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The plant growth regulator mepiquat chloride (1,1-dimethylpiperidinium chloride, DPC) has been successfully used worldwide in cotton production. Fortified DPC (DPC+) can slightly damage young tissues of the epidermis, which has shown potential in cotton chemical topping in China. The underlying mechanism remains unclear. We investigated whether apical meristem and leaf morpho-physiological traits contribute to delayed growth of the main stem and increased seed yield in DPC or DPC+ as a chemical inhibitor. Two different DPC-sensitive varieties (Xinluzao 60, L60; Jinken 1402, JK1402) were field-grown using three different topping treatments manual topping (MT), no topping (NT) and chemical topping (DPC+ and DPC) in irrigated arid lands of Xinjiang for two years. The plant height decreased by 1.4–13.6% for the DPC+ and DPC treatments compared with the NT treatment and increased by 3.8 –9.2% compared with the MT treatment. The thickness of the leaves, palisade tissue (Pt) and spongy tissue (St) increased by 5.1–21.5% under DPC treatment compared with other treatments. The 3-indoleacetic acid (IAA) content of the leaves significantly increased by 25.0–93.8% at 10 days under the DPC treatment compared with that under the MT and NT treatments. The zeatin riboside (ZR) content of the leaves and apical buds increased up to 7.5 times at 40 days under the DPC+ and DPC treatments compared with that under the NT treatment. The accumulation of reproductive organ biomass and proportion of reproductive organ dry matter to total dry matter under the DPC+ and DPC treatments increased by 2.0–39.7% compared with that under the MT and NT treatments. The seed cotton yield between the DPC+ and DPC treatments showed no significant difference. However, the seed cotton yield of JK1402 under the DPC+ and DPC treatments significantly increased by 9.5–11.7% compared with that under the MT and NT treatments. The main stem length was significantly correlated with the stem length of the upper part and gibberellin (GA) content in the apical buds. The leaf Pt and ZR contents were significantly correlated with the boll weight and seed cotton yield. Collectively, the data suggest that improved morpho-physiological traits of the apical part, such as an increase in the IAA and GA contents in the apical buds, leaf Pt and ZR contents, and boll weight, inhibited growth of the main stem and increased seed cotton yield for DPC, which is cheaper than DPC+ as a chemical inhibitor under chemical regulation during the whole growth period. • Chemical topping delays growth of the upper main stem. • Chemical topping enhances thickness and ZR contents of leaves. • DPC can increase boll weight and seed cotton yield in DPC-sensitive varieties. • DPC has the potential to replace manual and other chemical topping agents. [ABSTRACT FROM AUTHOR]