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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.

Aquaporins (AQPs) are integral transmembrane proteins well known as channels involved in the mobilization of water, small uncharged molecules and gases. In this work, the main objective was to carry out a comprehensive study of AQP encoding genes in Prunus avium (cv. Mazzard F12/1) on a genome-wide scale and describe their transcriptional behaviors in organs and in response to different abiotic stresses. A total of 28 non-redundant AQP genes were identified in Prunus spp. Genomes, which were phylogenetically grouped into five subfamilies (seven PIPs, eight NIPs, eight TIPs, three SIPs and two XIPs). Bioinformatic analyses revealed a high synteny and remarkable conservation of structural features among orthologs of different Prunus genomes. Several cis-acting regulatory elements (CREs) related to stress regulation were detected (ARE, WRE3, WUN, STRE, LTR, MBS, DRE, AT-rich and TC-rich). The above could be accounting for the expression variations associated with plant organs and, especially, each abiotic stress analyzed. Gene expressions of different PruavAQPs were shown to be preferentially associated with different stresses. PruavXIP2;1 and PruavXIP1;1 were up-regulated in roots at 6 h and 72 h of hypoxia, and in PruavXIP2;1 a slight induction of expression was also detected in leaves. Drought treatment strongly down-regulated PruavTIP4;1 but only in roots. Salt stress exhibited little or no variation in roots, except for PruavNIP4;1 and PruavNIP7;1, which showed remarkable gene repression and induction, respectively. Interestingly, PruavNIP4;1, the AQP most expressed in cherry roots subjected to cold temperatures, also showed this pattern in roots under high salinity. Similarly, PruavNIP4;2 consistently was up-regulated at 72 h of heat and drought treatments. From our evidence is possible to propose candidate genes for the development of molecular markers for selection processes in breeding programs for rootstocks and/or varieties of cherry.