. When applied before flowering (early defoliation – ED), it can also decrease cluster compactness and regulate yield in high-yielding varieties. This study aimed to evaluate the impact of ED on the physiology and metabolism of Aragonez (syn. Tempranillo) berries along the ripening period. The experiment was set up in 2013 at a commercial vineyard located in the Lisbon winegrowing region.

Read More

Oxidability of wines made from Spanish minority grape varieties

The phenolic profile of a wine plays an essential role in its oxidative capacity and in both white and red wines it defines its shelf life[1]. The study of minority varieties to produce wines with peculiar characteristics necessarily includes the phenolic and oxidative characterization of the wines produced. This paper presents the study of wines made from 24 minority and majority white and red grape varieties, focusing on phenolic characteristics (total phenols, slightly polymerized phenols, highly polymerized phenols, anthocyanins…), color, as well as parameters related to the oxidability of the wines and their capacity to consume oxygen [2].

Read More

New crossbreed winegrape genotypes cultivated under rainfed conditions in a semi-arid Mediterranean region

Traditional drought tolerant varieties such as Cabernet Sauvignon, Monastrell, and Syrah [1], have been used as parents in the grapevine breeding program initiated by the Instituto Murciano de Investigación y Desarrollo Agrario y Medioambiental (IMIDA) in 1997 [2]. This work presents the results of evaluating three new genotypes obtained from crosses between ‘Monastrell’ and ‘Cabernet Sauvignon’ (MC16 and MC80) and between ‘Monastrell’ and ‘Syrah’ (MS104), comparing their performance under conditions of water scarcity and high temperatures with that of their respective parental varieties. For this purpose, the six genotypes were cultivated under controlled irrigation conditions (60% ETc) and rainfed conditions.

Read More