Commercial fruit trees are usually formed by the combination of a rootstock and a scion to broaden the adaptability of scion cultivars to soil and climatic conditions, facilitate agricultural management, and/or increase productivity. In the different cultivated species of the genus Prunus, rootstocks having a wide range of uses are scarce, because of rootstock/ scion graft incompatibilities that prevent the establishment of a strong and lasting functional union. Graft incompatibility is a problem in cherry, almond, and apricot than in peach or plum. In general, closely related cultivars and species tend to be compatible, but taxonomically distant plants often manifest incompatibility. This review will focus on the knowledge currently available on the metabolic response during the formation and establishment of the stock/scion graft union in order to help the effort for identify future metabolic markers to be used in breeding programs. The physiological, metabolic and molecular mechanisms that cause incompatibility remain unclear and several hypotheses have been proposed to explain it, mostly based on herbaceous species. Few studies are available to explain incompatibility in woody plants. Various phenolic compounds are known to affect cell division, development and differentiation at the graft union. Flavonol (catechins and proanthocyanidins) concentrations increase shortly after grafting and, as a result of the stress induced during the healing response, vacuolar membrane disruption occurs resulting in the escape of phenols from the vacuole into the cytoplasmic matrix, causing dysfunctions in the growth of certain tissues (xylem and phloem), interference with the synthesis of lignin or inducing hormonal imbalances. All these abnormalities result in mechanical weakening of the union, which may manifest during the first year after grafting (translocated incompatibility) or may appear several years later (localized incompatibility), leading to major economic losses. More research is needed to fully understand the mechanism of graft incompatibility, particularly in woody plants. This knowledge is essential to develop molecular markers useful in rootstock breeding programs.

The current global agricultural challenges imply the need to generate new technologies and farming systems. In this context, rootstocks are an essential component in modern agriculture. Most currently used are those clonally propagated and there are several ongoing efforts to develop this type of plant material. Despite this tendency, lesser number of rootstock breeding programs exists in comparison to the large number of breeding programs for scion cultivars. In the case of rootstocks, traits evaluated in new selection lines are quite different: From the agronomic standpoint vigor is a key issue in order to establish high-density orchards. Other important agronomic traits include compatibility with a wide spectrum of cultivars from different species, good tolerance to root hypoxia, water use efficiency, aptitude to extract or exclude certain soil nutrients, and tolerance to soil or water salinity. Biotic stresses are also important: Resistance/tolerance to pests and diseases, such as nematodes, soil-borne fungi, crown gall, bacterial canker, and several virus, viroids, and phytoplasms. In this sense, the creation of new rootstocks at Centro de Estudios Avanzados en Fruticultura (CEAF) offers an alternative to stone fruit crop, particularly in Chile, where just a few alternatives are commercially available, and there are site-specific problems. The implementation of molecular markers in order to give support to the phenotypic evaluation of plant breeding has great potential assisting the selection of new genotypes of rootstocks. Marker-Assisted Selection (MAS) can shorten the time required to obtain new cultivars and can make the process more cost-effective than selection based exclusively on phenotype, but more basic research is needed to well understood the molecular and physiological mechanisms behind the studied trait.

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Plants are permanently facing challenges imposed by the environment which, in the context of the current scenario of global climate change, implies a constant process of adaptation to survive and even, in the case of crops, at least maintain yield. O2 deficiency at the rhizosphere level, i.e., root hypoxia, is one of the factors with the greatest impact at whole-plant level. At cellular level, this O2 deficiency provokes a disturbance in the energy metabolism which has notable consequences on the yield of plant crops. In this sense, although several physiological studies describe processes involved in plant adaptation to root hypoxia in woody fruit trees, with emphasis on the negative impacts on photosynthetic rate, there are very few studies that include -omics strategies for specifically understanding these processes in the roots of such species. Through a de novo assembly approach, a comparative transcriptome study of waterlogged Prunus spp. genotypes contrasting in their tolerance to root hypoxia was revisited in order to gain a deeper insight into the reconfiguration of pivotal pathways involved in energy metabolism. This re-analysis describes the classically altered pathways seen in the roots of woody fruit trees under hypoxia, but also routes that link them to pathways involved with nitrogen assimilation and the maintenance of cytoplasmic pH and glycolytic flow. In addition, the effects of root hypoxia on the transcription of genes related to the mitochondrial oxidative phosphorylation system, responsible for providing adenosine triphosphate (ATP) to the cell, are discussed in terms of their roles in the energy balance, reactive oxygen species (ROS) metabolism and aerenchyma formation. This review compiles key findings that help to explain the trait of tolerance to root hypoxia in woody fruit species, giving special attention to their strategies for managing the energy crisis. Finally, research challenges addressing less-explored topics in recovery and stress memory in woody fruit trees are pointed out.