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…

Do wine sulphites affect gut microbiota? An in vitro study of their digestion in the gastrointestinal tract

“Sulphites” and mainly sulphur dioxide (SO2) is by far the most widely used additive (E-220/INS 220) in winemaking and likely the most difficult to replace. The well-known antioxidant, antioxidasic and antimicrobial properties of SO2 make this molecule a practically essential tool, not only in winemaking, but also in the production of other food products. The current trend in winemaking is the reduction of this unfriendly additive due to its negative effects on health and environmental. In particular, it could cause headaches and intolerance/allergic reactions in sensitive individuals. Wine is considered one of the major contributors of exposure of SO2 in the adult population, when this beverage is included in the diet.

Viticultural heritage in mountain territories of Catalonia: prospecting in the region of Osona, northern Spain

The recovery of ancestral or minority vine varieties has been gaining great interest in recent years, among other reasons because it is likely that some of these varieties, due to the fact that they are found in relict areas, have a greater potential for adaptation to external factors (biotic or abiotic) and can minimize the effects that climate change is causing in viticulture. Varieties that can be grown at altitude are currently being sought to combat rising temperatures and prolonged extreme drought conditions. In Catalonia, the Pyrenean expansion of vineyard cultivation is documented from the 10th century and has been related to the “small climatic optimum” (9th-12th centuries) and also to seigniorial power.[1] But different adverse climatic periods and the arrival of Phylloxera by the late 19th century made many of these crops disappear.[2]

Effects of heat and water stress on grapevine health: primary and secondary metabolism

Grapevine resilience to climate change has become one of the most pressing topics in the Viticulture & Enology field. Vineyard health demands understanding the mechanisms that explain the direct and indirect interactions between environmental stressors. The current climate change scenario, where drought and heat-wave are more frequent and intense, strongly demands improving our knowledge of environmental stresses. During a heatwave, the ambient temperature rises above the plant’s average tolerance threshold and, generally, above 35 oC plant’s adaptation to heat stress is activated.

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.

Adsorption of tetraconazole by organic residues and vineyard organically-amended soils 

Spain is the country with the largest wine-producing area in the EU and its productivity is largely controlled applying fungicides. However, residues of these compounds can move and contaminate surface and groundwater. The objective of this work was to evaluate the capacity of bioadsorbents from different origin to adsorb and immobilize tetraconazole by themselves or when applied as organic soil amendment, and to prevent soil and water contamination by this fungicide. The adsorption of tetraconazole by 3 organic residues: spent mushroom substrate (SMS), green compost (GC) and vine pruning sawdust (VP), as well as by vineyard soils unamended and amended individually with these residues at 1.5% (w/w) was evaluated using the batch equilibrium technique.