A Concise Review on Multi-Omics Data Integration for Terroir Analysis in Vitis vinifera

Abstract

Vitis vinifera (grapevine) is one of the most important fruit crops, both for fresh consumption and wine and spirit production. The term terroir is frequently used in viticulture and the wine industry to relate wine sensory attributes to its geographic origin. Although, it can be cultivated in a wide range of environments, differences in growing conditions have a significant impact on fruit traits that ultimately affect wine quality. Understanding how fruit quality and yield are controlled at a molecular level in grapevine in response to environmental cues has been a major driver of research. Advances in the area of genomics, epigenomics, transcriptomics, proteomics and metabolomics, have significantly increased our knowledge on the abiotic regulation of yield and quality in many crop species, including V. vinifera. The integrated analysis of multiple 'omics' can give us the opportunity to better understand how plants modulate their response to different environments. However, 'omics' technologies provide a large amount of biological data and its interpretation is not always straightforward, especially when different 'omic' results are combined. Here we examine the current strategies used to integrate multi-omics, and how these have been used in V. vinifera. In addition, we also discuss the importance of including epigenomics data when integrating omics data as epigenetic mechanisms could play a major role as an intermediary between the environment and the genome.

Keywords: Vitis vinifera; data integration; environment; epigenetics; metabolomics; multi-omics; transcriptomics.

FIGURE 1

A conceptual view of some of the terroir factors that contribute to vine balance, fruit composition and wine quality. ^∗Vine genome/s refers to the possibility of the scion and rootstock used in a vineyard could be from different varieties/species (Modified from: Smart et al., 1985 and reproduced with permission from the copyright holder).

FIGURE 2

Data integration workflow for four omics technologies in addition to environmental data, and fruit and wine quality data (Modified from Wanichthanarak et al., 2015 and reproduced with permission from the copyright holder).