γ-Aminobutyric Acid Promotes Chloroplast Ultrastructure, Antioxidant Capacity, and Growth of Waterlogged Maize Seedlings

γ-aminobutyric acid (GABA) is a small signaling molecule that accumulates rapidly in plants exposed to various stresses; however, it has not been applied in regulating waterlogging tolerance in maize seedlings. Here, the effect of exogenous application of GABA in the determined optimal concentration was performed on seedlings of two maize cultivars under waterlogging treatments initiated at 3-leaf (V3) and 5-leaf stages (V5) in repeated experiments in 2016 and 2017. Chloroplast ultrastructure, photosynthesis, antioxidant capacity, and reactive oxygen species (ROS) production in the leaves were examined and compared with the corresponding values under normal soil water treatment (CK) and waterlogging treatment (WL). Compared with WL treatment, application of GABA significantly increased aboveground and root dry matter by 19.0% and 61.0%, promoted photosynthetic rate and chlorophyll content by 19.8% and 36.0%, increased the number of grana per chloroplast by 36.0%, fortified antioxidants (SOD, POD, CAT, GR, APX, VC) activities by 14.7–42.7%, and reduced the content of MDA, H2O2, and O2− by 30.5%, 32.5%, and 21.8%, respectively (p < 0.05). Collectively, GABA application was shown to promote the growth of maize seedlings under waterlogging, by down regulating ROIs-producing enzymes, activating antioxidant defense systems, and improving chloroplast ultrastructure and photosynthetic traits.