Transcriptomic and physiological analyses reveal drought adaptation strategies in drought-tolerant and -susceptible watermelon genotypes

•Study provides comprehensive understanding of watermelon adaption strategies to drought.•Melatonin functions as upstream of ABA in inducing wax biosynthesis and drought tolerance.•Higher abilities in synthesis of ABA, melatonin, wax, osmopretectants, and antioxidants confer drought tolerance.•Growth retardation is an important way to save and redistribute resources for drought-susceptible genotype. Drought stress has become one of the most urgent environmental hazards for horticultural crops. In this research, we analyzed watermelon adaptation strategies to drought stress in drought-tolerant (M20) and -susceptible (Y34) genotypes via transcriptomic and physiological analyses. After drought stress, a total of 6228 and 4311 differentially expressed genes (DEGs) were observed in Y34 and M20, respectively. Numerous DEGs were involved in various defense responses such as antioxidation, protein protection, osmotic adjustment, wax accumulation, hormone signaling, and melatonin biosynthesis. Accordingly, the contents of ABA, melatonin, wax, and some osmoprotectants were increased by drought stress in both Y34 and especially M20. Exogenous application of melatonin or ABA induced wax accumulation and drought tolerance and melatonin may function upstream of ABA. In comparison to Y34, M20 was more able to activate ABA signaling, melatonin biosynthesis, osmotic adjustment, antioxidation, and wax accumulation under drought stress. These stronger responses confer M20 tolerance to drought. Photosynthesis and most DEGs involved in photosynthesis and cell growth were decreased by drought stress in both M20 and especially Y34. For drought-susceptible genotypes, growth retardation may be an important mechanism for saving and redistributing resources in order to reprogram stress signaling networks.