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As an indoleamine molecule, melatonin mediates many physiological processes in plants. We investigated its role in regulating growth, ion homeostasis, and the response to oxidative stress in Malus hupehensis Rehd. under high-salinity conditions. Stressed plants had reduced growth and a marked decline in their net photosynthetic rates and chlorophyll contents. However, pretreatment with 0.1 μM melatonin significantly alleviated this growth inhibition and enabled plants to maintain an improved photosynthetic capacity. The addition of melatonin also lessened the amount of oxidative damage brought on by salinity, perhaps by directly scavenging H2O2 or enhancing the activities of antioxidative enzymes such as ascorbate peroxidase, catalase, and peroxidase. We also investigated whether melatonin might control the expression of ion-channel genes under salinity. Here, MdNHX1 and MdAKT1 were greatly up-regulated in the leaves, which possibly contributed to the maintenance of ion homeostasis and, thus, improved salinity resistance in plants exposed to exogenous melatonin.