Metabolomics and Transcriptomics Analyses of Two Contrasting Cherry Rootstocks in Response to Drought Stress

SIMPLE SUMMARY: Drought is one of the main factors affecting sweet cherry yields, and cherry rootstocks can provide a range of tree vigor levels to better match sweet cherries with the characteristics of the soil. To investigate the molecular responses of the cherry rootstocks to water deficiency, we performed transcriptomic and metabolomic analyses of two contrasting cherry rootstocks—Mahaleb CDR-1 and Gisela 5. The results revealed that differentially expressed metabolites related to the pathways of cyanoamino acid metabolism and phenylpropanoid biosynthesis may be key factors in the difference in drought resistance in the two rootstocks. Moreover, six central metabolites—3-cyanoalanine, phenylalanine, quinic acid, asparagine, p-benzoquinone, and phytosphingosine—were identified as potential biological markers of the drought response in cherries and may be key factors in the difference in drought resistance, along with caffeic acid and chlorogenic acid. Furthermore, we selected 17 differentially expressed genes as core candidate genes and the mechanism of a drought-tolerant cherry rootstock (DT) in response to drought is summarized. This study can provide a valuable insight into the molecular mechanisms behind drought resistance and will be beneficial to those aiming to breed promising new cherry cultivars. ABSTRACT: Drought is one of the main factors affecting sweet cherry yields, and cherry rootstocks can provide a range of tree vigor levels to better match sweet cherries with the characteristics of the soil. To investigate the molecular events of the cherry to water deficiency, we performed transcriptomic and metabolomic analyses of Prunus mahaleb CDR-1 (drought-tolerant cherry rootstock (DT)) and P. cerasus × P. canescens Gisela 5 (drought-susceptible cherry rootstock (DS)), respectively. The results revealed 253 common drought-responsive genes in leaves and roots in DT and 17 in DS; 59 upregulated metabolites were explored in leaves in DT and 19 were explored in DS. Differentially expressed metabolites related to the cyanoamino acid metabolism pathway and phenylpropanoid biosynthesis pathway may be key factors in the difference in drought resistance in the two rootstocks. Moreover, six central metabolites—3-cyanoalanine, phenylalanine, quinic acid, asparagine, p-benzoquinone, and phytosphingosine—were identified as potential biological markers of drought response in cherries and may be key factors in the difference in drought resistance, along with caffeic acid and chlorogenic acid. We also selected 17 differentially expressed genes as core candidate genes and the mechanism of DT in response to drought is summarized.