Grafting, the careful selection of rootstocks and scions, has played a crucial role maintaining Chilean avocado fruit quality standards in a scenario in which climate change and drought-related issues have considerably decreased avocado fruit production in the last fifteen years. The historical use of seedling rootstocks in Chile has experienced a recent shift towards clonal rootstocks, driven by the potential to produce more consistent and predictable crops. This research aims to compare Hass avocado plants grafted on Mexicola seedling and Dusa^® clonal rootstocks in a soilless and protected system using (i) a differential expression analysis of root and leaf samples and (ii) a fruit transcriptomic and metabolomic integration analysis to improve our understanding of rootstock–scion interaction and its impact on avocado tree performance and fruit quality. The results demonstrated that no significant transcriptomic and metabolomic differences were identified at fruit level in the ready-to-eat (RTE) stage for Hass avocado fruit from both rootstocks. However, Hass avocados grafted on the clonal rootstock showed greater aerial growth and slightly increased fruit size than the seedling rootstock due to the enrichment of cell wall-remodeling genes as revealed in leaves and fruit at harvest stage.

Avocados (Persea americana Mill.) are one of the crops with the highest water footprints in Chile and the production is at risk due to severe and frequent droughts. The current production is mostly based on sexually (seed) propagated rootstocks, while clonally propagated rootstocks are on the rise. In a recent study, we found differences in aerial, root growth and water use efficiency between trees grown on these two different rootstocks under controlled continuous fertigation and environmental conditions. In this study, we further describe possible mechanisms which drive the differences. Avocado cv. “Hass” grafted on “Dusa” (D, clonally propagated) and “Mexicola” (M, sexually propagated) rootstocks and different root segments (3, 5 and 8 cm from root tip) were investigated using a combination of hydraulic measurements and polar metabolite (GC-MS) techniques. The results show significant differences in root hydraulic properties, indicating that “Mexicola” fine roots have higher water uptake capacity. The polar metabolites analysis revealed 13 compounds significantly different between rootstocks while nine were found significantly different among root segments. Principal component analysis (PCA) revealed differences between rootstocks and root segments. The data presented here highlight the importance of considering key physiological knowledge in avocado rootstocks breeding programs to be better prepared for future challenging environmental conditions.